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Bosco N, Goldberg A, Zhao X, Mays JC, Cheng P, Johnson AF, Bianchi JJ, Toscani C, Di Tommaso E, Katsnelson L, Annuar D, Mei S, Faitelson RE, Pesselev IY, Mohamed KS, Mermerian A, Camacho-Hernandez EM, Gionco CA, Manikas J, Tseng YS, Sun Z, Fani S, Keegan S, Lippman SM, Fenyö D, Giunta S, Santaguida S, Davoli T. KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres. Cell 2023; 186:1985-2001.e19. [PMID: 37075754 PMCID: PMC10676289 DOI: 10.1016/j.cell.2023.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/17/2022] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer. Here, we describe KaryoCreate (karyotype CRISPR-engineered aneuploidy technology), a system that enables the generation of chromosome-specific aneuploidies by co-expression of an sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to mutant KNL1. We design unique and highly specific sgRNAs for 19 of the 24 chromosomes. Expression of these constructs leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny, with an average efficiency of 8% for gains and 12% for losses (up to 20%) validated across 10 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, frequent in gastrointestinal cancers, promotes resistance to TGF-β, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe an innovative technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.
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Affiliation(s)
- Nazario Bosco
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleah Goldberg
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Xin Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joseph C Mays
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Pan Cheng
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Adam F Johnson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joy J Bianchi
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Cecilia Toscani
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Elena Di Tommaso
- Department of Biology and Biotechnology Charles Darwin, University of Rome "La Sapienza", 00185 Rome, Italy
| | - Lizabeth Katsnelson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Dania Annuar
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sally Mei
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Roni E Faitelson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Ilan Y Pesselev
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Kareem S Mohamed
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Angela Mermerian
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Elaine M Camacho-Hernandez
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Courtney A Gionco
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Julie Manikas
- Department of Cell Biology, NYU Langone Health, New York, NY, USA
| | - Yi-Shuan Tseng
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Zhengxi Sun
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Somayeh Fani
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Scott M Lippman
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Simona Giunta
- Department of Biology and Biotechnology Charles Darwin, University of Rome "La Sapienza", 00185 Rome, Italy
| | - Stefano Santaguida
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Teresa Davoli
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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Ferrari KJ, Amato S, Noberini R, Toscani C, Fernández-Pérez D, Rossi A, Conforti P, Zanotti M, Bonaldi T, Tamburri S, Pasini D. Intestinal differentiation involves cleavage of histone H3 N-terminal tails by multiple proteases. Nucleic Acids Res 2021; 49:791-804. [PMID: 33398338 PMCID: PMC7826276 DOI: 10.1093/nar/gkaa1228] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/14/2022] Open
Abstract
The proteolytic cleavage of histone tails, also termed histone clipping, has been described as a mechanism for permanent removal of post-translational modifications (PTMs) from histone proteins. Such activity has been ascribed to ensure regulatory function in key cellular processes such as differentiation, senescence and transcriptional control, for which different histone-specific proteases have been described. However, all these studies were exclusively performed using cell lines cultured in vitro and no clear evidence that histone clipping is regulated in vivo has been reported. Here we show that histone H3 N-terminal tails undergo extensive cleavage in the differentiated cells of the villi in mouse intestinal epithelium. Combining biochemical methods, 3D organoid cultures and in vivo approaches, we demonstrate that intestinal H3 clipping is the result of multiple proteolytic activities. We identified Trypsins and Cathepsin L as specific H3 tail proteases active in small intestinal differentiated cells and showed that their proteolytic activity is differentially affected by the PTM pattern of histone H3 tails. Together, our findings provide in vivo evidence of H3 tail proteolysis in mammalian tissues, directly linking H3 clipping to cell differentiation.
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Affiliation(s)
- Karin Johanna Ferrari
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Roberta Noberini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Cecilia Toscani
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Daniel Fernández-Pérez
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alessandra Rossi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Pasquale Conforti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simone Tamburri
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Diego Pasini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
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