1
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Fagiani F, Pedrini E, Taverna S, Brambilla E, Murtaj V, Podini P, Ruffini F, Butti E, Braccia C, Andolfo A, Magliozzi R, Smirnova L, Kuhlmann T, Quattrini A, Calabresi PA, Reich DS, Martino G, Panina-Bordignon P, Absinta M. A glia-enriched stem cell 3D model of the human brain mimics the glial-immune neurodegenerative phenotypes of multiple sclerosis. Cell Rep Med 2024; 5:101680. [PMID: 39121861 DOI: 10.1016/j.xcrm.2024.101680] [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: 06/06/2023] [Revised: 01/12/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024]
Abstract
The role of central nervous system (CNS) glia in sustaining self-autonomous inflammation and driving clinical progression in multiple sclerosis (MS) is gaining scientific interest. We applied a single transcription factor (SOX10)-based protocol to accelerate oligodendrocyte differentiation from human induced pluripotent stem cell (hiPSC)-derived neural precursor cells, generating self-organizing forebrain organoids. These organoids include neurons, astrocytes, oligodendroglia, and hiPSC-derived microglia to achieve immunocompetence. Over 8 weeks, organoids reproducibly generated mature CNS cell types, exhibiting single-cell transcriptional profiles similar to the adult human brain. Exposed to inflamed cerebrospinal fluid (CSF) from patients with MS, organoids properly mimic macroglia-microglia neurodegenerative phenotypes and intercellular communication seen in chronic active MS. Oligodendrocyte vulnerability emerged by day 6 post-MS-CSF exposure, with nearly 50% reduction. Temporally resolved organoid data support and expand on the role of soluble CSF mediators in sustaining downstream events leading to oligodendrocyte death and inflammatory neurodegeneration. Such findings support the implementation of this organoid model for drug screening to halt inflammatory neurodegeneration.
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Affiliation(s)
- Francesca Fagiani
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Edoardo Pedrini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Stefano Taverna
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Elena Brambilla
- Division of Neuroscience, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Valentina Murtaj
- Division of Neuroscience, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Paola Podini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Francesca Ruffini
- Division of Neuroscience, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Erica Butti
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Clarissa Braccia
- ProMeFa, Proteomics and Metabolomics Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Annapaola Andolfo
- ProMeFa, Proteomics and Metabolomics Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Roberta Magliozzi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Lena Smirnova
- Center for Alternatives to Animal Testing, Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital of Münster, 48149 Münster, Germany
| | - Angelo Quattrini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Division of Neuroscience, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gianvito Martino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Division of Neuroscience, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Paola Panina-Bordignon
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Division of Neuroscience, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Martina Absinta
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Division of Neuroscience, Vita-Salute San Raffaele University, 20132 Milan, Italy; Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA.
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2
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Pitchai FNN, Tanner EJ, Khetan N, Vasen G, Levrel C, Kumar AJ, Pandey S, Ordonez T, Barnette P, Spencer D, Jung SY, Glazier J, Thompson C, Harvey-Vera A, Son HI, Son HI, Strathdee SA, Holguin L, Urak R, Burnett J, Burgess W, Busman-Sahay K, Estes JD, Hessell A, Fennessey CM, Keele BF, Haigwood NL, Weinberger LS. Engineered deletions of HIV replicate conditionally to reduce disease in nonhuman primates. Science 2024; 385:eadn5866. [PMID: 39116226 DOI: 10.1126/science.adn5866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 06/06/2024] [Indexed: 08/10/2024]
Abstract
Antiviral therapies with reduced frequencies of administration and high barriers to resistance remain a major goal. For HIV, theories have proposed that viral-deletion variants, which conditionally replicate with a basic reproductive ratio [R0] > 1 (termed "therapeutic interfering particles" or "TIPs"), could parasitize wild-type virus to constitute single-administration, escape-resistant antiviral therapies. We report the engineering of a TIP that, in rhesus macaques, reduces viremia of a highly pathogenic model of HIV by >3log10 following a single intravenous injection. Animal lifespan was significantly extended, TIPs conditionally replicated and were continually detected for >6 months, and sequencing data showed no evidence of viral escape. A single TIP injection also suppressed virus replication in humanized mice and cells from persons living with HIV. These data provide proof of concept for a potential new class of single-administration antiviral therapies.
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Affiliation(s)
- Fathima N Nagoor Pitchai
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Elizabeth J Tanner
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Neha Khetan
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Gustavo Vasen
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Clara Levrel
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Arjun J Kumar
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Shilpi Pandey
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Tracy Ordonez
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Philip Barnette
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - David Spencer
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
- Absci Corporation, Vancouver, WA, USA
| | - Seung-Yong Jung
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Joshua Glazier
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Cassandra Thompson
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Hye-In Son
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- US-Mexico Border Health Commission, Tijuana, Mexico
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Hye-In Son
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Steffanie A Strathdee
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Leo Holguin
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ryan Urak
- Center for Gene Therapy, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - John Burnett
- Center for Gene Therapy, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William Burgess
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
- Faculty of Health, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- School of Health and Biomedical Sciences College of Science, Engineering and Health RMIT University, Melbourne, Australia
| | - Ann Hessell
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nancy L Haigwood
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Leor S Weinberger
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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3
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Tooley K, Jerby L, Escobar G, Krovi SH, Mangani D, Dandekar G, Cheng H, Madi A, Goldschmidt E, Lambden C, Krishnan RK, Rozenblatt-Rosen O, Regev A, Anderson AC. Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity. Cell Rep Med 2024; 5:101640. [PMID: 38959885 PMCID: PMC11293343 DOI: 10.1016/j.xcrm.2024.101640] [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: 05/31/2023] [Revised: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
CD8+ T cells must persist and function in diverse tumor microenvironments to exert their effects. Thus, understanding common underlying expression programs could better inform the next generation of immunotherapies. We apply a generalizable matrix factorization algorithm that recovers both shared and context-specific expression programs from diverse datasets to a single-cell RNA sequencing (scRNA-seq) compendium of 33,161 CD8+ T cells from 132 patients with seven human cancers. Our meta-single-cell analyses uncover a pan-cancer T cell dysfunction program that predicts clinical non-response to checkpoint blockade in melanoma and highlights CXCR6 as a pan-cancer marker of chronically activated T cells. Cxcr6 is trans-activated by AP-1 and repressed by TCF1. Using mouse models, we show that Cxcr6 deletion in CD8+ T cells increases apoptosis of PD1+TIM3+ cells, dampens CD28 signaling, and compromises tumor growth control. Our study uncovers a TCF1:CXCR6 axis that counterbalances PD1-mediated suppression of CD8+ cell responses and is essential for effective anti-tumor immunity.
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Affiliation(s)
- Katherine Tooley
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulia Escobar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - S Harsha Krovi
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Davide Mangani
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gitanjali Dandekar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanning Cheng
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Goldschmidt
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Conner Lambden
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh K Krishnan
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ana C Anderson
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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4
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Dehaen N, Van Hul M, Mignion L, Kouakou AN, Cani PD, Jordan BF. Luciferase transduction and selection protocol for reliable in vivo bioluminescent measurements in cancer research. Heliyon 2024; 10:e33356. [PMID: 39035528 PMCID: PMC11259842 DOI: 10.1016/j.heliyon.2024.e33356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024] Open
Abstract
Bioluminescence imaging has become an essential non-invasive tool in cancer research for monitoring various cellular processes and tumor progression in vivo. In this article, we aimed to propose a transduction and selection protocol for reliable in vivo bioluminescent measurements in immunocompetent mouse models. Using two different heterogenous luciferase-expressing cell models, we underlined factors influencing transduction. The protocol was tested through an in vitro luciferase activity assay as well as using in vivo longitudinal monitoring of metastases formation (In Vivo Imaging System®). The data were cross validated with histological assessment. Our results demonstrated stable and proportional in vitro and in vivo bioluminescent signals correlating with actual metastatic burden. Furthermore, ex vivo analysis confirmed the accuracy of bioluminescent imaging in quantifying metastatic surface area. This protocol should ensure reliable and reproducible measurements in cancer research utilizing luciferase-positive cell lines, confirming the validity and accuracy of preclinical studies in immunocompetent models.
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Affiliation(s)
- Natacha Dehaen
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Matthias Van Hul
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Lionel Mignion
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Nuclear and Electron Spin Technologies (NEST) Platform, Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Axell-Natalie Kouakou
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Bioanalysis and Pharmacology of Bioactive Lipids (BPBL), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Patrice D. Cani
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), WELBIO department, WEL Research Institute, Wavre, Belgium
- Institute of Experimental and Clinical Research (IREC), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Bénédicte F. Jordan
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Nuclear and Electron Spin Technologies (NEST) Platform, Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
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5
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Portela-Lomba M, Simón D, Callejo-Móstoles M, de la Fuente G, Fernández de Sevilla D, García-Escudero V, Moreno-Flores MT, Sierra J. Generation of functional neurons from adult human mucosal olfactory ensheathing glia by direct lineage conversion. Cell Death Dis 2024; 15:478. [PMID: 38961086 PMCID: PMC11222439 DOI: 10.1038/s41419-024-06862-9] [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: 10/09/2023] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
A recent approach to promote central nervous system (CNS) regeneration after injury or disease is direct conversion of somatic cells to neurons. This is achieved by transduction of viral vectors that express neurogenic transcription factors. In this work we propose adult human mucosal olfactory ensheathing glia (hmOEG) as a candidate for direct reprogramming to neurons due to its accessibility and to its well-characterized neuroregenerative capacity. After induction of hmOEG with the single neurogenic transcription factor NEUROD1, the cells under study exhibited morphological and immunolabeling neuronal features, fired action potentials and expressed glutamatergic and GABAergic markers. In addition, after engraftment of transduced hmOEG cells in the mouse hippocampus, these cells showed specific neuronal labeling. Thereby, if we add to the neuroregenerative capacity of hmOEG cultures the conversion to neurons of a fraction of their population through reprogramming techniques, the engraftment of hmOEG and hmOEG-induced neurons could be a procedure to enhance neural repair after central nervous system injury.
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Affiliation(s)
- María Portela-Lomba
- School of Experimental Sciences, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Spain
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Diana Simón
- School of Experimental Sciences, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Spain
| | - Marta Callejo-Móstoles
- Department of Anatomy, Histology and Neuroscience, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Gemma de la Fuente
- Department of Anatomy, Histology and Neuroscience, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - David Fernández de Sevilla
- Department of Anatomy, Histology and Neuroscience, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Vega García-Escudero
- Department of Anatomy, Histology and Neuroscience, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - M Teresa Moreno-Flores
- Department of Anatomy, Histology and Neuroscience, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Javier Sierra
- School of Experimental Sciences, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Spain.
- School of Medicine, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Spain.
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6
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Gravina T, Favero F, Rosano S, Parab S, Diaz Alcalde A, Bussolino F, Doronzo G, Corà D. Integrative Bioinformatics Analysis Reveals a Transcription Factor EB-Driven MicroRNA Regulatory Network in Endothelial Cells. Int J Mol Sci 2024; 25:7123. [PMID: 39000232 PMCID: PMC11241138 DOI: 10.3390/ijms25137123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Various human diseases are triggered by molecular alterations influencing the fine-tuned expression and activity of transcription factors, usually due to imbalances in targets including protein-coding genes and non-coding RNAs, such as microRNAs (miRNAs). The transcription factor EB (TFEB) modulates human cellular networks, overseeing lysosomal biogenesis and function, plasma-membrane trafficking, autophagic flux, and cell cycle progression. In endothelial cells (ECs), TFEB is essential for the maintenance of endothelial integrity and function, ensuring vascular health. However, the comprehensive regulatory network orchestrated by TFEB remains poorly understood. Here, we provide novel mechanistic insights into how TFEB regulates the transcriptional landscape in primary human umbilical vein ECs (HUVECs), using an integrated approach combining high-throughput experimental data with dedicated bioinformatics analysis. By analyzing HUVECs ectopically expressing TFEB using ChIP-seq and examining both polyadenylated mRNA and small RNA sequencing data from TFEB-silenced HUVECs, we have developed a bioinformatics pipeline mapping the different gene regulatory interactions driven by TFEB. We show that TFEB directly regulates multiple miRNAs, which in turn post-transcriptionally modulate a broad network of target genes, significantly expanding the repertoire of gene programs influenced by this transcription factor. These insights may have significant implications for vascular biology and the development of novel therapeutics for vascular disease.
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Affiliation(s)
- Teresa Gravina
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Francesco Favero
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Stefania Rosano
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Sushant Parab
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Alejandra Diaz Alcalde
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
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7
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Simoni M, Menegazzi C, Fracassi C, Biffi CC, Genova F, Tenace NP, Lucianò R, Raimondi A, Tacchetti C, Brugarolas J, Mazza D, Bernardi R. PML restrains p53 activity and cellular senescence in clear cell renal cell carcinoma. EMBO Mol Med 2024; 16:1324-1351. [PMID: 38730056 PMCID: PMC11178789 DOI: 10.1038/s44321-024-00077-3] [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: 02/22/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Clear-cell renal cell carcinoma (ccRCC), the major subtype of RCC, is frequently diagnosed at late/metastatic stage with 13% 5-year disease-free survival. Functional inactivation of the wild-type p53 protein is implicated in ccRCC therapy resistance, but the detailed mechanisms of p53 malfunction are still poorly characterized. Thus, a better understanding of the mechanisms of disease progression and therapy resistance is required. Here, we report a novel ccRCC dependence on the promyelocytic leukemia (PML) protein. We show that PML is overexpressed in ccRCC and that PML depletion inhibits cell proliferation and relieves pathologic features of anaplastic disease in vivo. Mechanistically, PML loss unleashed p53-dependent cellular senescence thus depicting a novel regulatory axis to limit p53 activity and senescence in ccRCC. Treatment with the FDA-approved PML inhibitor arsenic trioxide induced PML degradation and p53 accumulation and inhibited ccRCC expansion in vitro and in vivo. Therefore, by defining non-oncogene addiction to the PML gene, our work uncovers a novel ccRCC vulnerability and lays the foundation for repurposing an available pharmacological intervention to restore p53 function and chemosensitivity.
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Affiliation(s)
- Matilde Simoni
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Menegazzi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Fracassi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudia C Biffi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Medical Advisor, Sanofi, Milan, Italy
| | - Francesca Genova
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nazario Pio Tenace
- Department of Pathology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Roberta Lucianò
- Department of Pathology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Raimondi
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Carlo Tacchetti
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Universita' Vita-Salute San Raffaele, Milan, Italy
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rosa Bernardi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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8
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Giménez Y, Palacios M, Sánchez-Domínguez R, Zorbas C, Peral J, Puzik A, Ugalde L, Alberquilla O, Villanueva M, Río P, Gálvez E, Da Costa L, Strullu M, Catala A, Ruiz-Llobet A, Segovia JC, Sevilla J, Strahm B, Niemeyer CM, Beléndez C, Leblanc T, Lafontaine DL, Bueren J, Navarro S. Lentivirus-mediated gene therapy corrects ribosomal biogenesis and shows promise for Diamond Blackfan anemia. JCI Insight 2024; 9:e171650. [PMID: 38775150 PMCID: PMC11141922 DOI: 10.1172/jci.insight.171650] [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: 05/12/2023] [Accepted: 04/10/2024] [Indexed: 06/02/2024] Open
Abstract
This study lays the groundwork for future lentivirus-mediated gene therapy in patients with Diamond Blackfan anemia (DBA) caused by mutations in ribosomal protein S19 (RPS19), showing evidence of a new safe and effective therapy. The data show that, unlike patients with Fanconi anemia (FA), the hematopoietic stem cell (HSC) reservoir of patients with DBA was not significantly reduced, suggesting that collection of these cells should not constitute a remarkable restriction for DBA gene therapy. Subsequently, 2 clinically applicable lentiviral vectors were developed. In the former lentiviral vector, PGK.CoRPS19 LV, a codon-optimized version of RPS19 was driven by the phosphoglycerate kinase promoter (PGK) already used in different gene therapy trials, including FA gene therapy. In the latter one, EF1α.CoRPS19 LV, RPS19 expression was driven by the elongation factor alpha short promoter, EF1α(s). Preclinical experiments showed that transduction of DBA patient CD34+ cells with the PGK.CoRPS19 LV restored erythroid differentiation, and demonstrated the long-term repopulating properties of corrected DBA CD34+ cells, providing evidence of improved erythroid maturation. Concomitantly, long-term restoration of ribosomal biogenesis was verified using a potentially novel method applicable to patients' blood cells, based on ribosomal RNA methylation analyses. Finally, in vivo safety studies and proviral insertion site analyses showed that lentivirus-mediated gene therapy was nontoxic.
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Affiliation(s)
- Yari Giménez
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Manuel Palacios
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Rebeca Sánchez-Domínguez
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Christiane Zorbas
- RNA Molecular Biology, Fonds de la Recherche Scientifique (FRS/FNRS), Université libre de Bruxelles (ULB), Biopark campus, Gosselies, Belgium
| | - Jorge Peral
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Alexander Puzik
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laura Ugalde
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Omaira Alberquilla
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Mariela Villanueva
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Paula Río
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | | | - Lydie Da Costa
- AP-HP, Hematology diagnostic laboratory, Hôpital Robert-Debré, Paris, France
- University of Paris; Hematim, UR4666, UPJV; LABEX GR-EX, Paris, France
| | - Marion Strullu
- AP-HP, service Immuno-Hématologie pédiatique, Hôpital R. Debré, Paris, France
| | | | | | - Jose Carlos Segovia
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | | | - Brigitte Strahm
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charlotte M. Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cristina Beléndez
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Sección de Hematología y Oncología Pediátricas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Thierry Leblanc
- AP-HP, service Immuno-Hématologie pédiatique, Hôpital R. Debré, Paris, France
| | - Denis L.J. Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (FRS/FNRS), Université libre de Bruxelles (ULB), Biopark campus, Gosselies, Belgium
| | - Juan Bueren
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
| | - Susana Navarro
- Division of Hematopoietic Innovative Therapies, CIEMAT, Madrid, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain
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9
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Andronikou C, Burdova K, Dibitetto D, Lieftink C, Malzer E, Kuiken HJ, Gogola E, Ray Chaudhuri A, Beijersbergen RL, Hanzlikova H, Jonkers J, Rottenberg S. PARG-deficient tumor cells have an increased dependence on EXO1/FEN1-mediated DNA repair. EMBO J 2024; 43:1015-1042. [PMID: 38360994 PMCID: PMC10943112 DOI: 10.1038/s44318-024-00043-2] [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: 06/26/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Targeting poly(ADP-ribose) glycohydrolase (PARG) is currently explored as a therapeutic approach to treat various cancer types, but we have a poor understanding of the specific genetic vulnerabilities that would make cancer cells susceptible to such a tailored therapy. Moreover, the identification of such vulnerabilities is of interest for targeting BRCA2;p53-deficient tumors that have acquired resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) through loss of PARG expression. Here, by performing whole-genome CRISPR/Cas9 drop-out screens, we identify various genes involved in DNA repair to be essential for the survival of PARG;BRCA2;p53-deficient cells. In particular, our findings reveal EXO1 and FEN1 as major synthetic lethal interactors of PARG loss. We provide evidence for compromised replication fork progression, DNA single-strand break repair, and Okazaki fragment processing in PARG;BRCA2;p53-deficient cells, alterations that exacerbate the effects of EXO1/FEN1 inhibition and become lethal in this context. Since this sensitivity is dependent on BRCA2 defects, we propose to target EXO1/FEN1 in PARPi-resistant tumors that have lost PARG activity. Moreover, EXO1/FEN1 targeting may be a useful strategy for enhancing the effect of PARG inhibitors in homologous recombination-deficient tumors.
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Affiliation(s)
- Christina Andronikou
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Kamila Burdova
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Diego Dibitetto
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Elke Malzer
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD, Rotterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hana Hanzlikova
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Oncode Institute, Amsterdam, The Netherlands.
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland.
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland.
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10
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Medaer L, Veys K, Gijsbers R. Current Status and Prospects of Viral Vector-Based Gene Therapy to Treat Kidney Diseases. Hum Gene Ther 2024; 35:139-150. [PMID: 38386502 DOI: 10.1089/hum.2023.184] [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] [Indexed: 02/24/2024] Open
Abstract
Inherited kidney diseases are among the leading causes of chronic kidney disease, reducing the quality of life and resulting in substantial socioeconomic impact. The advent of early genetic testing and the growing understanding of the molecular basis and pathophysiology of these disorders have opened avenues for novel treatment strategies. Viral vector-based gene therapies have evolved from experimental treatments for rare diseases to potent platforms that carry the intrinsic potential to provide a cure with a single application. Several gene therapy products have reached the market, and the numbers are only expected to increase. Still, none target inherited kidney diseases. Gene transfer to the kidney has lagged when compared to other tissue-directed therapies such as hepatic, neuromuscular, and ocular tissues. Systemic delivery of genetic information to tackle kidney disease is challenging. The pharma industry is taking steps to take on kidney disease and to translate the current research into the therapeutic arena. In this review, we provide an overview of the current viral vector-based approaches and their potential. We discuss advances in platforms and injection routes that have been explored to enhance gene delivery toward kidney cells in animal models, and how these can fuel the development of viable gene therapy products for humans.
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Affiliation(s)
- Louise Medaer
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, Faculty of Medicine
| | - Koenraad Veys
- Laboratory of Paediatric Nephrology, Department of Development and Regeneration, Faculty of Medicine
| | - Rik Gijsbers
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, Faculty of Medicine
- Leuven Viral Vector Core, Faculty of Medicine; KU Leuven, Leuven, Belgium
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11
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Valeri E, Unali G, Piras F, Abou-Alezz M, Pais G, Benedicenti F, Lidonnici MR, Cuccovillo I, Castiglioni I, Arévalo S, Spinozzi G, Merelli I, Behrendt R, Oo A, Kim B, Landau NR, Ferrari G, Montini E, Kajaste-Rudnitski A. Removal of innate immune barriers allows efficient transduction of quiescent human hematopoietic stem cells. Mol Ther 2024; 32:124-139. [PMID: 37990494 PMCID: PMC10787167 DOI: 10.1016/j.ymthe.2023.11.020] [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: 05/23/2023] [Revised: 09/29/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
Quiescent human hematopoietic stem cells (HSC) are ideal targets for gene therapy applications due to their preserved stemness and repopulation capacities; however, they have not been exploited extensively because of their resistance to genetic manipulation. We report here the development of a lentiviral transduction protocol that overcomes this resistance in long-term repopulating quiescent HSC, allowing their efficient genetic manipulation. Mechanistically, lentiviral vector transduction of quiescent HSC was found to be restricted at the level of vector entry and by limited pyrimidine pools. These restrictions were overcome by the combined addition of cyclosporin H (CsH) and deoxynucleosides (dNs) during lentiviral vector transduction. Clinically relevant transduction levels were paired with higher polyclonal engraftment of long-term repopulating HSC as compared with standard ex vivo cultured controls. These findings identify the cell-intrinsic barriers that restrict the transduction of quiescent HSC and provide a means to overcome them, paving the way for the genetic engineering of unstimulated HSC.
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Affiliation(s)
- Erika Valeri
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Vita-Salute San Raffaele University, School of Medicine, 20132 Milan, Italy
| | - Giulia Unali
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Vita-Salute San Raffaele University, School of Medicine, 20132 Milan, Italy
| | - Francesco Piras
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Monah Abou-Alezz
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Giulia Pais
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maria Rosa Lidonnici
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Ivan Cuccovillo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Ilaria Castiglioni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sergio Arévalo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Rayk Behrendt
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Adrian Oo
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU School of Medicine, New York, NY 10016, USA
| | - Giuliana Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Vita-Salute San Raffaele University, School of Medicine, 20132 Milan, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Anna Kajaste-Rudnitski
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy.
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12
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Fracassi C, Ugge' M, Abdelhalim M, Zapparoli E, Simoni M, Magliulo D, Mazza D, Lazarevic D, Morelli M, Collas P, Bernardi R. PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer. Nucleic Acids Res 2023; 51:11024-11039. [PMID: 37823593 PMCID: PMC10639071 DOI: 10.1093/nar/gkad819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
The promyelocytic leukemia (PML) protein organizes nuclear aggregates known as PML nuclear bodies (PML-NBs), where many transcription factors localize to be regulated. In addition, associations of PML and PML-NBs with chromatin are described in various cell types, further implicating PML in transcriptional regulation. However, a complete understanding of the functional consequences of PML association to DNA in cellular contexts where it promotes relevant phenotypes is still lacking. We examined PML chromatin association in triple-negative breast cancer (TNBC) cell lines, where it exerts important oncogenic functions. We find that PML associates discontinuously with large heterochromatic PML-associated domains (PADs) that contain discrete gene-rich euchromatic sub-domains locally depleted of PML. PML promotes heterochromatic organization in PADs and expression of pro-metastatic genes embedded in these sub-domains. Importantly, this occurs outside PML-NBs, suggesting that nucleoplasmic PML exerts a relevant gene regulatory function. We also find that PML plays indirect regulatory roles in TNBC cells by promoting the expression of pro-metastatic genes outside PADs. Our findings suggest that PML is an important transcriptional regulator of pro-oncogenic metagenes in TNBC cells, via transcriptional regulation and epigenetic organization of heterochromatin domains that embed regions of local transcriptional activity.
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Affiliation(s)
- Cristina Fracassi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Martina Ugge'
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ettore Zapparoli
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Matilde Simoni
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Daniela Magliulo
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Marco J Morelli
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Rosa Bernardi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
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13
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Indrigo M, Morella I, Orellana D, d'Isa R, Papale A, Parra R, Gurgone A, Lecca D, Cavaccini A, Tigaret CM, Cagnotto A, Jones K, Brooks S, Ratto GM, Allen ND, Lelos MJ, Middei S, Giustetto M, Carta AR, Tonini R, Salmona M, Hall J, Thomas K, Brambilla R, Fasano S. Nuclear ERK1/2 signaling potentiation enhances neuroprotection and cognition via Importinα1/KPNA2. EMBO Mol Med 2023; 15:e15984. [PMID: 37792911 PMCID: PMC10630888 DOI: 10.15252/emmm.202215984] [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: 03/10/2022] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023] Open
Abstract
Cell signaling is central to neuronal activity and its dysregulation may lead to neurodegeneration and cognitive decline. Here, we show that selective genetic potentiation of neuronal ERK signaling prevents cell death in vitro and in vivo in the mouse brain, while attenuation of ERK signaling does the opposite. This neuroprotective effect mediated by an enhanced nuclear ERK activity can also be induced by the novel cell penetrating peptide RB5. In vitro administration of RB5 disrupts the preferential interaction of ERK1 MAP kinase with importinα1/KPNA2 over ERK2, facilitates ERK1/2 nuclear translocation, and enhances global ERK activity. Importantly, RB5 treatment in vivo promotes neuroprotection in mouse models of Huntington's (HD), Alzheimer's (AD), and Parkinson's (PD) disease, and enhances ERK signaling in a human cellular model of HD. Additionally, RB5-mediated potentiation of ERK nuclear signaling facilitates synaptic plasticity, enhances cognition in healthy rodents, and rescues cognitive impairments in AD and HD models. The reported molecular mechanism shared across multiple neurodegenerative disorders reveals a potential new therapeutic target approach based on the modulation of KPNA2-ERK1/2 interactions.
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Affiliation(s)
- Marzia Indrigo
- Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific InstituteMilanoItaly
| | - Ilaria Morella
- Neuroscience and Mental Health Innovation Institute, School of BiosciencesCardiff UniversityCardiffUK
| | - Daniel Orellana
- Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific InstituteMilanoItaly
| | - Raffaele d'Isa
- Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific InstituteMilanoItaly
| | - Alessandro Papale
- Neuroscience and Mental Health Innovation Institute, School of BiosciencesCardiff UniversityCardiffUK
| | - Riccardo Parra
- NEST, Istituto Nanoscienze CNR, and Scuola Normale SuperiorePisaItaly
| | | | - Daniela Lecca
- Department of Biomedical SciencesUniversity of CagliariCagliariItaly
| | - Anna Cavaccini
- Neuromodulation of Cortical and Subcortical Circuits LaboratoryFondazione Istituto Italiano di TecnologiaGenovaItaly
| | - Cezar M Tigaret
- Neuroscience and Mental Health Research Institute, School of MedicineCardiff UniversityCardiffUK
| | - Alfredo Cagnotto
- Dipartimento di Biochimica e Farmacologia MolecolareIstituto di Ricerche Farmacologiche Mario Negri‐IRCCSMilanoItaly
| | | | - Simon Brooks
- School of BiosciencesCardiff UniversityCardiffUK
| | | | | | | | - Silvia Middei
- Institute of Cell Biology and Neurobiology CNRRomaItaly
| | - Maurizio Giustetto
- Department of NeuroscienceUniversity of TorinoTorinoItaly
- National Institute of NeuroscienceTorinoItaly
| | - Anna R Carta
- Department of Biomedical SciencesUniversity of CagliariCagliariItaly
| | - Raffaella Tonini
- Neuromodulation of Cortical and Subcortical Circuits LaboratoryFondazione Istituto Italiano di TecnologiaGenovaItaly
| | - Mario Salmona
- Dipartimento di Biochimica e Farmacologia MolecolareIstituto di Ricerche Farmacologiche Mario Negri‐IRCCSMilanoItaly
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, School of MedicineCardiff UniversityCardiffUK
| | - Kerrie Thomas
- Neuroscience and Mental Health Research Institute, School of MedicineCardiff UniversityCardiffUK
| | - Riccardo Brambilla
- Neuroscience and Mental Health Innovation Institute, School of BiosciencesCardiff UniversityCardiffUK
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”Università degli Studi di PaviaPaviaItaly
| | - Stefania Fasano
- Neuroscience and Mental Health Innovation Institute, School of BiosciencesCardiff UniversityCardiffUK
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14
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Magliulo D, Simoni M, Caserta C, Fracassi C, Belluschi S, Giannetti K, Pini R, Zapparoli E, Beretta S, Uggè M, Draghi E, Rossari F, Coltella N, Tresoldi C, Morelli MJ, Di Micco R, Gentner B, Vago L, Bernardi R. The transcription factor HIF2α partakes in the differentiation block of acute myeloid leukemia. EMBO Mol Med 2023; 15:e17810. [PMID: 37807875 PMCID: PMC10630882 DOI: 10.15252/emmm.202317810] [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: 04/05/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
One of the defining features of acute myeloid leukemia (AML) is an arrest of myeloid differentiation whose molecular determinants are still poorly defined. Pharmacological removal of the differentiation block contributes to the cure of acute promyelocytic leukemia (APL) in the absence of cytotoxic chemotherapy, but this approach has not yet been translated to non-APL AMLs. Here, by investigating the function of hypoxia-inducible transcription factors HIF1α and HIF2α, we found that both genes exert oncogenic functions in AML and that HIF2α is a novel regulator of the AML differentiation block. Mechanistically, we found that HIF2α promotes the expression of transcriptional repressors that have been implicated in suppressing AML myeloid differentiation programs. Importantly, we positioned HIF2α under direct transcriptional control by the prodifferentiation agent all-trans retinoic acid (ATRA) and demonstrated that HIF2α blockade cooperates with ATRA to trigger AML cell differentiation. In conclusion, we propose that HIF2α inhibition may open new therapeutic avenues for AML treatment by licensing blasts maturation and leukemia debulking.
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Affiliation(s)
- Daniela Magliulo
- Division of Experimental OncologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Matilde Simoni
- Division of Experimental OncologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Carolina Caserta
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
| | - Cristina Fracassi
- Division of Experimental OncologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Serena Belluschi
- Vita Salute San Raffaele University School of MedicineMilanItaly
- Present address:
MogrifyCambridgeUK
| | - Kety Giannetti
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
| | - Raffaella Pini
- Center for Omics SciencesIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Ettore Zapparoli
- Center for Omics SciencesIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
| | - Martina Uggè
- Division of Experimental OncologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Eleonora Draghi
- Unit of Immunogenetics, Leukemia Genomics and ImmunobiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Federico Rossari
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
- Vita Salute San Raffaele University School of MedicineMilanItaly
| | - Nadia Coltella
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
| | - Cristina Tresoldi
- Unit of Hematology and Bone Marrow TransplantationIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Marco J Morelli
- Center for Omics SciencesIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
- Present address:
Ludwig Institute for Cancer researchLausanne UniversityLausanneSwitzerland
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and ImmunobiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Rosa Bernardi
- Division of Experimental OncologyIRCCS San Raffaele Scientific InstituteMilanItaly
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15
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Bhin J, Yemelyanenko J, Chao X, Klarenbeek S, Opdam M, Malka Y, Hoekman L, Kruger D, Bleijerveld O, Brambillasca CS, Sprengers J, Siteur B, Annunziato S, van Haren MJ, Martin NI, van de Ven M, Peters D, Agami R, Linn SC, Boven E, Altelaar M, Jonkers J, Zingg D, Wessels LF. MYC is a clinically significant driver of mTOR inhibitor resistance in breast cancer. J Exp Med 2023; 220:e20211743. [PMID: 37642941 PMCID: PMC10465700 DOI: 10.1084/jem.20211743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 05/18/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Targeting the PI3K-AKT-mTOR pathway is a promising therapeutic strategy for breast cancer treatment. However, low response rates and development of resistance to PI3K-AKT-mTOR inhibitors remain major clinical challenges. Here, we show that MYC activation drives resistance to mTOR inhibitors (mTORi) in breast cancer. Multiomic profiling of mouse invasive lobular carcinoma (ILC) tumors revealed recurrent Myc amplifications in tumors that acquired resistance to the mTORi AZD8055. MYC activation was associated with biological processes linked to mTORi response and counteracted mTORi-induced translation inhibition by promoting translation of ribosomal proteins. In vitro and in vivo induction of MYC conferred mTORi resistance in mouse and human breast cancer models. Conversely, AZD8055-resistant ILC cells depended on MYC, as demonstrated by the synergistic effects of mTORi and MYCi combination treatment. Notably, MYC status was significantly associated with poor response to everolimus therapy in metastatic breast cancer patients. Thus, MYC is a clinically relevant driver of mTORi resistance that may stratify breast cancer patients for mTOR-targeted therapies.
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Affiliation(s)
- Jinhyuk Bhin
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
- Department of Biomedical System Informatics, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Julia Yemelyanenko
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Xue Chao
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yuval Malka
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dinja Kruger
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Medical Oncology, Amsterdam University Medical Center, Vrije Universiteit Amsterdam/Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Onno Bleijerveld
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Chiara S. Brambillasca
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Justin Sprengers
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bjørn Siteur
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stefano Annunziato
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Matthijs J. van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Peters
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Reuven Agami
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sabine C. Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Epie Boven
- Department of Medical Oncology, Amsterdam University Medical Center, Vrije Universiteit Amsterdam/Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Maarten Altelaar
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Daniel Zingg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Lodewyk F.A. Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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16
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Uceda-Castro R, Margarido AS, Song JY, de Gooijer MC, Messal HA, Chambers CR, Nobis M, Çitirikkaya CH, Hahn K, Seinstra D, Herrmann D, Timpson P, Wesseling P, van Tellingen O, Vennin C, van Rheenen J. BCRP drives intrinsic chemoresistance in chemotherapy-naïve breast cancer brain metastasis. SCIENCE ADVANCES 2023; 9:eabp9530. [PMID: 37851804 PMCID: PMC10584345 DOI: 10.1126/sciadv.abp9530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/14/2023] [Indexed: 10/20/2023]
Abstract
Although initially successful, treatments with chemotherapy often fail because of the recurrence of chemoresistant metastases. Since these tumors develop after treatment, resistance is generally thought to occur in response to chemotherapy. However, alternative mechanisms of intrinsic chemoresistance in the chemotherapy-naïve setting may exist but remain poorly understood. Here, we study drug-naïve murine breast cancer brain metastases (BCBMs) to identify how cancer cells growing in a secondary site can acquire intrinsic chemoresistance without cytotoxic agent exposure. We demonstrate that drug-naïve murine breast cancer cells that form cancer lesions in the brain undergo vascular mimicry and concomitantly express the adenosine 5'-triphosphate-binding cassette transporter breast cancer resistance protein (BCRP), a common marker of brain endothelial cells. We reveal that expression of BCRP by the BCBM tumor cells protects them against doxorubicin and topotecan. We conclude that BCRP overexpression can cause intrinsic chemoresistance in cancer cells growing in metastatic sites without prior chemotherapy exposure.
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Affiliation(s)
- Rebeca Uceda-Castro
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Andreia S. Margarido
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mark C. de Gooijer
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Hendrik A. Messal
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Cecilia R. Chambers
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Max Nobis
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ceren H. Çitirikkaya
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kerstin Hahn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Danielle Seinstra
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, Amsterdam, Netherlands
| | - David Herrmann
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Paul Timpson
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, Amsterdam, Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Mouse Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Claire Vennin
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
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17
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Escobar G, Tooley K, Oliveras JP, Huang L, Cheng H, Bookstaver ML, Edwards C, Froimchuk E, Xue C, Mangani D, Krishnan RK, Hazel N, Rutigliani C, Jewell CM, Biasco L, Anderson AC. Tumor immunogenicity dictates reliance on TCF1 in CD8 + T cells for response to immunotherapy. Cancer Cell 2023; 41:1662-1679.e7. [PMID: 37625402 PMCID: PMC10529353 DOI: 10.1016/j.ccell.2023.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 06/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023]
Abstract
Stem-like CD8+ T cells are regulated by T cell factor 1 (TCF1) and are considered requisite for immune checkpoint blockade (ICB) response. However, recent findings indicate that reliance on TCF1+CD8+ T cells for ICB efficacy may differ across tumor contexts. We find that TCF1 is essential for optimal priming of tumor antigen-specific CD8+ T cells and ICB response in poorly immunogenic tumors that accumulate TOX+ dysfunctional T cells, but is dispensable for T cell priming and therapy response in highly immunogenic tumors that efficiently expand transitory effectors. Importantly, improving T cell priming by vaccination or by enhancing antigen presentation on tumors rescues the defective responses of TCF1-deficient CD8+ T cells upon ICB in poorly immunogenic tumors. Our study highlights TCF1's role during the early stages of anti-tumor CD8+ T cell responses with important implications for guiding optimal therapeutic interventions in cancers with low TCF1+CD8+ T cells and low-neo-antigen expression.
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Affiliation(s)
- Giulia Escobar
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Katherine Tooley
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Joan Pagès Oliveras
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Linglin Huang
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Hanning Cheng
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Michelle L Bookstaver
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Camilla Edwards
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Eugene Froimchuk
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Chang Xue
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Davide Mangani
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh K Krishnan
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Natanael Hazel
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Carola Rutigliani
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher M Jewell
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA; US Department of Veterans Affairs, VA Maryland Health Care System, Baltimore, MD 21201, USA
| | - Luca Biasco
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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18
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Passeri L, Andolfi G, Bassi V, Russo F, Giacomini G, Laudisa C, Marrocco I, Cesana L, Di Stefano M, Fanti L, Sgaramella P, Vitale S, Ziparo C, Auricchio R, Barera G, Di Nardo G, Troncone R, Gianfrani C, Annoni A, Passerini L, Gregori S. Tolerogenic IL-10-engineered dendritic cell-based therapy to restore antigen-specific tolerance in T cell mediated diseases. J Autoimmun 2023; 138:103051. [PMID: 37224733 DOI: 10.1016/j.jaut.2023.103051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/06/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023]
Abstract
Tolerogenic dendritic cells play a critical role in promoting antigen-specific tolerance via dampening of T cell responses, induction of pathogenic T cell exhaustion and antigen-specific regulatory T cells. Here we efficiently generate tolerogenic dendritic cells by genetic engineering of monocytes with lentiviral vectors co-encoding for immunodominant antigen-derived peptides and IL-10. These transduced dendritic cells (designated DCIL-10/Ag) secrete IL-10 and efficiently downregulate antigen-specific CD4+ and CD8+ T cell responses from healthy subjects and celiac disease patients in vitro. In addition, DCIL-10/Ag induce antigen-specific CD49b+LAG-3+ T cells, which display the T regulatory type 1 (Tr1) cell gene signature. Administration of DCIL-10/Ag resulted in the induction of antigen-specific Tr1 cells in chimeric transplanted mice and the prevention of type 1 diabetes in pre-clinical disease models. Subsequent transfer of these antigen-specific T cells completely prevented type 1 diabetes development. Collectively these data indicate that DCIL-10/Ag represent a platform to induce stable antigen-specific tolerance to control T-cell mediated diseases.
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Affiliation(s)
- Laura Passeri
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Grazia Andolfi
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Virginia Bassi
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy; University of Rome Tor Vergata, Via Cracovia 50, 00133, Rome, Italy
| | - Fabio Russo
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Giorgia Giacomini
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Cecilia Laudisa
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Ilaria Marrocco
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Luca Cesana
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Marina Di Stefano
- Department of Paediatrics, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Lorella Fanti
- Gastroenterology and Gastrointestinal Endoscopy Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Paola Sgaramella
- Department of Paediatrics, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Serena Vitale
- Institute of Biochemistry and Cell Biology, CNR, via P.Castellino 11, 80131, Naples, Italy
| | - Chiara Ziparo
- NESMOS Department, School of Medicine and Psychology, Sapienza University of Rome, Sant'Andrea University Hospital, Via di Grottarossa 1035, 00189, Rome, Italy
| | - Renata Auricchio
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), Department of Translational Medical Science, Section of Pediatrics, Via Pansini 5, 80131, University Federico II, Naples, Italy
| | - Graziano Barera
- Department of Paediatrics, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Giovanni Di Nardo
- NESMOS Department, School of Medicine and Psychology, Sapienza University of Rome, Sant'Andrea University Hospital, Via di Grottarossa 1035, 00189, Rome, Italy
| | - Riccardo Troncone
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), Department of Translational Medical Science, Section of Pediatrics, Via Pansini 5, 80131, University Federico II, Naples, Italy
| | - Carmen Gianfrani
- Institute of Biochemistry and Cell Biology, CNR, via P.Castellino 11, 80131, Naples, Italy
| | - Andrea Annoni
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Laura Passerini
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Silvia Gregori
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy.
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19
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Bhin J, Paes Dias M, Gogola E, Rolfs F, Piersma SR, de Bruijn R, de Ruiter JR, van den Broek B, Duarte AA, Sol W, van der Heijden I, Andronikou C, Kaiponen TS, Bakker L, Lieftink C, Morris B, Beijersbergen RL, van de Ven M, Jimenez CR, Wessels LFA, Rottenberg S, Jonkers J. Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors. Cell Rep 2023; 42:112538. [PMID: 37209095 DOI: 10.1016/j.celrep.2023.112538] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023] Open
Abstract
BRCA1 and BRCA2 both function in DNA double-strand break repair by homologous recombination (HR). Due to their HR defect, BRCA1/2-deficient cancers are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPis), but they eventually acquire resistance. Preclinical studies yielded several PARPi resistance mechanisms that do not involve BRCA1/2 reactivation, but their relevance in the clinic remains elusive. To investigate which BRCA1/2-independent mechanisms drive spontaneous resistance in vivo, we combine molecular profiling with functional analysis of HR of matched PARPi-naive and PARPi-resistant mouse mammary tumors harboring large intragenic deletions that prevent reactivation of BRCA1/2. We observe restoration of HR in 62% of PARPi-resistant BRCA1-deficient tumors but none in the PARPi-resistant BRCA2-deficient tumors. Moreover, we find that 53BP1 loss is the prevalent resistance mechanism in HR-proficient BRCA1-deficient tumors, whereas resistance in BRCA2-deficient tumors is mainly induced by PARG loss. Furthermore, combined multi-omics analysis identifies additional genes and pathways potentially involved in modulating PARPi response.
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Affiliation(s)
- Jinhyuk Bhin
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Biomedical System Informatics, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mariana Paes Dias
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Frank Rolfs
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Bram van den Broek
- Division of Cell Biology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Alexandra A Duarte
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Wendy Sol
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Christina Andronikou
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Taina S Kaiponen
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Lara Bakker
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
| | - Sven Rottenberg
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
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20
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Ariano C, Costanza F, Akman M, Riganti C, Corà D, Casanova E, Astanina E, Comunanza V, Bussolino F, Doronzo G. TFEB inhibition induces melanoma shut-down by blocking the cell cycle and rewiring metabolism. Cell Death Dis 2023; 14:314. [PMID: 37160873 PMCID: PMC10170071 DOI: 10.1038/s41419-023-05828-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/11/2023]
Abstract
Melanomas are characterised by accelerated cell proliferation and metabolic reprogramming resulting from the contemporary dysregulation of the MAPK pathway, glycolysis and the tricarboxylic acid (TCA) cycle. Here, we suggest that the oncogenic transcription factor EB (TFEB), a key regulator of lysosomal biogenesis and function, controls melanoma tumour growth through a transcriptional programme targeting ERK1/2 activity and glucose, glutamine and cholesterol metabolism. Mechanistically, TFEB binds and negatively regulates the promoter of DUSP-1, which dephosphorylates ERK1/2. In melanoma cells, TFEB silencing correlates with ERK1/2 dephosphorylation at the activation-related p-Thr185 and p-Tyr187 residues. The decreased ERK1/2 activity synergises with TFEB control of CDK4 expression, resulting in cell proliferation blockade. Simultaneously, TFEB rewires metabolism, influencing glycolysis, glucose and glutamine uptake, and cholesterol synthesis. In TFEB-silenced melanoma cells, cholesterol synthesis is impaired, and the uptake of glucose and glutamine is inhibited, leading to a reduction in glycolysis, glutaminolysis and oxidative phosphorylation. Moreover, the reduction in TFEB level induces reverses TCA cycle, leading to fatty acid production. A syngeneic BRAFV600E melanoma model recapitulated the in vitro study results, showing that TFEB silencing sustains the reduction in tumour growth, increase in DUSP-1 level and inhibition of ERK1/2 action, suggesting a pivotal role for TFEB in maintaining proliferative melanoma cell behaviour and the operational metabolic pathways necessary for meeting the high energy demands of melanoma cells.
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Affiliation(s)
- C Ariano
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - F Costanza
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - M Akman
- Department of Oncology, University of Torino, Torino, Italy
| | - C Riganti
- Department of Oncology, University of Torino, Torino, Italy
| | - D Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases - CAAD, Novara, Italy
| | - E Casanova
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - E Astanina
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - V Comunanza
- Department of Oncology, University of Torino, Torino, Italy
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - F Bussolino
- Department of Oncology, University of Torino, Torino, Italy.
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy.
| | - G Doronzo
- Department of Oncology, University of Torino, Torino, Italy.
- Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy.
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21
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Lizcano-Perret B, Lardinois C, Wavreil F, Hauchamps P, Herinckx G, Sorgeloos F, Vertommen D, Gatto L, Michiels T. Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic. PLoS Pathog 2022; 18:e1011042. [PMID: 36508477 PMCID: PMC9779665 DOI: 10.1371/journal.ppat.1011042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/22/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Proteins from some unrelated pathogens, including small RNA viruses of the family Picornaviridae, large DNA viruses such as Kaposi sarcoma-associated herpesvirus and even bacteria of the genus Yersinia can recruit cellular p90-ribosomal protein S6 kinases (RSKs) through a common linear motif and maintain the kinases in an active state. On the one hand, pathogens' proteins might hijack RSKs to promote their own phosphorylation (direct target model). On the other hand, some data suggested that pathogens' proteins might dock the hijacked RSKs toward a third interacting partner, thus redirecting the kinase toward a specific substrate. We explored the second hypothesis using the Cardiovirus leader protein (L) as a paradigm. The L protein is known to trigger nucleocytoplasmic trafficking perturbation, which correlates with hyperphosphorylation of phenylalanine-glycine (FG)-nucleoporins (FG-NUPs) such as NUP98. Using a biotin ligase fused to either RSK or L, we identified FG-NUPs as primary partners of the L-RSK complex in infected cells. An L protein mutated in the central RSK-interaction motif was readily targeted to the nuclear envelope whereas an L protein mutated in the C-terminal domain still interacted with RSK but failed to interact with the nuclear envelope. Thus, L uses distinct motifs to recruit RSK and to dock the L-RSK complex toward the FG-NUPs. Using an analog-sensitive RSK2 mutant kinase, we show that, in infected cells, L can trigger RSK to use NUP98 and NUP214 as direct substrates. Our data therefore illustrate a novel virulence mechanism where pathogens' proteins hijack and retarget cellular protein kinases toward specific substrates, to promote their replication or to escape immunity.
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Affiliation(s)
- Belén Lizcano-Perret
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Cécile Lardinois
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Fanny Wavreil
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Philippe Hauchamps
- Computational Biology and Bioinformatics unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Gaëtan Herinckx
- MASSPROT platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Frédéric Sorgeloos
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Didier Vertommen
- MASSPROT platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Thomas Michiels
- Molecular Virology unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- * E-mail:
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22
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MYC promotes immune-suppression in triple-negative breast cancer via inhibition of interferon signaling. Nat Commun 2022; 13:6579. [PMID: 36323660 PMCID: PMC9630413 DOI: 10.1038/s41467-022-34000-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
The limited efficacy of immune checkpoint inhibitor treatment in triple-negative breast cancer (TNBC) patients is attributed to sparse or unresponsive tumor-infiltrating lymphocytes, but the mechanisms that lead to a therapy resistant tumor immune microenvironment are incompletely known. Here we show a strong correlation between MYC expression and loss of immune signatures in human TNBC. In mouse models of TNBC proficient or deficient of breast cancer type 1 susceptibility gene (BRCA1), MYC overexpression dramatically decreases lymphocyte infiltration in tumors, along with immune signature remodelling. MYC-mediated suppression of inflammatory signalling induced by BRCA1/2 inactivation is confirmed in human TNBC cell lines. Moreover, MYC overexpression prevents the recruitment and activation of lymphocytes in both human and mouse TNBC co-culture models. Chromatin-immunoprecipitation-sequencing reveals that MYC, together with its co-repressor MIZ1, directly binds promoters of multiple interferon-signalling genes, resulting in their downregulation. MYC overexpression thus counters tumor growth inhibition by a Stimulator of Interferon Genes (STING) agonist via suppressing induction of interferon signalling. Together, our data reveal that MYC suppresses innate immunity and facilitates tumor immune escape, explaining the poor immunogenicity of MYC-overexpressing TNBCs.
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23
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Wolff JH, Mikkelsen JG. Delivering genes with human immunodeficiency virus-derived vehicles: still state-of-the-art after 25 years. J Biomed Sci 2022; 29:79. [PMID: 36209077 PMCID: PMC9548131 DOI: 10.1186/s12929-022-00865-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Viruses are naturally endowed with the capacity to transfer genetic material between cells. Following early skepticism, engineered viruses have been used to transfer genetic information into thousands of patients, and genetic therapies are currently attracting large investments. Despite challenges and severe adverse effects along the way, optimized technologies and improved manufacturing processes are driving gene therapy toward clinical translation. Fueled by the outbreak of AIDS in the 1980s and the accompanying focus on human immunodeficiency virus (HIV), lentiviral vectors derived from HIV have grown to become one of the most successful and widely used vector technologies. In 2022, this vector technology has been around for more than 25 years. Here, we celebrate the anniversary by portraying the vector system and its intriguing properties. We dive into the technology itself and recapitulate the use of lentiviral vectors for ex vivo gene transfer to hematopoietic stem cells and for production of CAR T-cells. Furthermore, we describe the adaptation of lentiviral vectors for in vivo gene delivery and cover the important contribution of lentiviral vectors to basic molecular research including their role as carriers of CRISPR genome editing technologies. Last, we dwell on the emerging capacity of lentiviral particles to package and transfer foreign proteins.
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Affiliation(s)
- Jonas Holst Wolff
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark
| | - Jacob Giehm Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark.
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24
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Astanina E, Doronzo G, Corà D, Neri F, Oliviero S, Genova T, Mussano F, Middonti E, Vallariello E, Cencioni C, Valdembri D, Serini G, Limana F, Foglio E, Ballabio A, Bussolino F. The TFEB-TGIF1 axis regulates EMT in mouse epicardial cells. Nat Commun 2022; 13:5191. [PMID: 36057632 PMCID: PMC9440911 DOI: 10.1038/s41467-022-32855-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a complex and pivotal process involved in organogenesis and is related to several pathological processes, including cancer and fibrosis. During heart development, EMT mediates the conversion of epicardial cells into vascular smooth muscle cells and cardiac interstitial fibroblasts. Here, we show that the oncogenic transcription factor EB (TFEB) is a key regulator of EMT in epicardial cells and that its genetic overexpression in mouse epicardium is lethal due to heart defects linked to impaired EMT. TFEB specifically orchestrates the EMT-promoting function of transforming growth factor (TGF) β, and this effect results from activated transcription of thymine-guanine-interacting factor (TGIF)1, a TGFβ/Smad pathway repressor. The Tgif1 promoter is activated by TFEB, and in vitro and in vivo findings demonstrate its increased expression when Tfeb is overexpressed. Furthermore, Tfeb overexpression in vitro prevents TGFβ-induced EMT, and this effect is abolished by Tgif1 silencing. Tfeb loss of function, similar to that of Tgif1, sensitizes cells to TGFβ, inducing an EMT response to low doses of TGFβ. Together, our findings reveal an unexpected function of TFEB in regulating EMT, which might provide insights into injured heart repair and control of cancer progression. Epithelial-mesenchymal transition (EMT) is a complex process involved in organogenesis. Here, the authors show that the transcription factor EB (TFEB) regulates EMT in epicardium during heart development by tuning sensitivity to TGFβ signaling.
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Affiliation(s)
- Elena Astanina
- Department of Oncology, University of Torino, Torino, Italy. .,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy.
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, Università degli Studi del Piemonte Orientale, Novara, Italy
| | - Francesco Neri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Tullio Genova
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Federico Mussano
- CIR Dental School, Department of Surgical Sciences, University of Torino, Via Nizza 230, 10126, Turin, Italy
| | - Emanuele Middonti
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Edoardo Vallariello
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Chiara Cencioni
- Institute for Systems Analysis and Computer Science "A. Ruberti", National Research Council (IASI-CNR), Rome, Italy
| | - Donatella Valdembri
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Guido Serini
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Federica Limana
- San Raffaele Open University, Rome, Italy.,Laboratory of Cellular and Molecular Pathology, IRCCS San Raffaele Pisana, Rome, Italy
| | - Eleonora Foglio
- Technoscience, Parco Scientifico e Tecnologico Pontino, 04100, Latina, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Federico Bussolino
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
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25
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Yew CHT, Gurumoorthy N, Nordin F, Tye GJ, Wan Kamarul Zaman WS, Tan JJ, Ng MH. Integrase deficient lentiviral vector: prospects for safe clinical applications. PeerJ 2022; 10:e13704. [PMID: 35979475 PMCID: PMC9377332 DOI: 10.7717/peerj.13704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/19/2022] [Indexed: 01/17/2023] Open
Abstract
HIV-1 derived lentiviral vector is an efficient transporter for delivering desired genetic materials into the targeted cells among many viral vectors. Genetic material transduced by lentiviral vector is integrated into the cell genome to introduce new functions, repair defective cell metabolism, and stimulate certain cell functions. Various measures have been administered in different generations of lentiviral vector systems to reduce the vector's replicating capabilities. Despite numerous demonstrations of an excellent safety profile of integrative lentiviral vectors, the precautionary approach has prompted the development of integrase-deficient versions of these vectors. The generation of integrase-deficient lentiviral vectors by abrogating integrase activity in lentiviral vector systems reduces the rate of transgenes integration into host genomes. With this feature, the integrase-deficient lentiviral vector is advantageous for therapeutic implementation and widens its clinical applications. This short review delineates the biology of HIV-1-erived lentiviral vector, generation of integrase-deficient lentiviral vector, recent studies involving integrase-deficient lentiviral vectors, limitations, and prospects for neoteric clinical use.
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Affiliation(s)
- Chee-Hong Takahiro Yew
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Universiti Kebangsaan Malaysia Medical Centre (UKMMC), Kuala Lumpur, Malaysia
| | - Narmatha Gurumoorthy
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Universiti Kebangsaan Malaysia Medical Centre (UKMMC), Kuala Lumpur, Malaysia
| | - Fazlina Nordin
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Universiti Kebangsaan Malaysia Medical Centre (UKMMC), Kuala Lumpur, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | | | - Jun Jie Tan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia (USM), Bertam, Kepala Batas, Pulau Pinang, Malaysia
| | - Min Hwei Ng
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Universiti Kebangsaan Malaysia Medical Centre (UKMMC), Kuala Lumpur, Malaysia
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26
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Zingg D, Bhin J, Yemelyanenko J, Kas SM, Rolfs F, Lutz C, Lee JK, Klarenbeek S, Silverman IM, Annunziato S, Chan CS, Piersma SR, Eijkman T, Badoux M, Gogola E, Siteur B, Sprengers J, de Klein B, de Goeij-de Haas RR, Riedlinger GM, Ke H, Madison R, Drenth AP, van der Burg E, Schut E, Henneman L, van Miltenburg MH, Proost N, Zhen H, Wientjens E, de Bruijn R, de Ruiter JR, Boon U, de Korte-Grimmerink R, van Gerwen B, Féliz L, Abou-Alfa GK, Ross JS, van de Ven M, Rottenberg S, Cuppen E, Chessex AV, Ali SM, Burn TC, Jimenez CR, Ganesan S, Wessels LFA, Jonkers J. Truncated FGFR2 is a clinically actionable oncogene in multiple cancers. Nature 2022; 608:609-617. [PMID: 35948633 PMCID: PMC9436779 DOI: 10.1038/s41586-022-05066-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/03/2022] [Indexed: 12/13/2022]
Abstract
Somatic hotspot mutations and structural amplifications and fusions that affect fibroblast growth factor receptor 2 (encoded by FGFR2) occur in multiple types of cancer1. However, clinical responses to FGFR inhibitors have remained variable1–9, emphasizing the need to better understand which FGFR2 alterations are oncogenic and therapeutically targetable. Here we apply transposon-based screening10,11 and tumour modelling in mice12,13, and find that the truncation of exon 18 (E18) of Fgfr2 is a potent driver mutation. Human oncogenomic datasets revealed a diverse set of FGFR2 alterations, including rearrangements, E1–E17 partial amplifications, and E18 nonsense and frameshift mutations, each causing the transcription of E18-truncated FGFR2 (FGFR2ΔE18). Functional in vitro and in vivo examination of a compendium of FGFR2ΔE18 and full-length variants pinpointed FGFR2-E18 truncation as single-driver alteration in cancer. By contrast, the oncogenic competence of FGFR2 full-length amplifications depended on a distinct landscape of cooperating driver genes. This suggests that genomic alterations that generate stable FGFR2ΔE18 variants are actionable therapeutic targets, which we confirmed in preclinical mouse and human tumour models, and in a clinical trial. We propose that cancers containing any FGFR2 variant with a truncated E18 should be considered for FGFR-targeted therapies. Truncation of exon 18 of FGFR2 (FGFR2ΔE18) is a potent driver mutation in mice and humans, and FGFR-targeted therapy should be considered for patients with cancer expressing stable FGFR2ΔE18 variants.
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Affiliation(s)
- Daniel Zingg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Jinhyuk Bhin
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julia Yemelyanenko
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Sjors M Kas
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Frank Rolfs
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | | | - Sjoerd Klarenbeek
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Stefano Annunziato
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Chang S Chan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Timo Eijkman
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Madelon Badoux
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Bjørn Siteur
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Justin Sprengers
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bim de Klein
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Richard R de Goeij-de Haas
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gregory M Riedlinger
- Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA.,Department of Pathology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Hua Ke
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA
| | | | - Anne Paulien Drenth
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Eva Schut
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Linda Henneman
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martine H van Miltenburg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Ellen Wientjens
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ute Boon
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | | | - Bastiaan van Gerwen
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Luis Féliz
- Incyte Biosciences International, Morges, Switzerland
| | - Ghassan K Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Medical College at Cornell University, New York, NY, USA
| | - Jeffrey S Ross
- Foundation Medicine, Cambridge, MA, USA.,Upstate University Hospital, Upstate Medical University, Syracuse, NY, USA
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
| | - Edwin Cuppen
- Oncode Institute, Utrecht, The Netherlands.,Hartwig Medical Foundation, Amsterdam, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Shridar Ganesan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA.
| | - Lodewyk F A Wessels
- Oncode Institute, Utrecht, The Netherlands. .,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Oncode Institute, Utrecht, The Netherlands.
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27
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Gioelli N, Neilson LJ, Wei N, Villari G, Chen W, Kuhle B, Ehling M, Maione F, Willox S, Brundu S, Avanzato D, Koulouras G, Mazzone M, Giraudo E, Yang XL, Valdembri D, Zanivan S, Serini G. Neuropilin 1 and its inhibitory ligand mini-tryptophanyl-tRNA synthetase inversely regulate VE-cadherin turnover and vascular permeability. Nat Commun 2022; 13:4188. [PMID: 35858913 PMCID: PMC9300702 DOI: 10.1038/s41467-022-31904-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
The formation of a functional blood vessel network relies on the ability of endothelial cells (ECs) to dynamically rearrange their adhesive contacts in response to blood flow and guidance cues, such as vascular endothelial growth factor-A (VEGF-A) and class 3 semaphorins (SEMA3s). Neuropilin 1 (NRP1) is essential for blood vessel development, independently of its ligands VEGF-A and SEMA3, through poorly understood mechanisms. Grounding on unbiased proteomic analysis, we report here that NRP1 acts as an endocytic chaperone primarily for adhesion receptors on the surface of unstimulated ECs. NRP1 localizes at adherens junctions (AJs) where, interacting with VE-cadherin, promotes its basal internalization-dependent turnover and favors vascular permeability initiated by histamine in both cultured ECs and mice. We identify a splice variant of tryptophanyl-tRNA synthetase (mini-WARS) as an unconventionally secreted extracellular inhibitory ligand of NRP1 that, by stabilizing it at the AJs, slows down both VE-cadherin turnover and histamine-elicited endothelial leakage. Thus, our work shows a role for NRP1 as a major regulator of AJs plasticity and reveals how mini-WARS acts as a physiological NRP1 inhibitory ligand in the control of VE-cadherin endocytic turnover and vascular permeability.
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Affiliation(s)
- Noemi Gioelli
- Department of Oncology, University of Torino School of Medicine, Candiolo (TO), Italy
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy
| | | | - Na Wei
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Giulia Villari
- Department of Oncology, University of Torino School of Medicine, Candiolo (TO), Italy
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy
| | - Wenqian Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Manuel Ehling
- Center for Cancer Biology, Department of Oncology, University of Leuven, Leuven, 3000, Belgium
- Center for Cancer Biology, VIB, Leuven, 3000, Belgium
| | - Federica Maione
- Department of Oncology, University of Torino School of Medicine, Candiolo (TO), Italy
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy
| | - Sander Willox
- Center for Cancer Biology, Department of Oncology, University of Leuven, Leuven, 3000, Belgium
- Center for Cancer Biology, VIB, Leuven, 3000, Belgium
| | - Serena Brundu
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy
- Department of Science and Drug Technology, University of Torino, Torino, Italy
| | - Daniele Avanzato
- Department of Oncology, University of Torino School of Medicine, Candiolo (TO), Italy
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy
| | | | - Massimiliano Mazzone
- Center for Cancer Biology, Department of Oncology, University of Leuven, Leuven, 3000, Belgium
- Center for Cancer Biology, VIB, Leuven, 3000, Belgium
- Department of Science and Drug Technology, University of Torino, Torino, Italy
- Molecular Biotechnology Center (MBC), University of Torino, Torino, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Enrico Giraudo
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy
- Department of Science and Drug Technology, University of Torino, Torino, Italy
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Donatella Valdembri
- Department of Oncology, University of Torino School of Medicine, Candiolo (TO), Italy
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Guido Serini
- Department of Oncology, University of Torino School of Medicine, Candiolo (TO), Italy.
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo (TO), Italy.
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Margarido AS, Uceda-Castro R, Hahn K, de Bruijn R, Kester L, Hofland I, Lohuis J, Seinstra D, Broeks A, Jonkers J, Broekman MLD, Wesseling P, Vennin C, Vizoso M, van Rheenen J. Epithelial-to-Mesenchymal Transition Drives Invasiveness of Breast Cancer Brain Metastases. Cancers (Basel) 2022; 14:cancers14133115. [PMID: 35804890 PMCID: PMC9264851 DOI: 10.3390/cancers14133115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 12/30/2022] Open
Abstract
(1) Background: an increasing number of breast cancer patients develop lethal brain metastases (BM). The complete removal of these tumors by surgery becomes complicated when cells infiltrate into the brain parenchyma. However, little is known about the nature of these invading cells in breast cancer brain metastasis (BCBM). (2) Methods: we use intravital microscopy through a cranial window to study the behavior of invading cells in a mouse model of BCBM. (3) Results: we demonstrate that BCBM cells that escape from the metastatic mass and infiltrate into brain parenchyma undergo epithelial-to-mesenchymal transition (EMT). Moreover, cells undergoing EMT revert to an epithelial state when growing tumor masses in the brain. Lastly, through multiplex immunohistochemistry, we confirm the presence of these infiltrative cells in EMT in patient samples. (4) Conclusions: together, our data identify the critical role of EMT in the invasive behavior of BCBM, which warrants further consideration to target those cells when treating BCBM.
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Affiliation(s)
- Andreia S. Margarido
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
| | - Rebeca Uceda-Castro
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
| | - Kerstin Hahn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Lennart Kester
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
| | - Ingrid Hofland
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (I.H.); (A.B.)
| | - Jeroen Lohuis
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
| | - Danielle Seinstra
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, 1081 HV Amsterdam, The Netherlands; (D.S.); (P.W.)
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (I.H.); (A.B.)
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
| | - Marike L. D. Broekman
- Department of Neurosurgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
- Department of Neurosurgery, Haaglanden Medical Center, Lijnbaan, 2512 VA The Hague, The Netherlands
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, 1081 HV Amsterdam, The Netherlands; (D.S.); (P.W.)
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Claire Vennin
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
| | - Miguel Vizoso
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
- Correspondence: (M.V.); (J.v.R.)
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (A.S.M.); (R.U.-C.); (K.H.); (R.d.B.); (L.K.); (J.L.); (J.J.); (C.V.)
- Correspondence: (M.V.); (J.v.R.)
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29
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Ariano C, Riganti C, Corà D, Valdembri D, Mana G, Astanina E, Serini G, Bussolino F, Doronzo G. TFEB controls integrin-mediated endothelial cell adhesion by the regulation of cholesterol metabolism. Angiogenesis 2022; 25:471-492. [PMID: 35545719 PMCID: PMC9519734 DOI: 10.1007/s10456-022-09840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
The dynamic integrin-mediated adhesion of endothelial cells (ECs) to the surrounding ECM is fundamental for angiogenesis both in physiological and pathological conditions, such as embryonic development and cancer progression. The dynamics of EC-to-ECM adhesions relies on the regulation of the conformational activation and trafficking of integrins. Here, we reveal that oncogenic transcription factor EB (TFEB), a known regulator of lysosomal biogenesis and metabolism, also controls a transcriptional program that influences the turnover of ECM adhesions in ECs by regulating cholesterol metabolism. We show that TFEB favors ECM adhesion turnover by promoting the transcription of genes that drive the synthesis of cholesterol, which promotes the aggregation of caveolin-1, and the caveolin-dependent endocytosis of integrin β1. These findings suggest that TFEB might represent a novel target for the pharmacological control of pathological angiogenesis and bring new insights in the mechanism sustaining TFEB control of endocytosis.
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Affiliation(s)
- Camilla Ariano
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - Chiara Riganti
- Department of Oncology, University of Torino, Torino, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases-CAAD, Novara, Italy
| | - Donatella Valdembri
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - Giulia Mana
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - Elena Astanina
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - Guido Serini
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, Candiolo, Italy. .,Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy.
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, Candiolo, Italy. .,Candiolo Cancer Institute- FPO-IRCCS, Candiolo, Italy.
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30
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Comprehensive characterization of pre- and post-treatment samples of breast cancer reveal potential mechanisms of chemotherapy resistance. NPJ Breast Cancer 2022; 8:60. [PMID: 35523804 PMCID: PMC9076915 DOI: 10.1038/s41523-022-00428-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/12/2022] [Indexed: 12/23/2022] Open
Abstract
When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk is significantly higher if no complete pathologic response is achieved. Identification of the underlying resistance mechanisms is essential to select treatments with maximal efficacy and minimal toxicity. Here we employed gene expression profiles derived from 317 HER2-negative treatment-naïve breast cancer biopsies of patients who underwent neoadjuvant chemotherapy, deep whole exome, and RNA-sequencing profiles of 22 matched pre- and post-treatment tumors, and treatment outcome data to identify biomarkers of response and resistance mechanisms. Molecular profiling of treatment-naïve breast cancer samples revealed that expression levels of proliferation, immune response, and extracellular matrix (ECM) organization combined predict response to chemotherapy. Triple negative patients with high proliferation, high immune response and low ECM expression had a significantly better treatment response and survival benefit (HR 0.29, 95% CI 0.10–0.85; p = 0.02), while in ER+ patients the opposite was seen (HR 4.73, 95% CI 1.51–14.8; p = 0.008). The characterization of paired pre-and post-treatment samples revealed that aberrations of known cancer genes were either only present in the pre-treatment sample (CDKN1B) or in the post-treatment sample (TP53, APC, CTNNB1). Proliferation-associated genes were frequently down-regulated in post-treatment ER+ tumors, but not in triple negative tumors. Genes involved in ECM were upregulated in the majority of post-chemotherapy samples. Genomic and transcriptomic differences between pre- and post-chemotherapy samples are common and may reveal potential mechanisms of therapy resistance. Our results show a wide range of distinct, but related mechanisms, with a prominent role for proliferation- and ECM-related genes.
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31
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Krivdova G, Voisin V, Schoof EM, Marhon SA, Murison A, McLeod JL, Gabra MM, Zeng AGX, Aigner S, Yee BA, Shishkin AA, Van Nostrand EL, Hermans KG, Trotman-Grant AC, Mbong N, Kennedy JA, Gan OI, Wagenblast E, De Carvalho DD, Salmena L, Minden MD, Bader GD, Yeo GW, Dick JE, Lechman ER. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML. Cell Rep 2022; 38:110481. [PMID: 35263585 PMCID: PMC11185845 DOI: 10.1016/j.celrep.2022.110481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 11/18/2022] Open
Abstract
Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSCs) point to shared core stemness properties. However, discordance between mRNA and protein signatures highlights an important role for post-transcriptional regulation by microRNAs (miRNAs) in governing this critical nexus. Here, we identify miR-130a as a regulator of HSC self-renewal and differentiation. Enforced expression of miR-130a impairs B lymphoid differentiation and expands long-term HSCs. Integration of protein mass spectrometry and chimeric AGO2 crosslinking and immunoprecipitation (CLIP) identifies TBL1XR1 as a primary miR-130a target, whose loss of function phenocopies miR-130a overexpression. Moreover, we report that miR-130a is highly expressed in t(8;21) acute myeloid leukemia (AML), where it is critical for maintaining the oncogenic molecular program mediated by the AML1-ETO complex. Our study establishes that identification of the comprehensive miRNA targetome within primary cells enables discovery of genes and molecular networks underpinning stemness properties of normal and leukemic cells.
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Affiliation(s)
- Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Erwin M Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jessica L McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Martino M Gabra
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexander A Shishkin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Karin G Hermans
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Program of Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Aaron C Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Division of Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON M4N3M5, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leonardo Salmena
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Gary D Bader
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada.
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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Paes Dias M, Rottenberg S, Jonkers J. Functional genetic dropout screens and in vivo validation of candidate therapeutic targets using mouse mammary tumoroids. STAR Protoc 2022; 3:101132. [PMID: 35146447 PMCID: PMC8801381 DOI: 10.1016/j.xpro.2022.101132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We have previously developed 3D tumoroids derived from genetically engineered mouse models (GEMMs) of BRCA1/2-deficient breast cancer. Here, we describe how to genetically modify tumoroids, use them for functional genetic dropout screens, and carry out orthotopic transplantation of modified tumoroids. The purpose of this protocol is to screen for therapeutic targets and allow rapid and straightforward in vivo validation of the candidate targets. For complete details on the use and execution of this protocol, please refer to Paes Dias et al. (2021b). Functional genetic dropout screens using BRCA1/2-deficient mouse mammary tumoroids Screen analysis and identification of candidate drug targets In vitro genetic modification and orthotopic transplantation of tumoroids Rapid and straightforward testing of candidate drug targets in vivo
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Affiliation(s)
- Mariana Paes Dias
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
- Oncode Institute, 1066CX Amsterdam, the Netherlands
- Corresponding author
| | - Sven Rottenberg
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland
| | - Jos Jonkers
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
- Oncode Institute, 1066CX Amsterdam, the Netherlands
- Corresponding author
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33
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Choteau M, Scohy A, Messe S, Luyckx M, Dechamps M, Montiel V, Yombi JC, Gruson D, Limaye N, Michiels T, Dumoutier L. Development of SARS-CoV2 humoral response including neutralizing antibodies is not sufficient to protect patients against fatal infection. Sci Rep 2022; 12:2077. [PMID: 35136139 PMCID: PMC8827092 DOI: 10.1038/s41598-022-06038-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/18/2022] [Indexed: 12/23/2022] Open
Abstract
More than a year after the start of the pandemic, COVID-19 remains a global health emergency. Although the immune response against SARS-CoV-2 has been extensively studied, some points remain controversial. One is the role of antibodies in viral clearance and modulation of disease severity. While passive transfer of neutralizing antibodies protects against SARS-CoV-2 infection in animal models, titers of anti-SARS-CoV-2 antibodies have been reported to be higher in patients suffering from more severe forms of the disease. A second key question for pandemic management and vaccine design is the persistence of the humoral response. Here, we characterized the antibody response in 187 COVID-19 patients, ranging from asymptomatic individuals to patients who died from COVID-19, and including patients who recovered. We developed in-house ELISAs to measure titers of IgG, IgM and IgA directed against the RBD or N regions in patient serum or plasma, and a spike-pseudotyped neutralization assay to analyse seroneutralization. Higher titers of virus-specific antibodies were detected in patients with severe COVID-19, including deceased patients, compared to asymptomatic patients. This demonstrates that fatal infection is not associated with defective humoral response. Finally, most of recovered patients still had anti-SARS-CoV-2 IgG more than 3 months after infection.
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Affiliation(s)
- Mathilde Choteau
- Experimental Medicine Unit, de Duve Institute, Université Catholique de Louvain, 74 Avenue Hippocrate, 1200, Brussels, Belgium
| | - Anaïs Scohy
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, Brussels, Belgium
- Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Stéphane Messe
- Virology Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Mathieu Luyckx
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
- Tumor Infiltrating Lymphocytes Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Mélanie Dechamps
- Pôle de Recherche Cardiovasculaire (CARD), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
- Cardiovascular Intensive Care, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Virginie Montiel
- Intensive Care, Cliniques Universitaires Saint-Luc, Brussels, Belgium
- Pôle de Recherche Pharmacologie et de Thérapeutique (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Jean Cyr Yombi
- Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
- Department of Internal Medicine and Infectious Diseases, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Damien Gruson
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, Brussels, Belgium
- Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Nisha Limaye
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Thomas Michiels
- Virology Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Laure Dumoutier
- Experimental Medicine Unit, de Duve Institute, Université Catholique de Louvain, 74 Avenue Hippocrate, 1200, Brussels, Belgium.
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34
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Stravalaci M, Pagani I, Paraboschi EM, Pedotti M, Doni A, Scavello F, Mapelli SN, Sironi M, Perucchini C, Varani L, Matkovic M, Cavalli A, Cesana D, Gallina P, Pedemonte N, Capurro V, Clementi N, Mancini N, Invernizzi P, Bayarri-Olmos R, Garred P, Rappuoli R, Duga S, Bottazzi B, Uguccioni M, Asselta R, Vicenzi E, Mantovani A, Garlanda C. Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules. Nat Immunol 2022; 23:275-286. [DOI: 10.1038/s41590-021-01114-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/09/2021] [Indexed: 12/11/2022]
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Paes Dias M, Tripathi V, van der Heijden I, Cong K, Manolika EM, Bhin J, Gogola E, Galanos P, Annunziato S, Lieftink C, Andújar-Sánchez M, Chakrabarty S, Smith GCM, van de Ven M, Beijersbergen RL, Bartkova J, Rottenberg S, Cantor S, Bartek J, Ray Chaudhuri A, Jonkers J. Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps. Mol Cell 2021; 81:4692-4708.e9. [PMID: 34555355 DOI: 10.1016/j.molcel.2021.09.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 07/20/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.
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Affiliation(s)
- Mariana Paes Dias
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Vivek Tripathi
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD Rotterdam, the Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Ke Cong
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eleni-Maria Manolika
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD Rotterdam, the Netherlands
| | - Jinhyuk Bhin
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Robotics and Screening Center, Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Panagiotis Galanos
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
| | - Stefano Annunziato
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Robotics and Screening Center, Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Miguel Andújar-Sánchez
- Pathology Department, Complejo Hospitalario Universitario Insular, Las Palmas, Gran Canaria, Spain
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Karnataka 576104, India
| | - Graeme C M Smith
- Artios Pharma, Glenn Berge Building, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Robotics and Screening Center, Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jirina Bartkova
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen 2100, Denmark; Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm 171 77, Sweden
| | - Sven Rottenberg
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland
| | - Sharon Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen 2100, Denmark; Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm 171 77, Sweden
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD Rotterdam, the Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, 1066CX Amsterdam, the Netherlands.
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Role of TGFβ1 and WNT6 in FGF2 and BMP4-driven endothelial differentiation of murine embryonic stem cells. Angiogenesis 2021; 25:113-128. [PMID: 34478025 PMCID: PMC8813801 DOI: 10.1007/s10456-021-09815-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/13/2021] [Indexed: 11/21/2022]
Abstract
Embryonic stem cells (ES) are a valuable source of endothelial cells. By co-culturing ES cells with the stromal PA6 cells, the endothelial commitment can be achieved by adding exogenous FGF2 or BMP4. In this work, the molecular pathways that direct the differentiation of ES cells toward endothelium in response to FGF2 are evaluated and compared to those activated by BMP4. To this purpose the genes expression profiles of both ES/PA6 co-cultures and of pure cultures of PA6 cells were obtained by microarray technique at different time points. The bioinformatics processing of the data indicated TGFβ1 as the most represented upstream regulator in FGF2-induced endothelial commitment while WNT pathway as the most represented in BMP4-activated endothelial differentiation. Loss of function experiments were performed to validate the importance of TGFβ1 and WNT6 respectively in FGF2 and BMP4-induced endothelial differentiation. The loss of TGFβ1 expression significantly impaired the accomplishment of the endothelial commitment unless exogenous recombinant TGFβ1 was added to the culture medium. Similarly, silencing WNT6 expression partially affected the endothelial differentiation of the ES cells upon BMP4 stimulation. Such dysfunction was recovered by the addition of recombinant WNT6 to the culture medium. The ES/PA6 co-culture system recreates an in vitro complete microenvironment in which endothelial commitment is accomplished in response to alternative signals through different mechanisms. Given the importance of WNT and TGFβ1 in mediating the crosstalk between tumor and stromal cells this work adds new insights in the mechanism of tumor angiogenesis and of its possible inhibition.
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Dieter SM, Siegl C, Codó PL, Huerta M, Ostermann-Parucha AL, Schulz E, Zowada MK, Martin S, Laaber K, Nowrouzi A, Blatter M, Kreth S, Westermann F, Benner A, Uhrig U, Putzker K, Lewis J, Haegebarth A, Mumberg D, Holton SJ, Weiske J, Toepper LM, Scheib U, Siemeister G, Ball CR, Kuster B, Stoehr G, Hahne H, Johannes S, Lange M, Herbst F, Glimm H. Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer. Cell Rep 2021; 36:109394. [PMID: 34289372 DOI: 10.1016/j.celrep.2021.109394] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/08/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of-but not all-spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.
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Affiliation(s)
- Sebastian M Dieter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany.
| | | | - Paula L Codó
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; CureVac AG, 60325 Frankfurt am Main, Germany
| | - Mario Huerta
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Anna L Ostermann-Parucha
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Erik Schulz
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Martina K Zowada
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Sylvia Martin
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Karin Laaber
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Ali Nowrouzi
- Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Mona Blatter
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Sina Kreth
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Kerstin Putzker
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Andrea Haegebarth
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Dominik Mumberg
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Simon J Holton
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Joerg Weiske
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Lena-Marit Toepper
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Ulrike Scheib
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Gerhard Siemeister
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | | | | | - Sarah Johannes
- Bayer AG, Research & Development, Pharmaceuticals, 42117 Wuppertal, Germany
| | - Martin Lange
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Friederike Herbst
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany.
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Parrini M, Naskar S, Alberti M, Colombi I, Morelli G, Rocchi A, Nanni M, Piccardi F, Charles S, Ronzitti G, Mingozzi F, Contestabile A, Cancedda L. Restoring neuronal chloride homeostasis with anti-NKCC1 gene therapy rescues cognitive deficits in a mouse model of Down syndrome. Mol Ther 2021; 29:3072-3092. [PMID: 34058387 PMCID: PMC8531145 DOI: 10.1016/j.ymthe.2021.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/27/2021] [Accepted: 05/18/2021] [Indexed: 01/24/2023] Open
Abstract
A common feature of diverse brain disorders is the alteration of GABA-mediated inhibition because of aberrant, intracellular chloride homeostasis induced by changes in the expression and/or function of chloride transporters. Notably, pharmacological inhibition of the chloride importer NKCC1 is able to rescue brain-related core deficits in animal models of these pathologies and in some human clinical studies. Here, we show that reducing NKCC1 expression by RNA interference in the Ts65Dn mouse model of Down syndrome (DS) restores intracellular chloride concentration, efficacy of gamma-aminobutyric acid (GABA)-mediated inhibition, and neuronal network dynamics in vitro and ex vivo. Importantly, adeno-associated virus (AAV)-mediated, neuron-specific NKCC1 knockdown in vivo rescues cognitive deficits in diverse behavioral tasks in Ts65Dn animals. Our results highlight a mechanistic link between NKCC1 expression and behavioral abnormalities in DS mice and establish a molecular target for new therapeutic approaches, including gene therapy, to treat brain disorders characterized by neuronal chloride imbalance.
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Affiliation(s)
- Martina Parrini
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Shovan Naskar
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Micol Alberti
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Ilaria Colombi
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Giovanni Morelli
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Anna Rocchi
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, 16132 Genoa, Italy; IRCSS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Marina Nanni
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Federica Piccardi
- Animal Facility, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Severine Charles
- Genethon, 91000 Evry, France; Paris-Saclay University, University Evry, Inserm, Integrare research unit UMR_S951, 91000 Evry, France
| | - Giuseppe Ronzitti
- Genethon, 91000 Evry, France; Paris-Saclay University, University Evry, Inserm, Integrare research unit UMR_S951, 91000 Evry, France
| | - Federico Mingozzi
- Genethon, 91000 Evry, France; Paris-Saclay University, University Evry, Inserm, Integrare research unit UMR_S951, 91000 Evry, France
| | - Andrea Contestabile
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy.
| | - Laura Cancedda
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy; Dulbecco Telethon Institute, 00185 Rome, Italy.
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Peruzzotti-Jametti L, Bernstock JD, Willis CM, Manferrari G, Rogall R, Fernandez-Vizarra E, Williamson JC, Braga A, van den Bosch A, Leonardi T, Krzak G, Kittel Á, Benincá C, Vicario N, Tan S, Bastos C, Bicci I, Iraci N, Smith JA, Peacock B, Muller KH, Lehner PJ, Buzas EI, Faria N, Zeviani M, Frezza C, Brisson A, Matheson NJ, Viscomi C, Pluchino S. Neural stem cells traffic functional mitochondria via extracellular vesicles. PLoS Biol 2021; 19:e3001166. [PMID: 33826607 PMCID: PMC8055036 DOI: 10.1371/journal.pbio.3001166] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/19/2021] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
Neural stem cell (NSC) transplantation induces recovery in animal models of central nervous system (CNS) diseases. Although the replacement of lost endogenous cells was originally proposed as the primary healing mechanism of NSC grafts, it is now clear that transplanted NSCs operate via multiple mechanisms, including the horizontal exchange of therapeutic cargoes to host cells via extracellular vesicles (EVs). EVs are membrane particles trafficking nucleic acids, proteins, metabolites and metabolic enzymes, lipids, and entire organelles. However, the function and the contribution of these cargoes to the broad therapeutic effects of NSCs are yet to be fully understood. Mitochondrial dysfunction is an established feature of several inflammatory and degenerative CNS disorders, most of which are potentially treatable with exogenous stem cell therapeutics. Herein, we investigated the hypothesis that NSCs release and traffic functional mitochondria via EVs to restore mitochondrial function in target cells. Untargeted proteomics revealed a significant enrichment of mitochondrial proteins spontaneously released by NSCs in EVs. Morphological and functional analyses confirmed the presence of ultrastructurally intact mitochondria within EVs with conserved membrane potential and respiration. We found that the transfer of these mitochondria from EVs to mtDNA-deficient L929 Rho0 cells rescued mitochondrial function and increased Rho0 cell survival. Furthermore, the incorporation of mitochondria from EVs into inflammatory mononuclear phagocytes restored normal mitochondrial dynamics and cellular metabolism and reduced the expression of pro-inflammatory markers in target cells. When transplanted in an animal model of multiple sclerosis, exogenous NSCs actively transferred mitochondria to mononuclear phagocytes and induced a significant amelioration of clinical deficits. Our data provide the first evidence that NSCs deliver functional mitochondria to target cells via EVs, paving the way for the development of novel (a)cellular approaches aimed at restoring mitochondrial dysfunction not only in multiple sclerosis, but also in degenerative neurological diseases.
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Affiliation(s)
- Luca Peruzzotti-Jametti
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | - Joshua D. Bernstock
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
- National Institutes of Health (NINDS/NIH), Bethesda, Maryland, United States of America
| | - Cory M. Willis
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | - Giulia Manferrari
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | - Rebecca Rogall
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | | | - James C. Williamson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Alice Braga
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | - Aletta van den Bosch
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | - Tommaso Leonardi
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Grzegorz Krzak
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | - Ágnes Kittel
- Institute of Experimental Medicine, Eötvös Lorand Research Network, Budapest, Hungary
| | - Cristiane Benincá
- MRC Mitochondrial Biology Unit, University of Cambridge, United Kingdom
| | - Nunzio Vicario
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Italy
| | | | - Carlos Bastos
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Iacopo Bicci
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
| | - Nunzio Iraci
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Italy
| | - Jayden A. Smith
- Cambridge Innovation Technologies Consulting (CITC) Limited, United Kingdom
| | - Ben Peacock
- NanoFCM Co., Ltd, Nottingham, United Kingdom
| | | | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Edit Iren Buzas
- Semmelweis University, Budapest, Hungary
- HCEMM Kft HU, Budapest, Hungary
- ELKH-SE, Budapest, Hungary
| | - Nuno Faria
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, United Kingdom
| | - Christian Frezza
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge United Kingdom
| | | | - Nicholas J. Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Carlo Viscomi
- MRC Mitochondrial Biology Unit, University of Cambridge, United Kingdom
| | - Stefano Pluchino
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, United Kingdom
- Cambridge Innovation Technologies Consulting (CITC) Limited, United Kingdom
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40
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Johnson NM, Alvarado AF, Moffatt TN, Edavettal JM, Swaminathan TA, Braun SE. HIV-based lentiviral vectors: origin and sequence differences. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 21:451-465. [PMID: 33981779 PMCID: PMC8065252 DOI: 10.1016/j.omtm.2021.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/23/2021] [Indexed: 12/11/2022]
Abstract
Three gene therapy strategies have received US Food and Drug Administration (FDA) approval; one includes HIV-1-based lentiviral vectors. These vectors incorporate features to provide long-term gene transfer and expression while minimizing generation of a replication-competent virus or pathogenicity. Importantly, the coding regions of viral proteins were deleted, and the cis-acting regulatory elements were retained. With the use of representative vectors developed for clinical/commercial applications, we compared the vector backbone sequences to the initial sources of the HIV-1. All vectors included required elements: 5′ long terminal repeat (LTR) through the Ψ packaging signal, central polypurine tract/chain termination sequence (cPPT/CTS), Rev responsive element (RRE), and 3′ LTR, including a poly(A) signal. The Ψ signaling sequence demonstrated the greatest similarity between all vectors with only minor changes. The 3′ LTR was the most divergent sequence with a range of deletions. The RRE length varied between vectors. Phylogenetic analysis of the cPPT/CTS indicated multiple sources, perhaps because of its later inclusion into lentiviral vector systems, whereas other regions revealed node clusters around the HIV-1 reference genomes HXB2 and NL4-3. We examine the function of each region in a lentiviral vector, the molecular differences between vectors, and where optimization may guide development of the lentiviral delivery systems.
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Affiliation(s)
- Nathan M Johnson
- Division of Immunology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA
| | - Anna Francesca Alvarado
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Trey N Moffatt
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Joshua M Edavettal
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Tarun A Swaminathan
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Stephen E Braun
- Division of Immunology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA.,Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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41
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Targeting CX3CR1 Suppresses the Fanconi Anemia DNA Repair Pathway and Synergizes with Platinum. Cancers (Basel) 2021; 13:cancers13061442. [PMID: 33810010 PMCID: PMC8004634 DOI: 10.3390/cancers13061442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/22/2022] Open
Abstract
The C-X3-C motif chemokine receptor 1 (CX3CR1, fractalkine receptor) is associated with neoplastic transformation, inflammation, neurodegenerative diseases and aging, and the small molecule inhibitor KAND567 targeting CX3CR1 (CX3CR1i) is evaluated in clinical trials for acute systemic inflammation upon SARS-CoV-2 infections. Here we identify a hitherto unknown role of CX3CR1 in Fanconi anemia (FA) pathway mediated repair of DNA interstrand crosslinks (ICLs) in replicating cells. FA pathway activation triggers CX3CR1 nuclear localization which facilitates assembly of the key FA protein FANCD2 into foci. Interfering with CX3CR1 function upon ICL-induction results in inability of replicating cells to progress from S phase, replication fork stalling and impaired chromatin recruitment of key FA pathway factors. Consistent with defective FA repair, CX3CR1i results in increased levels of residual cisplatin-DNA adducts and decreased cell survival. Importantly, CX3CR1i synergizes with platinum agents in a nonreversible manner in proliferation assays including platinum resistant models. Taken together, our results reveal an unanticipated interplay between CX3CR1 and the FA pathway and show for the first time that a clinical-phase small molecule inhibitor targeting CX3CR1 might show benefit in improving responses to DNA crosslinking chemotherapeutics.
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Goitre L, Fornelli C, Zotta A, Perrelli A, Retta SF. Production of KRIT1-knockout and KRIT1-knockin Mouse Embryonic Fibroblasts as Cellular Models of CCM Disease. Methods Mol Biol 2021; 2152:151-167. [PMID: 32524551 DOI: 10.1007/978-1-0716-0640-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The development of distinct cellular and animal models has allowed the identification and characterization of molecular mechanisms underlying the pathogenesis of cerebral cavernous malformation (CCM) disease. This is a major cerebrovascular disorder of proven genetic origin, affecting 0.5% of the population. Three disease genes have been identified: CCM1/KRIT1, CCM2, and CCM3. These genes encode for proteins implicated in the regulation of major cellular structures and mechanisms, such as cell-cell and cell-matrix adhesion, actin cytoskeleton dynamics, and endothelial-to-mesenchymal transition, suggesting that they may act as pleiotropic regulators of cellular homeostasis. Indeed, accumulated evidence in cellular and animal models demonstrates that emerged pleiotropic functions of CCM proteins are mainly due to their ability to modulate redox-sensitive pathways and mechanisms involved in adaptive responses to oxidative stress and inflammation, thus contributing to the preservation of cellular homeostasis and stress defenses. In particular, we demonstrated that KRIT1 loss-of-function affects master regulators of cellular redox homeostasis and responses to oxidative stress, including major redox-sensitive transcriptional factors and antioxidant proteins, and autophagy, suggesting that altered redox signaling and oxidative stress contribute to CCM pathogenesis, and opening novel preventive and therapeutic perspectives.In this chapter, we describe materials and methods for isolation of mouse embryonic fibroblast (MEF) cells from homozygous KRIT1-knockout mouse embryos, and their transduction with a lentiviral vector encoding KRIT1 to generate cellular models of CCM disease that contributed significantly to the identification of pathogenetic mechanisms.
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Affiliation(s)
- Luca Goitre
- Department of Clinical and Biological Science, University of Torino, Orbassano (Torino), Italy. .,CCM Italia Research Network, Torino, Italy.
| | - Claudia Fornelli
- Department of Clinical and Biological Science, University of Torino, Orbassano (Torino), Italy.,CCM Italia Research Network, Torino, Italy
| | - Alessia Zotta
- Department of Clinical and Biological Science, University of Torino, Orbassano (Torino), Italy.,CCM Italia Research Network, Torino, Italy
| | - Andrea Perrelli
- CCM Italia Research Network, Torino, Italy.,Department of Clinical and Biological Science, School of Medicine and Surgery, University of Torino, Orbassano (Torino), Italy
| | - Saverio Francesco Retta
- CCM Italia Research Network, Torino, Italy. .,Department of Clinical and Biological Science, School of Medicine and Surgery, University of Torino, Orbassano (Torino), Italy.
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43
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Wright H, Aylwin CF, Toro CA, Ojeda SR, Lomniczi A. Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression. Sci Rep 2021; 11:1996. [PMID: 33479437 PMCID: PMC7819995 DOI: 10.1038/s41598-021-81689-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Female puberty is subject to Polycomb Group (PcG)-dependent transcriptional repression. Kiss1, a puberty-activating gene, is a key target of this silencing mechanism. Using a gain-of-function approach and a systems biology strategy we now show that EED, an essential PcG component, acts in the arcuate nucleus of the hypothalamus to alter the functional organization of a gene network involved in the stimulatory control of puberty. A central node of this network is Kdm6b, which encodes an enzyme that erases the PcG-dependent histone modification H3K27me3. Kiss1 is a first neighbor in the network; genes encoding glutamatergic receptors and potassium channels are second neighbors. By repressing Kdm6b expression, EED increases H3K27me3 abundance at these gene promoters, reducing gene expression throughout a gene network controlling puberty activation. These results indicate that Kdm6b repression is a basic mechanism used by PcG to modulate the biological output of puberty-activating gene networks.
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Affiliation(s)
- Hollis Wright
- Division of Neuroscience, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA
| | - Carlos F Aylwin
- Division of Neuroscience, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA
| | - Carlos A Toro
- Division of Neuroscience, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA
| | - Sergio R Ojeda
- Division of Neuroscience, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA
| | - Alejandro Lomniczi
- Division of Neuroscience, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA.
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44
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Luis A. The Old and the New: Prospects for Non-Integrating Lentiviral Vector Technology. Viruses 2020; 12:v12101103. [PMID: 33003492 PMCID: PMC7600637 DOI: 10.3390/v12101103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Lentiviral vectors have been developed and used in multiple gene and cell therapy applications. One of their main advantages over other vectors is the ability to integrate the genetic material into the genome of the host. However, this can also be a disadvantage as it may lead to insertional mutagenesis. To address this, non-integrating lentiviral vectors (NILVs) were developed. To generate NILVs, it is possible to introduce mutations in the viral enzyme integrase and/or mutations on the viral DNA recognised by integrase (the attachment sites). NILVs are able to stably express transgenes from episomal DNA in non-dividing cells or transiently if the target cells divide. It has been shown that these vectors are able to transduce multiple cell types and tissues. These characteristics make NILVs ideal vectors to use in vaccination and immunotherapies, among other applications. They also open future prospects for NILVs as tools for the delivery of CRISPR/Cas9 components, a recent revolutionary technology now widely used for gene editing and repair.
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Affiliation(s)
- Apolonia Luis
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
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Jofra Hernández R, Calabria A, Sanvito F, De Mattia F, Farinelli G, Scala S, Visigalli I, Carriglio N, De Simone M, Vezzoli M, Cecere F, Migliavacca M, Basso-Ricci L, Omrani M, Benedicenti F, Norata R, Rancoita PMV, Di Serio C, Albertini P, Cristofori P, Naldini L, Gentner B, Montini E, Aiuti A, Mortellaro A. Hematopoietic Tumors in a Mouse Model of X-linked Chronic Granulomatous Disease after Lentiviral Vector-Mediated Gene Therapy. Mol Ther 2020; 29:86-102. [PMID: 33010230 PMCID: PMC7791081 DOI: 10.1016/j.ymthe.2020.09.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/03/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Chronic granulomatous disease (CGD) is a rare inherited disorder due to loss-of-function mutations in genes encoding the NADPH oxidase subunits. Hematopoietic stem and progenitor cell (HSPC) gene therapy (GT) using regulated lentiviral vectors (LVs) has emerged as a promising therapeutic option for CGD patients. We performed non-clinical Good Laboratory Practice (GLP) and laboratory-grade studies to assess the safety and genotoxicity of LV targeting myeloid-specific Gp91phox expression in X-linked chronic granulomatous disease (XCGD) mice. We found persistence of gene-corrected cells for up to 1 year, restoration of Gp91phox expression and NADPH oxidase activity in XCGD phagocytes, and reduced tissue inflammation after LV-mediated HSPC GT. Although most of the mice showed no hematological or biochemical toxicity, a small subset of XCGD GT mice developed T cell lymphoblastic lymphoma (2.94%) and myeloid leukemia (5.88%). No hematological malignancies were identified in C57BL/6 mice transplanted with transduced XCGD HSPCs. Integration pattern analysis revealed an oligoclonal composition with rare dominant clones harboring vector insertions near oncogenes in mice with tumors. Collectively, our data support the long-term efficacy of LV-mediated HSPC GT in XCGD mice and provide a safety warning because the chronic inflammatory XCGD background may contribute to oncogenesis.
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Affiliation(s)
- Raisa Jofra Hernández
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy; GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Sanvito
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy; Pathology Unit, Department of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabiola De Mattia
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giada Farinelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ilaria Visigalli
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicola Carriglio
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maura De Simone
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Michela Vezzoli
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Cecere
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maddalena Migliavacca
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy; Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Basso-Ricci
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maryam Omrani
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rossana Norata
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Clelia Di Serio
- University Centre for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Paola Albertini
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Patrizia Cristofori
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy; Non-Clinical Safety In Vivo Translation Research, Glaxo Smith Kline, Ware, UK
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy; Medical School, Vita-Salute San Raffaele University, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy; Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy; Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy; Medical School, Vita-Salute San Raffaele University, Milan, Italy.
| | - Alessandra Mortellaro
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
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46
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Sena-Esteves M, Gao G. Introducing Genes into Mammalian Cells: Viral Vectors. Cold Spring Harb Protoc 2020; 2020:095513. [PMID: 32457039 DOI: 10.1101/pdb.top095513] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the years, many different viral vector systems have been developed to take advantage of the specific biological properties and tropisms of a large number of mammalian viruses. As a result, researchers wanting to introduce and/or express genes in mammalian cells have many options, as discussed here.
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47
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Pavani G, Laurent M, Fabiano A, Cantelli E, Sakkal A, Corre G, Lenting PJ, Concordet JP, Toueille M, Miccio A, Amendola M. Ex vivo editing of human hematopoietic stem cells for erythroid expression of therapeutic proteins. Nat Commun 2020; 11:3778. [PMID: 32728076 PMCID: PMC7391635 DOI: 10.1038/s41467-020-17552-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 07/06/2020] [Indexed: 11/30/2022] Open
Abstract
Targeted genome editing has a great therapeutic potential to treat disorders that require protein replacement therapy. To develop a platform independent of specific patient mutations, therapeutic transgenes can be inserted in a safe and highly transcribed locus to maximize protein expression. Here, we describe an ex vivo editing approach to achieve efficient gene targeting in human hematopoietic stem/progenitor cells (HSPCs) and robust expression of clinically relevant proteins by the erythroid lineage. Using CRISPR-Cas9, we integrate different transgenes under the transcriptional control of the endogenous α-globin promoter, recapitulating its high and erythroid-specific expression. Erythroblasts derived from targeted HSPCs secrete different therapeutic proteins, which retain enzymatic activity and cross-correct patients’ cells. Moreover, modified HSPCs maintain long-term repopulation and multilineage differentiation potential in transplanted mice. Overall, we establish a safe and versatile CRISPR-Cas9-based HSPC platform for different therapeutic applications, including hemophilia and inherited metabolic disorders. A platform for systemic therapeutic transgene expression independent of patient mutations needs a safe and highly transcribed locus. Here the authors ex vivo edit HPSCs using CRISPR-Cas9 to integrate transgenes under the α-globin promoter to achieve erythroid specific expression.
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Affiliation(s)
- Giulia Pavani
- Genethon, 91000, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Marine Laurent
- Genethon, 91000, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Anna Fabiano
- Genethon, 91000, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Erika Cantelli
- Genethon, 91000, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Aboud Sakkal
- Genethon, 91000, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Guillaume Corre
- Genethon, 91000, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Peter J Lenting
- Laboratory of Hemostasis-Inflammation-Thrombosis, UMR_S1176, Inserm, Univ. Paris-Sud, Université Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
| | - Jean-Paul Concordet
- National Museum of Natural History, UMR_1154 Inserm, UMR_7196 CNRS, Univ Sorbonne, Paris, France
| | | | - Annarita Miccio
- Université de Paris, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, F-75015, Paris, France
| | - Mario Amendola
- Genethon, 91000, Evry, France. .,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France.
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48
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Abstract
A widely used third-generation lentiviral packaging system produces virus with enhanced biosafety by eliminating HIV accessory genes and separating packaging elements into three different plasmids. However, for certain vectors such as pLKO.1, third-generation safety features reduce lentiviral titers due to the lack of the accessory gene tat. Here we present a way to improve virus production and target gene knockdown with a modified pLKO.1 CMV pLKO.1C) vector and optimized packaging construct ratios. Replacing the pLKO.1 RSV promoter with the Cytomegalovirus promoter yielded an average of threefold higher titer than standard pLKO.1 packaged using the third-generation system, while optimizing the packaging vector ratios further increased titer and yielded an average of tenfold higher titer than pLKO.1 packaged with the second-generation system. Substituting the Rous Sarcoma Virus promoter of pLKO.1 with the Cytomegalovirus promoter dramatically enhanced virus production with the third-generation packaging system. Higher titers and improved target gene knockdown were achieved by optimizing the ratio of viral packaging constructs. This study suggests an approach to generate and deliver lentiviruses with maximized efficacy while maintaining biosafety.
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49
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Annunziato S, Lutz C, Henneman L, Bhin J, Wong K, Siteur B, van Gerwen B, de Korte‐Grimmerink R, Zafra MP, Schatoff EM, Drenth AP, van der Burg E, Eijkman T, Mukherjee S, Boroviak K, Wessels LFA, van de Ven M, Huijbers IJ, Adams DJ, Dow LE, Jonkers J. In situ CRISPR-Cas9 base editing for the development of genetically engineered mouse models of breast cancer. EMBO J 2020; 39:e102169. [PMID: 31930530 PMCID: PMC7049816 DOI: 10.15252/embj.2019102169] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022] Open
Abstract
Genetically engineered mouse models (GEMMs) of cancer have proven to be of great value for basic and translational research. Although CRISPR-based gene disruption offers a fast-track approach for perturbing gene function and circumvents certain limitations of standard GEMM development, it does not provide a flexible platform for recapitulating clinically relevant missense mutations in vivo. To this end, we generated knock-in mice with Cre-conditional expression of a cytidine base editor and tested their utility for precise somatic engineering of missense mutations in key cancer drivers. Upon intraductal delivery of sgRNA-encoding vectors, we could install point mutations with high efficiency in one or multiple endogenous genes in situ and assess the effect of defined allelic variants on mammary tumorigenesis. While the system also produces bystander insertions and deletions that can stochastically be selected for when targeting a tumor suppressor gene, we could effectively recapitulate oncogenic nonsense mutations. We successfully applied this system in a model of triple-negative breast cancer, providing the proof of concept for extending this flexible somatic base editing platform to other tissues and tumor types.
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Affiliation(s)
- Stefano Annunziato
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Catrin Lutz
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Linda Henneman
- Transgenic Core FacilityMouse Clinic for Cancer and Aging (MCCA)The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jinhyuk Bhin
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Division of Molecular CarcinogenesisThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Kim Wong
- Wellcome Trust Sanger InstituteCambridgeUK
| | - Bjørn Siteur
- Preclinical Intervention UnitMouse Clinic for Cancer and Aging (MCCA)The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Bas van Gerwen
- Preclinical Intervention UnitMouse Clinic for Cancer and Aging (MCCA)The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Renske de Korte‐Grimmerink
- Preclinical Intervention UnitMouse Clinic for Cancer and Aging (MCCA)The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Maria Paz Zafra
- Division of Hematology and Medical OncologyDepartment of MedicineSandra and Edward Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
| | - Emma M Schatoff
- Division of Hematology and Medical OncologyDepartment of MedicineSandra and Edward Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
- Weill Cornell/Rockefeller/Sloan Kettering Tri‐I MD‐PhD ProgramNew YorkNYUSA
| | - Anne Paulien Drenth
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Eline van der Burg
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Timo Eijkman
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Siddhartha Mukherjee
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | | | - Lodewyk FA Wessels
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Division of Molecular CarcinogenesisThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Marieke van de Ven
- Preclinical Intervention UnitMouse Clinic for Cancer and Aging (MCCA)The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Ivo J Huijbers
- Transgenic Core FacilityMouse Clinic for Cancer and Aging (MCCA)The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | | | - Lukas E Dow
- Division of Hematology and Medical OncologyDepartment of MedicineSandra and Edward Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
- Department of BiochemistrySandra and Edward Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
| | - Jos Jonkers
- Division of Molecular PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Cancer Genomics NetherlandsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
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50
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Rosano S, Corà D, Parab S, Zaffuto S, Isella C, Porporato R, Hoza RM, Calogero RA, Riganti C, Bussolino F, Noghero A. A regulatory microRNA network controls endothelial cell phenotypic switch during sprouting angiogenesis. eLife 2020; 9:48095. [PMID: 31976858 PMCID: PMC7299339 DOI: 10.7554/elife.48095] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
Angiogenesis requires the temporal coordination of the proliferation and the migration of endothelial cells. Here, we investigated the regulatory role of microRNAs (miRNAs) in harmonizing angiogenesis processes in a three-dimensional in vitro model. We described a microRNA network which contributes to the observed down- and upregulation of proliferative and migratory genes, respectively. Global analysis of miRNA-target gene interactions identified two sub-network modules, the first organized in upregulated miRNAs connected with downregulated target genes and the second with opposite features. miR-424-5p and miR-29a-3p were selected for the network validation. Gain- and loss-of-function approaches targeting these microRNAs impaired angiogenesis, suggesting that these modules are instrumental to the temporal coordination of endothelial migration and proliferation. Interestingly, miR-29a-3p and its targets belong to a selective biomarker that is able to identify colorectal cancer patients who are responding to anti-angiogenic treatments. Our results provide a view of higher-order interactions in angiogenesis that has potential to provide diagnostic and therapeutic insights.
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Affiliation(s)
- Stefania Rosano
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases - CAAD, Novara, Italy
| | - Sushant Parab
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Serena Zaffuto
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Claudio Isella
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | | | - Roxana Maria Hoza
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Raffaele A Calogero
- Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Alessio Noghero
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
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