101
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B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors. Nat Commun 2023; 14:488. [PMID: 36717582 PMCID: PMC9887000 DOI: 10.1038/s41467-023-36097-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Induced pluripotent stem cell (iPSC) reprogramming is inefficient and understanding the molecular mechanisms underlying this inefficiency holds the key to successfully control cellular identity. Here, we report 24 reprogramming roadblock genes identified by CRISPR/Cas9-mediated genome-wide knockout (KO) screening. Of these, depletion of the predicted KRAB zinc finger protein (KRAB-ZFP) Zfp266 strongly and consistently enhances murine iPSC generation in several reprogramming settings, emerging as the most robust roadblock. We show that ZFP266 binds Short Interspersed Nuclear Elements (SINEs) adjacent to binding sites of pioneering factors, OCT4 (POU5F1), SOX2, and KLF4, and impedes chromatin opening. Replacing the KRAB co-suppressor with co-activator domains converts ZFP266 from an inhibitor to a potent facilitator of iPSC reprogramming. We propose that the SINE-KRAB-ZFP interaction is a critical regulator of chromatin accessibility at regulatory elements required for efficient cellular identity changes. In addition, this work serves as a resource to further illuminate molecular mechanisms hindering reprogramming.
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102
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Vinceti A, De Lucia RR, Cremaschi P, Perron U, Karakoc E, Mauri L, Fernandez C, Kluczynski KH, Anderson DS, Iorio F. An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens. CELL REPORTS METHODS 2023; 3:100373. [PMID: 36814834 PMCID: PMC9939378 DOI: 10.1016/j.crmeth.2022.100373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/06/2022] [Accepted: 12/07/2022] [Indexed: 01/24/2023]
Abstract
A limitation of pooled CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes arising from copy-number-amplified genomics regions. To solve this issue, we previously developed CRISPRcleanR: a computational method implemented as R/python package and in a dockerized version. CRISPRcleanR detects and corrects biased responses to CRISPR-Cas9 targeting in an unsupervised fashion, accurately reducing false-positive signals while maintaining sensitivity in identifying relevant genetic dependencies. Here, we present CRISPRcleanR WebApp , a web application enabling access to CRISPRcleanR through an intuitive interface. CRISPRcleanR WebApp removes the complexity of R/python language user interactions; provides user-friendly access to a complete analytical pipeline, not requiring any data pre-processing and generating gene-level summaries of essentiality with associated statistical scores; and offers a range of interactively explorable plots while supporting a more comprehensive range of CRISPR guide RNAs' libraries than the original package. CRISPRcleanR WebApp is available at https://crisprcleanr-webapp.fht.org/.
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Affiliation(s)
- Alessandro Vinceti
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
| | - Riccardo Roberto De Lucia
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
| | - Paolo Cremaschi
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
| | - Umberto Perron
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
| | - Emre Karakoc
- Cancer Dependency Map Analytics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Luca Mauri
- ICT and Digitalisation, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
| | - Carlos Fernandez
- ICT and Digitalisation, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
| | | | - Daniel Stephen Anderson
- ICT and Digitalisation, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
| | - Francesco Iorio
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy
- Cancer Dependency Map Analytics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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103
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Exploring the Use of Cold Atmospheric Plasma to Overcome Drug Resistance in Cancer. Biomedicines 2023; 11:biomedicines11010208. [PMID: 36672716 PMCID: PMC9855365 DOI: 10.3390/biomedicines11010208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Drug resistance is a major problem in cancer treatment, as it limits the effectiveness of pharmacological agents and can lead to disease progression. Cold atmospheric plasma (CAP) is a technology that uses ionized gas (plasma) to generate reactive oxygen and nitrogen species (RONS) that can kill cancer cells. CAP is a novel approach for overcoming drug resistance in cancer. In recent years, there has been a growing interest in using CAP to enhance the effectiveness of chemotherapy drugs. In this review, we discuss the mechanisms behind this phenomenon and explore its potential applications in cancer treatment. Going through the existing literature on CAP and drug resistance in cancer, we highlight the challenges and opportunities for further research in this field. Our review suggests that CAP could be a promising option for overcoming drug resistance in cancer and warrants further investigation.
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104
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Liu H, Lv Z, Zhang G, Wang X, Wang Y, Wang K. Knowledge mapping and current trends of global research on CRISPR in the field of cancer. Front Cell Dev Biol 2023; 11:1178221. [PMID: 37200626 PMCID: PMC10185797 DOI: 10.3389/fcell.2023.1178221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
Background: Gene editing tools using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-related systems have revolutionized our understanding of cancer. The purpose of this study was to determine the distribution, collaboration, and direction of cancer research using CRISPR. Methods: Data from the Web of Science (WoS) Core Collection database were collected from 4,408 cancer publications related to CRISPR from 1 January 2013to 31 December 2022. The obtained data were analyzed using VOSviewer software for citation, co-citation, co-authorship, and co-occurrence analysis. Results: The number of annual publications has grown steadily over the past decade worldwide. The United States was shown, by far, to be the leading source of cancer publications, citations, and collaborations involving CRISPR than any other country, followed by China. Li Wei (Jilin University, China), and Harvard Medical School (Boston, MA, United States) were the author and institution with the most publications and active collaborations, respectively. The journal with the most contributions was Nature Communications (n = 147) and the journal with the most citations was Nature (n = 12,111). The research direction of oncogenic molecules, mechanisms, and cancer-related gene editing was indicated based on keyword analysis. Conclusion: The current study has provided a comprehensive overview of cancer research highlights and future trends of CRISPR, combined with a review of CRISPR applications in cancer to summarize and predict research directions and provide guidance to researchers.
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Affiliation(s)
- Han Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zongwei Lv
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Gong Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yuan Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Kefeng Wang, ; Yuan Wang,
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Kefeng Wang, ; Yuan Wang,
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105
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Wodi C, Belali T, Morse R, Porazinski S, Ladomery M. SPHINX-Based Combination Therapy as a Potential Novel Treatment Strategy for Acute Myeloid Leukaemia. Br J Biomed Sci 2023; 80:11041. [PMID: 36895328 PMCID: PMC9988938 DOI: 10.3389/bjbs.2023.11041] [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: 11/09/2022] [Accepted: 02/08/2023] [Indexed: 02/23/2023]
Abstract
Introduction: Dysregulated alternative splicing is a prominent feature of cancer. The inhibition and knockdown of the SR splice factor kinase SRPK1 reduces tumour growth in vivo. As a result several SPRK1 inhibitors are in development including SPHINX, a 3-(trifluoromethyl)anilide scaffold. The objective of this study was to treat two leukaemic cell lines with SPHINX in combination with the established cancer drugs azacitidine and imatinib. Materials and Methods: We selected two representative cell lines; Kasumi-1, acute myeloid leukaemia, and K562, BCR-ABL positive chronic myeloid leukaemia. Cells were treated with SPHINX concentrations up to 10μM, and in combination with azacitidine (up to 1.5 μg/ml, Kasumi-1 cells) and imatinib (up to 20 μg/ml, K562 cells). Cell viability was determined by counting the proportion of live cells and those undergoing apoptosis through the detection of activated caspase 3/7. SRPK1 was knocked down with siRNA to confirm SPHINX results. Results: The effects of SPHINX were first confirmed by observing reduced levels of phosphorylated SR proteins. SPHINX significantly reduced cell viability and increased apoptosis in Kasumi-1 cells, but less prominently in K562 cells. Knockdown of SRPK1 by RNA interference similarly reduced cell viability. Combining SPHINX with azacitidine augmented the effect of azacitidine in Kasumi-1 cells. In conclusion, SPHINX reduces cell viability and increases apoptosis in the acute myeloid leukaemia cell line Kasumi-1, but less convincingly in the chronic myeloid leukaemia cell line K562. Conclusion: We suggest that specific types of leukaemia may present an opportunity for the development of SRPK1-targeted therapies to be used in combination with established chemotherapeutic drugs.
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Affiliation(s)
- Chigeru Wodi
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | - Tareg Belali
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | - Ruth Morse
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | - Sean Porazinski
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Michael Ladomery
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
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106
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Bonamino MH, Correia EM. The CRISPR/Cas System in Human Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:59-71. [PMID: 37486516 DOI: 10.1007/978-3-031-33325-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The use of CRISPR as a genetic editing tool modified the oncology field from its basic to applied research for opening a simple, fast, and cheaper way to manipulate the genome. This chapter reviews some of the major uses of this technique for in vitro- and in vivo-based biological screenings, for cellular and animal model generation, and new derivative tools applied to cancer research. CRISPR has opened new frontiers increasing the knowledge about cancer, pointing to new solutions to overcome several challenges to better understand the disease and design better treatments.
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107
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Kong T, Laranjeira ABA, Yang K, Fisher DAC, Yu L, Poittevin De La Frégonnière L, Wang AZ, Ruzinova MB, Fowles JS, Fulbright MC, Cox MJ, Celik H, Challen GA, Huang S, Oh ST. DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression. NATURE CANCER 2023; 4:108-127. [PMID: 36581736 PMCID: PMC11288645 DOI: 10.1038/s43018-022-00486-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/08/2022] [Indexed: 12/31/2022]
Abstract
Myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed single-cell RNA sequencing on serial MPN and sAML patient stem and progenitor cells, identifying aberrantly increased expression of DUSP6 underlying disease transformation. Pharmacologic dual-specificity phosphatase (DUSP)6 targeting led to inhibition of S6 and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling while also reducing inflammatory cytokine production. DUSP6 perturbation further inhibited ribosomal S6 kinase (RSK)1, which we identified as a second indispensable candidate associated with poor clinical outcome. Ectopic expression of DUSP6 mediated JAK2-inhibitor resistance and exacerbated disease severity in patient-derived xenograft (PDX) models. Contrastingly, DUSP6 inhibition potently suppressed disease development across Jak2V617F and MPLW515L MPN mouse models and sAML PDXs without inducing toxicity in healthy controls. These findings underscore DUSP6 in driving disease transformation and highlight the DUSP6-RSK1 axis as a vulnerable, druggable pathway in myeloid malignancies.
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Affiliation(s)
- Tim Kong
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Angelo B A Laranjeira
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Daniel A C Fisher
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - LaYow Yu
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Laure Poittevin De La Frégonnière
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Anthony Z Wang
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Marianna B Ruzinova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jared S Fowles
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary C Fulbright
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Maggie J Cox
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Stephen T Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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108
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Meduri E, Breeze C, Marando L, Richardson SE, Huntly BJ. The RNA editing landscape in acute myeloid leukemia reveals associations with disease mutations and clinical outcome. iScience 2022; 25:105622. [PMID: 36465109 PMCID: PMC9713371 DOI: 10.1016/j.isci.2022.105622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/18/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Several studies have documented aberrant RNA editing patterns across multiple tumors across large patient cohorts from The Cancer Genome Atlas (TCGA). However, studies on understanding the role of RNA editing in acute myeloid leukemia (AML) have been limited to smaller sample sizes. Using high throughput transcriptomic data from the TCGA, we demonstrated higher levels of editing as a predictor of poor outcome within the AML patient samples. Moreover, differential editing patterns were observed across individual AML genotypes. We also could demonstrate a negative association between the degree of editing and mRNA abundance for some transcripts, identifying the potential regulatory potential of RNA-editing in altering gene expression in AML. Further edQTL analysis suggests potential cis-regulatory mechanisms in RNA editing variation. Our work suggests a functional and regulatory role of RNA editing in the pathogenesis of AML and we extended our analysis to gain insight into the factors influencing altered levels of editing.
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Affiliation(s)
- Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Charles Breeze
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals, Cambridge, UK
| | - Simon E. Richardson
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals, Cambridge, UK
| | - Brian J.P. Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals, Cambridge, UK
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109
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Keys HR, Knouse KA. Genome-scale CRISPR screening in a single mouse liver. CELL GENOMICS 2022; 2:100217. [PMID: 36643909 PMCID: PMC9835819 DOI: 10.1016/j.xgen.2022.100217] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/08/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022]
Abstract
A complete understanding of the genetic determinants underlying mammalian physiology and disease is limited by the capacity for high-throughput genetic dissection in the living organism. Genome-wide CRISPR screening is a powerful method for uncovering the genetic regulation of cellular processes, but the need to stably deliver single guide RNAs to millions of cells has largely restricted its implementation to ex vivo systems. There thus remains a need for accessible high-throughput functional genomics in vivo. Here, we establish genome-wide screening in the liver of a single mouse and use this approach to uncover regulation of hepatocyte fitness. We uncover pathways not identified in cell culture screens, underscoring the power of genetic dissection in the organism. The approach we developed is accessible, scalable, and adaptable to diverse phenotypes and applications. We have hereby established a foundation for high-throughput functional genomics in a living mammal, enabling comprehensive investigation of physiology and disease.
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Affiliation(s)
- Heather R. Keys
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kristin A. Knouse
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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110
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Liu ACH, Cathelin S, Yang Y, Dai DL, Ayyathan DM, Hosseini M, Minden MD, Tierens A, Chan SM. Targeting STAT5 Signaling Overcomes Resistance to IDH Inhibitors in Acute Myeloid Leukemia through Suppression of Stemness. Cancer Res 2022; 82:4325-4339. [PMID: 36150062 DOI: 10.1158/0008-5472.can-22-1293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/01/2022] [Accepted: 09/21/2022] [Indexed: 01/24/2023]
Abstract
Mutant isocitrate dehydrogenase 1 (IDH1) and IDH2 block the differentiation of acute myeloid leukemia (AML) cells through production of R-2-hydroxyglutarate (R-2-HG). IDH inhibitors can induce differentiation of AML cells by lowering R-2-HG but have limited clinical efficacy as single agents. Here, we performed a genome-wide CRISPR knockout screen in an Idh1-mutated hematopoietic progenitor cell line to identify genes that increased the differentiation response to ivosidenib, an IDH1 inhibitor. The screen identified C-type lectin member 5a (Clec5a), which encodes a spleen tyrosine kinase (SYK)-coupled surface receptor, as one of the top hits. Knockout of Clec5a and Syk rendered cells more sensitive to ivosidenib-induced differentiation through a reduction in STAT5-dependent expression of stemness-related genes, including genes in the homeobox (HOX) family. Importantly, direct inhibition of STAT5 activity was sufficient to increase the differentiation response to IDH inhibitors in primary human IDH1- and IDH2-mutated AML cells, including those harboring mutations in receptor tyrosine kinase (RTK) and MAPK genes that have been linked to drug resistance. In patient-derived xenograft models of IDH1-mutated AML, combination treatment with ivosidenib and the STAT5 inhibitor pimozide was superior to each agent alone in inducing differentiation in leukemic cells without compromising normal hematopoiesis. These findings demonstrate that STAT5 is a critical mediator of resistance to IDH inhibitors and provide the rationale for combining STAT5 and IDH inhibitors in the treatment of IDH-mutated AML. SIGNIFICANCE A CRISPR knockout screen identifies a mechanism of resistance to IDH inhibitors in AML involving activated STAT5 signaling, suggesting a potential strategy to improve the clinical efficacy of IDH inhibitors.
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Affiliation(s)
- Alex C H Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Severine Cathelin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yitong Yang
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David L Dai
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Mohsen Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark D Minden
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Anne Tierens
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven M Chan
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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111
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Liang JR, Corn JE. A CRISPR view on autophagy. Trends Cell Biol 2022; 32:1008-1022. [PMID: 35581059 DOI: 10.1016/j.tcb.2022.04.006] [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: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/21/2023]
Abstract
Autophagy is a fundamental pathway for the degradation of cytoplasmic content in response to pleiotropic extracellular and intracellular stimuli. Recent advances in the autophagy field have demonstrated that different organelles can also be specifically targeted for autophagy with broad implications on cellular and organismal health. This opens new dimensions in the autophagy field and more unanswered questions on the rationale and underlying mechanisms to degrade different organelles. Functional genomics via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-based screening has gained popularity in the autophagy field to understand the common and unique factors that are implicated in the signaling, recognition, and execution of different cargo-specific autophagies. We focus on recent applications of CRISPR-based screens in the autophagy field, their discoveries, and the future directions of autophagy screens.
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Affiliation(s)
- Jin Rui Liang
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland; Medical Research Council, Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland.
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112
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Zhao Y, Yu L, Wu X, Li H, Coombes KR, Au KF, Cheng L, Li L. CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression. Bioinformatics 2022; 38:5245-5252. [PMID: 36250792 PMCID: PMC9710553 DOI: 10.1093/bioinformatics/btac668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 09/26/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Clustered regularly interspaced short palindromic repeats (CRISPR)-based genetic perturbation screen is a powerful tool to probe gene function. However, experimental noises, especially for the lowly expressed genes, need to be accounted for to maintain proper control of false positive rate. METHODS We develop a statistical method, named CRISPR screen with Expression Data Analysis (CEDA), to integrate gene expression profiles and CRISPR screen data for identifying essential genes. CEDA stratifies genes based on expression level and adopts a three-component mixture model for the log-fold change of single-guide RNAs (sgRNAs). Empirical Bayesian prior and expectation-maximization algorithm are used for parameter estimation and false discovery rate inference. RESULTS Taking advantage of gene expression data, CEDA identifies essential genes with higher expression. Compared to existing methods, CEDA shows comparable reliability but higher sensitivity in detecting essential genes with moderate sgRNA fold change. Therefore, using the same CRISPR data, CEDA generates an additional hit gene list. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
- Biomedical Informatics Shared Resources, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Xue Wu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Kevin R Coombes
- Department of Population Health Sciences, Georgia Cancer Center at Augusta University, Augusta, GA 30912, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
- Biomedical Informatics Shared Resources, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Lijun Cheng
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Lang Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
- Biomedical Informatics Shared Resources, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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113
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Ten Years of CRISPRing Cancers In Vitro. Cancers (Basel) 2022; 14:cancers14235746. [PMID: 36497228 PMCID: PMC9738354 DOI: 10.3390/cancers14235746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
Cell lines have always constituted a good investigation tool for cancer research, allowing scientists to understand the basic mechanisms underlying the complex network of phenomena peculiar to the transforming path from a healthy to cancerous cell. The introduction of CRISPR in everyday laboratory activity and its relative affordability greatly expanded the bench lab weaponry in the daily attempt to better understand tumor biology with the final aim to mitigate cancer's impact in our lives. In this review, we aim to report how this genome editing technique affected in the in vitro modeling of different aspects of tumor biology, its several declinations, and analyze the advantages and drawbacks of each of them.
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114
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Funk L, Su KC, Ly J, Feldman D, Singh A, Moodie B, Blainey PC, Cheeseman IM. The phenotypic landscape of essential human genes. Cell 2022; 185:4634-4653.e22. [PMID: 36347254 PMCID: PMC10482496 DOI: 10.1016/j.cell.2022.10.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/01/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
Understanding the basis for cellular growth, proliferation, and function requires determining the roles of essential genes in diverse cellular processes, including visualizing their contributions to cellular organization and morphology. Here, we combined pooled CRISPR-Cas9-based functional screening of 5,072 fitness-conferring genes in human HeLa cells with microscopy-based imaging of DNA, the DNA damage response, actin, and microtubules. Analysis of >31 million individual cells identified measurable phenotypes for >90% of gene knockouts, implicating gene targets in specific cellular processes. Clustering of phenotypic similarities based on hundreds of quantitative parameters further revealed co-functional genes across diverse cellular activities, providing predictions for gene functions and associations. By conducting pooled live-cell screening of ∼450,000 cell division events for 239 genes, we additionally identified diverse genes with functional contributions to chromosome segregation. Our work establishes a resource detailing the consequences of disrupting core cellular processes that represents the functional landscape of essential human genes.
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Affiliation(s)
- Luke Funk
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kuan-Chung Su
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jimmy Ly
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - David Feldman
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Brittania Moodie
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA.
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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115
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Abe T, Horisawa Y, Kikuchi O, Ozawa-Umeta H, Kishimoto A, Katsuura Y, Imaizumi A, Hashimoto T, Shirakawa K, Takaori-Kondo A, Yusa K, Asakura T, Kakeya H, Kanai M. Pharmacologic characterization of TBP1901, a prodrug form of aglycone curcumin, and CRISPR-Cas9 screen for therapeutic targets of aglycone curcumin. Eur J Pharmacol 2022; 935:175321. [PMID: 36228744 DOI: 10.1016/j.ejphar.2022.175321] [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: 04/25/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022]
Abstract
Curcumin (aglycone curcumin) has antitumor properties in a variety of malignancies via the alteration of multiple cancer-related biological pathways; however, its clinical application has been hampered due to its poor bioavailability. To overcome this limitation, we have developed a synthesized curcumin β-D-glucuronide sodium salt (TBP1901), a prodrug form of aglycone curcumin. In this study, we aimed to clarify the pharmacologic characteristics of TBP1901. In β-glucuronidase (GUSB)-proficient mice, both curcumin β-D-glucuronide and its active metabolite, aglycone curcumin, were detected in the blood after TBP1901 injection, whereas only curcumin β-D-glucuronide was detected in GUSB-impaired mice, suggesting that GUSB plays a pivotal role in the conversion of TBP1901 into aglycone curcumin in vivo. TBP1901 itself had minimal antitumor effects in vitro, whereas it demonstrated significant antitumor effects in vivo. Genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 screen disclosed the genes associated with NF-κB signaling pathway and mitochondria were among the highest hit. In vitro, aglycone curcumin inhibited NF-kappa B signaling pathways whereas it caused production of reactive oxygen species (ROS). ROS scavenger, N-acetyl-L-cysteine, partially reversed antitumor effects of aglycone curcumin. In summary, TBP1901 can exert antitumor effects as a prodrug of aglycone curcumin through GUSB-dependent activation.
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Affiliation(s)
| | - Yoshihito Horisawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Kikuchi
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | | | | | | | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Yusa
- Stem Cell Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tadashi Asakura
- Radioisotope Research Facilities, Jikei University School of Medicine, Tokyo, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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116
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Dietary methionine starvation impairs acute myeloid leukemia progression. Blood 2022; 140:2037-2052. [PMID: 35984907 DOI: 10.1182/blood.2022017575] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
Targeting altered tumor cell metabolism might provide an attractive opportunity for patients with acute myeloid leukemia (AML). An amino acid dropout screen on primary leukemic stem cells and progenitor populations revealed a number of amino acid dependencies, of which methionine was one of the strongest. By using various metabolite rescue experiments, nuclear magnetic resonance-based metabolite quantifications and 13C-tracing, polysomal profiling, and chromatin immunoprecipitation sequencing, we identified that methionine is used predominantly for protein translation and to provide methyl groups to histones via S-adenosylmethionine for epigenetic marking. H3K36me3 was consistently the most heavily impacted mark following loss of methionine. Methionine depletion also reduced total RNA levels, enhanced apoptosis, and induced a cell cycle block. Reactive oxygen species levels were not increased following methionine depletion, and replacement of methionine with glutathione or N-acetylcysteine could not rescue phenotypes, excluding a role for methionine in controlling redox balance control in AML. Although considered to be an essential amino acid, methionine can be recycled from homocysteine. We uncovered that this is primarily performed by the enzyme methionine synthase and only when methionine availability becomes limiting. In vivo, dietary methionine starvation was not only tolerated by mice, but also significantly delayed both cell line and patient-derived AML progression. Finally, we show that inhibition of the H3K36-specific methyltransferase SETD2 phenocopies much of the cytotoxic effects of methionine depletion, providing a more targeted therapeutic approach. In conclusion, we show that methionine depletion is a vulnerability in AML that can be exploited therapeutically, and we provide mechanistic insight into how cells metabolize and recycle methionine.
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117
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Okuda H, Miyamoto R, Takahashi S, Kawamura T, Ichikawa J, Harada I, Tamura T, Yokoyama A. RNA-binding proteins of KHDRBS and IGF2BP families control the oncogenic activity of MLL-AF4. Nat Commun 2022; 13:6688. [PMID: 36335100 PMCID: PMC9637093 DOI: 10.1038/s41467-022-34558-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/27/2022] [Indexed: 11/08/2022] Open
Abstract
Chromosomal translocation generates the MLL-AF4 fusion gene, which causes acute leukemia of multiple lineages. MLL-AF4 is a strong oncogenic driver that induces leukemia without additional mutations and is the most common cause of pediatric leukemia. However, establishment of a murine disease model via retroviral transduction has been difficult owning to a lack of understanding of its regulatory mechanisms. Here, we show that MLL-AF4 protein is post-transcriptionally regulated by RNA-binding proteins, including those of KHDRBS and IGF2BP families. MLL-AF4 translation is inhibited by ribosomal stalling, which occurs at regulatory sites containing AU-rich sequences recognized by KHDRBSs. Synonymous mutations disrupting the association of KHDRBSs result in proper translation of MLL-AF4 and leukemic transformation. Consequently, the synonymous MLL-AF4 mutant induces leukemia in vivo. Our results reveal that post-transcriptional regulation critically controls the oncogenic activity of MLL-AF4; these findings might be valuable in developing novel therapies via modulation of the activity of RNA-binding proteins.
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Affiliation(s)
- Hiroshi Okuda
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan ,grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan
| | - Ryo Miyamoto
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan
| | - Satoshi Takahashi
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan ,grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Kyoto University Graduate School of Medicine, Kyoto, Kyoto Japan
| | - Takeshi Kawamura
- grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology (RCAST), The University of Tokyo, Bunkyo, Tokyo Japan
| | - Juri Ichikawa
- grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan
| | - Ibuki Harada
- grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan
| | - Tomohiko Tamura
- grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan ,grid.268441.d0000 0001 1033 6139Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa Japan
| | - Akihiko Yokoyama
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan ,grid.272242.30000 0001 2168 5385National Cancer Center Research Institute, Chuo, Tokyo Japan
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The methyltransferase domain of DNMT1 is an essential domain in acute myeloid leukemia independent of DNMT3A mutation. Commun Biol 2022; 5:1174. [PMID: 36329185 PMCID: PMC9633652 DOI: 10.1038/s42003-022-04139-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Aberrant DNA methylation patterns are a prominent feature of cancer. Methylation of DNA is mediated by the DNA methyltransferase (DNMT) protein family, which regulates de novo (DNMT3A and DNMT3B) and maintenance (DNMT1) methylation. Mutations in DNMT3A are observed in approximately 22% of acute myeloid leukemia (AML). We hypothesized that DNMT1 or DNMT3B could function as a synthetic lethal therapeutic strategy for DNMT3A-mutant AML. CRISPR-Cas9 tiling screens were performed to identify functional domains within DNMT1/DNMT3B that exhibited greater dependencies in DNMT3A mutant versus wild-type cell lines. Although increased sensitivity to DNMT1 mutation was observed in some DNMT3A mutant cellular models tested, the subtlety of these results prevents us from basing any conclusions on a synthetic lethal relationship between DNMT1 and DNMT3A. Our data suggests that a therapeutic window for DNMT1 methyltransferase inhibition in DNMT3A-driven AML may exist, but validation in more biologically relevant models is required.
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119
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Hoberecht L, Perampalam P, Lun A, Fortin JP. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Nat Commun 2022; 13:6568. [PMID: 36323688 PMCID: PMC9630310 DOI: 10.1038/s41467-022-34320-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced CRISPR applications. Here, we present a new ecosystem of R packages, called crisprVerse, that enables efficient gRNA design and annotation for a multitude of CRISPR technologies. This includes CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR base editing (CRISPRbe) and CRISPR knockdown (CRISPRkd). The core package, crisprDesign, offers a user-friendly and unified interface to add off-target annotations, rich gene and SNP annotations, and on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. The crisprVerse ecosystem is open-source and deployed through the Bioconductor project ( https://github.com/crisprVerse ).
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Affiliation(s)
- Luke Hoberecht
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Aaron Lun
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jean-Philippe Fortin
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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120
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Dunn S, Eberlein C, Yu J, Gris-Oliver A, Ong SH, Yelland U, Cureton N, Staniszewska A, McEwen R, Fox M, Pilling J, Hopcroft P, Coker EA, Jaaks P, Garnett MJ, Isherwood B, Serra V, Davies BR, Barry ST, Lynch JT, Yusa K. AKT-mTORC1 reactivation is the dominant resistance driver for PI3Kβ/AKT inhibitors in PTEN-null breast cancer and can be overcome by combining with Mcl-1 inhibitors. Oncogene 2022; 41:5046-5060. [PMID: 36241868 PMCID: PMC9652152 DOI: 10.1038/s41388-022-02482-9] [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: 05/03/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
Abstract
The PI3K pathway is commonly activated in breast cancer, with PI3K-AKT pathway inhibitors used clinically. However, mechanisms that limit or enhance the therapeutic effects of PI3K-AKT inhibitors are poorly understood at a genome-wide level. Parallel CRISPR screens in 3 PTEN-null breast cancer cell lines identified genes mediating resistance to capivasertib (AKT inhibitor) and AZD8186 (PI3Kβ inhibitor). The dominant mechanism causing resistance is reactivated PI3K-AKT-mTOR signalling, but not other canonical signalling pathways. Deletion of TSC1/2 conferred resistance to PI3Kβi and AKTi through mTORC1. However, deletion of PIK3R2 and INPPL1 drove specific PI3Kβi resistance through AKT. Conversely deletion of PIK3CA, ERBB2, ERBB3 increased PI3Kβi sensitivity while modulation of RRAGC, LAMTOR1, LAMTOR4 increased AKTi sensitivity. Significantly, we found that Mcl-1 loss enhanced response through rapid apoptosis induction with AKTi and PI3Kβi in both sensitive and drug resistant TSC1/2 null cells. The combination effect was BAK but not BAX dependent. The Mcl-1i + PI3Kβ/AKTi combination was effective across a panel of breast cancer cell lines with PIK3CA and PTEN mutations, and delivered increased anti-tumor benefit in vivo. This study demonstrates that different resistance drivers to PI3Kβi and AKTi converge to reactivate PI3K-AKT or mTOR signalling and combined inhibition of Mcl-1 and PI3K-AKT has potential as a treatment strategy for PI3Kβi/AKTi sensitive and resistant breast tumours.
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Affiliation(s)
- Shanade Dunn
- Wellcome Sanger Institute, Cambridge, UK
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK
| | - Cath Eberlein
- Bioscience, Early Oncology, AstraZeneca, Alderley Park, UK
| | - Jason Yu
- Wellcome Sanger Institute, Cambridge, UK
- Molecular Biology of Metabolism Lab, The Francis Crick Institute, London, UK
| | | | | | - Urs Yelland
- Bioscience, Early Oncology, AstraZeneca, Alderley Park, UK
| | | | | | - Robert McEwen
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK
| | - Millie Fox
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK
| | | | | | | | | | | | | | - Violeta Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Simon T Barry
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK.
| | - James T Lynch
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Cambridge, UK.
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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121
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He C, Liu B, Wang HY, Wu L, Zhao G, Huang C, Liu Y, Shan B, Liu L. Inhibition of SRPK1, a key splicing regulator, exhibits antitumor and chemotherapeutic-sensitizing effects on extranodal NK/T-cell lymphoma cells. BMC Cancer 2022; 22:1100. [PMID: 36303126 PMCID: PMC9609466 DOI: 10.1186/s12885-022-10158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/06/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Increasing evidence has convincingly shown that abnormal pre-mRNA splicing is implicated in the development of most human malignancies. Serine/arginine-rich protein kinase 1 (SRPK1), a key splicing regulator, is reported to be overexpressed in leukemia and other cancer types, which suggests the therapeutic potential of targeting SRPK1. METHODS SRPK1 expression was measured in 41 ENKTL patients by immunohistochemistry and mRNA expression was analyzed by qRT‒PCR. We knocked down SRPK1 expression in the ENKTL cell line YT by siRNA transfection and inhibited SRPK1 using inhibitors (SPHINX31 and SRPIN340) in YT cells and peripheral blood lymphocytes (PBLs) isolated from ENKTL patients to investigate its role in cell proliferation and apoptosis. Then, RNA-seq analysis was performed to predict the potential signaling pathway by which SRPK1 inhibition induces cell death and further verified this prediction by Western blotting. RESULTS In the present study, we initially evaluated the clinical significance of SRPK1 in extranodal natural killer/T-cell lymphoma (ENKTL), a very aggressive subtype of non-Hodgkin lymphoma. The expression of SRPK1 in ENKLT patients was examined by immunohistochemistry and qRT‒PCR, which revealed SRPK1 overexpression in more than 60% of ENKTL specimens and its association with worse survival. Cellular experiments using the human ENKTL cell line YT and PBLs from ENKTL patients, demonstrated that inhibition of SRPK1 suppressed cell proliferation and induced apoptosis. Subsequently, we investigated the downstream targets of SRPK1 by RNA-seq analysis and found that SRPK1 inhibition induced ATF4/CHOP pathway activation and AKT1 inhibition. Furthermore, ENKTL patients presenting high SRPK1 expression showed resistance to cisplatin-based chemotherapy. The association of SRPK1 expression with cisplatin resistance was also confirmed in YT cells. SRPK1 overexpression via pLVX-SRPK1 plasmid transfection dramatically decreased the sensitivity of YT cells to cisplatin, while siRNA-mediated SRPK1 knockdown or SRPK1 inhibitor treatment significantly increased cisplatin cytotoxicity. CONCLUSION In summary, these results support that SRPK1 might be a useful clinical prognostic indicator and therapeutic target for ENKTL, especially for patients who relapse after cisplatin-based chemotherapies.
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Affiliation(s)
- Cuiying He
- Department of Hematology, The Fourth Hospital of Hebei Medical University, NO.169, TianShan Street, Shijiazhuang, 050035, Hebei, China
- Hebei Provincial Key Laboratory of Tumor Microenvironment and Drug Resistance, Shijiazhuang, China
- Hebei Medical University, Shijiazhuang, China
| | - Beichen Liu
- Department of Hematology, The Fourth Hospital of Hebei Medical University, NO.169, TianShan Street, Shijiazhuang, 050035, Hebei, China
- Hebei Provincial Key Laboratory of Tumor Microenvironment and Drug Resistance, Shijiazhuang, China
| | - Huan-You Wang
- Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - Lili Wu
- Department of Hematology, The Fourth Hospital of Hebei Medical University, NO.169, TianShan Street, Shijiazhuang, 050035, Hebei, China
| | - Guimin Zhao
- Department of Hematology, The Fourth Hospital of Hebei Medical University, NO.169, TianShan Street, Shijiazhuang, 050035, Hebei, China
| | - Chen Huang
- Department of Hematology, The Fourth Hospital of Hebei Medical University, NO.169, TianShan Street, Shijiazhuang, 050035, Hebei, China
| | - Yueping Liu
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Baoen Shan
- Hebei Medical University, Shijiazhuang, China.
- Research Center and Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Lihong Liu
- Department of Hematology, The Fourth Hospital of Hebei Medical University, NO.169, TianShan Street, Shijiazhuang, 050035, Hebei, China.
- Hebei Provincial Key Laboratory of Tumor Microenvironment and Drug Resistance, Shijiazhuang, China.
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122
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Valcarcel-Jimenez L, Rogerson C, Yong C, Schmidt C, Yang M, Cremades-Rodelgo M, Harle V, Offord V, Wong K, Mora A, Speed A, Caraffini V, Tran MGB, Maher ER, Stewart GD, Vanharanta S, Adams DJ, Frezza C. HIRA loss transforms FH-deficient cells. SCIENCE ADVANCES 2022; 8:eabq8297. [PMID: 36269833 PMCID: PMC9586478 DOI: 10.1126/sciadv.abq8297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/31/2022] [Indexed: 05/03/2023]
Abstract
Fumarate hydratase (FH) is a mitochondrial enzyme that catalyzes the reversible hydration of fumarate to malate in the tricarboxylic acid (TCA) cycle. Germline mutations of FH lead to hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a cancer syndrome characterized by a highly aggressive form of renal cancer. Although HLRCC tumors metastasize rapidly, FH-deficient mice develop premalignant cysts in the kidneys, rather than carcinomas. How Fh1-deficient cells overcome these tumor-suppressive events during transformation is unknown. Here, we perform a genome-wide CRISPR-Cas9 screen to identify genes that, when ablated, enhance the proliferation of Fh1-deficient cells. We found that the depletion of the histone cell cycle regulator (HIRA) enhances proliferation and invasion of Fh1-deficient cells in vitro and in vivo. Mechanistically, Hira loss activates MYC and its target genes, increasing nucleotide metabolism specifically in Fh1-deficient cells, independent of its histone chaperone activity. These results are instrumental for understanding mechanisms of tumorigenesis in HLRCC and the development of targeted treatments for patients.
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Affiliation(s)
- Lorea Valcarcel-Jimenez
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Connor Rogerson
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Cissy Yong
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christina Schmidt
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Ming Yang
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Monica Cremades-Rodelgo
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Victoria Harle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kim Wong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ariane Mora
- School of Chemistry and Molecular Biosciences, University of Queensland, Molecular Biosciences Building 76, St. Lucia, QLD 4072, Australia
| | - Alyson Speed
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Veronica Caraffini
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Maxine Gia Binh Tran
- UCL Division of Surgery and Interventional Science, Specialist Centre for Kidney Cancer, Royal Free Hospital, Pond Street, London NW3 2QG, UK
| | - Eamonn R. Maher
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sakari Vanharanta
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- Translational Cancer Medicine Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christian Frezza
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley ARD, Pimkin M, Paralkar VR. Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell 2022; 82:3826-3839.e9. [PMID: 36113481 PMCID: PMC9588704 DOI: 10.1016/j.molcel.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Ribosomal RNAs (rRNAs) are the most abundant cellular RNAs, and their synthesis from rDNA repeats by RNA polymerase I accounts for the bulk of all transcription. Despite substantial variation in rRNA transcription rates across cell types, little is known about cell-type-specific factors that bind rDNA and regulate rRNA transcription to meet tissue-specific needs. Using hematopoiesis as a model system, we mapped about 2,200 ChIP-seq datasets for 250 transcription factors (TFs) and chromatin proteins to human and mouse rDNA and identified robust binding of multiple TF families to canonical TF motifs on rDNA. Using a 47S-FISH-Flow assay developed for nascent rRNA quantification, we demonstrated that targeted degradation of C/EBP alpha (CEBPA), a critical hematopoietic TF with conserved rDNA binding, caused rapid reduction in rRNA transcription due to reduced RNA Pol I occupancy. Our work identifies numerous potential rRNA regulators and provides a template for dissection of TF roles in rRNA transcription.
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Affiliation(s)
- Charles Antony
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Subin S George
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Justin Blum
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patrick Somers
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chelsea L Thorsheim
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dexter J Wu-Corts
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuxi Ai
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Long Gao
- Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Kaosheng Lv
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Michel G Tremblay
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec, QC G1V 0A6, Canada
| | - Kai Tan
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland 0623, New Zealand; Digital Life Institute, University of Auckland, Auckland 0632, New Zealand
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Vikram R Paralkar
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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124
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Siebert AE, Corll J, Paige Gronevelt J, Levine L, Hobbs LM, Kenney C, Powell CLE, Battistuzzi FU, Davenport R, Mark Settles A, Brad Barbazuk W, Westrick RJ, Madlambayan GJ, Lal S. Genetic analysis of human RNA binding motif protein 48 (RBM48) reveals an essential role in U12-type intron splicing. Genetics 2022; 222:iyac129. [PMID: 36040194 PMCID: PMC9526058 DOI: 10.1093/genetics/iyac129] [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: 05/13/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
U12-type or minor introns are found in most multicellular eukaryotes and constitute ∼0.5% of all introns in species with a minor spliceosome. Although the biological significance for the evolutionary conservation of U12-type introns is debated, mutations disrupting U12 splicing cause developmental defects in both plants and animals. In human hematopoietic stem cells, U12 splicing defects disrupt proper differentiation of myeloid lineages and are associated with myelodysplastic syndrome, predisposing individuals to acute myeloid leukemia. Mutants in the maize ortholog of RNA binding motif protein 48 (RBM48) have aberrant U12-type intron splicing. Human RBM48 was recently purified biochemically as part of the minor spliceosome and shown to recognize the 5' end of the U6atac snRNA. In this report, we use CRISPR/Cas9-mediated ablation of RBM48 in human K-562 cells to show the genetic function of RBM48. RNA-seq analysis comparing wild-type and mutant K-562 genotypes found that 48% of minor intron-containing genes have significant U12-type intron retention in RBM48 mutants. Comparing these results to maize rbm48 mutants defined a subset of minor intron-containing genes disrupted in both species. Mutations in the majority of these orthologous minor intron-containing genes have been reported to cause developmental defects in both plants and animals. Our results provide genetic evidence that the primary defect of human RBM48 mutants is aberrant U12-type intron splicing, while a comparison of human and maize RNA-seq data identifies candidate genes likely to mediate mutant phenotypes of U12-type splicing defects.
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Affiliation(s)
- Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - J Paige Gronevelt
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Laurel Levine
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Linzi M Hobbs
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Catalina Kenney
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Christopher L E Powell
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Fabia U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - A Mark Settles
- Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Randal J Westrick
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Gerard J Madlambayan
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
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125
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Lalonde ME, Sasseville M, Gélinas AM, Milanese JS, Béland K, Drouin S, Haddad E, Marcotte R. Genome-wide CRISPR screens identify ferroptosis as a novel therapeutic vulnerability in acute lymphoblastic leukemia. Haematologica 2022; 108:382-393. [PMID: 36134452 PMCID: PMC9890019 DOI: 10.3324/haematol.2022.280786] [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: 02/02/2022] [Indexed: 02/03/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most frequent cancer diagnosed in children. Despite the great progress achieved over the last 40 years, with cure rates now exceeding 85%, refractory or relapsed ALL still exhibit a dismal prognosis. This poor outcome reflects the lack of treatment options specifically targeting relapsed or refractory ALL. In order to address this gap, we performed whole-genome CRISPR/Cas drop-out screens on a panel of seven B-ALL cell lines. Our results demonstrate that while there was a significant overlap in gene essentiality between ALL cell lines and other cancer types survival of ALL cell lines was dependent on several unique metabolic pathways, including an exquisite sensitivity to GPX4 depletion and ferroptosis induction. Detailed molecular analysis of B-ALL cells suggest that they are primed to undergo ferroptosis as they exhibit high steady-state oxidative stress potential, a low buffering capacity, and a disabled GPX4-independent secondary lipid peroxidation detoxification pathway. Finally, we validated the sensitivity of BALL to ferroptosis induction using patient-derived B-ALL samples.
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Affiliation(s)
- Marie-Eve Lalonde
- Human Health Therapeutics Research Center, National Research Council Canada
| | - Marc Sasseville
- Human Health Therapeutics Research Center, National Research Council Canada
| | - Anne-Marie Gélinas
- Human Health Therapeutics Research Center, National Research Council Canada
| | | | - Kathie Béland
- Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Quebec, Canada
| | - Simon Drouin
- Human Health Therapeutics Research Center, National Research Council Canada
| | - Elie Haddad
- Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Quebec, Canada
| | - Richard Marcotte
- Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, H4P 2R2.
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126
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Zhang P, Brinton LT, Gharghabi M, Sher S, Williams K, Cannon M, Walker JS, Canfield D, Beaver L, Cempre CB, Phillips H, Chen X, Yan P, Lehman A, Scherle P, Wang M, Vaddi K, Baiocchi R, Wang R, Sampath D, Alinari L, Blachly JS, Lapalombella R. Targeting OXPHOS de novo purine synthesis as the nexus of FLT3 inhibitor-mediated synergistic antileukemic actions. SCIENCE ADVANCES 2022; 8:eabp9005. [PMID: 36112677 PMCID: PMC9481139 DOI: 10.1126/sciadv.abp9005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 05/09/2023]
Abstract
Using a genome-wide CRISPR screen, we identified CDK9, DHODH, and PRMT5 as synthetic lethal partners with gilteritinib treatment in fms-like tyrosine kinase 3 (FLT3)-internal tandem duplication (ITD) acute myeloid leukemia (AML) and genetically and pharmacologically validated their roles in gilteritinib sensitivity. The presence of FLT3-ITD is associated with an increase in anaerobic glycolysis, rendering leukemia cells highly sensitive to inhibition of glycolysis. Supportive of this, our data show the enrichment of single guide RNAs targeting 28 glycolysis-related genes upon gilteritinib treatment, suggesting that switching from glycolysis to oxidative phosphorylation (OXPHOS) may represent a metabolic adaption of AML in gilteritinib resistance. CDK9i/FLT3i, DHODHi/FLT3i, and PRMT5i/FLT3i pairs mechanistically converge on OXPHOS and purine biosynthesis blockade, implying that targeting the metabolic functions of these three genes and/or proteins may represent attractive strategies to sensitize AML to gilteritinib treatment. Our findings provide the basis for maximizing therapeutic impact of FLT3-ITD inhibitors and a rationale for a clinical trial of these novel combinations.
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Affiliation(s)
- Pu Zhang
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Lindsey T. Brinton
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Mehdi Gharghabi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Steven Sher
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Katie Williams
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Matthew Cannon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Janek S. Walker
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Daniel Canfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Larry Beaver
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Casey B. Cempre
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Hannah Phillips
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Xuyong Chen
- Center for Childhood Cancer and Blood Diseases, Hematology/Oncology and BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, OH, USA
| | - Pearlly Yan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Amy Lehman
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | | | - Min Wang
- Prelude Therapeutics, Wilmington, DE, USA
| | - Kris Vaddi
- Prelude Therapeutics, Wilmington, DE, USA
| | - Robert Baiocchi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Diseases, Hematology/Oncology and BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, OH, USA
| | - Deepa Sampath
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - James S. Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Leukemia Research Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH, USA
| | - Rosa Lapalombella
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Leukemia Research Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH, USA
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127
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Kang K, Song Y, Kim I, Kim TJ. Therapeutic Applications of the CRISPR-Cas System. Bioengineering (Basel) 2022; 9:bioengineering9090477. [PMID: 36135023 PMCID: PMC9495783 DOI: 10.3390/bioengineering9090477] [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: 08/17/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The clustered regularly interspaced palindromic repeat (CRISPR)-Cas system has revolutionized genetic engineering due to its simplicity, stability, and precision since its discovery. This technology is utilized in a variety of fields, from basic research in medicine and biology to medical diagnosis and treatment, and its potential is unbounded as new methods are developed. The review focused on medical applications and discussed the most recent treatment trends and limitations, with an emphasis on CRISPR-based therapeutics for infectious disease, oncology, and genetic disease, as well as CRISPR-based diagnostics, screening, immunotherapy, and cell therapy. Given its promising results, the successful implementation of the CRISPR-Cas system in clinical practice will require further investigation into its therapeutic applications.
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Affiliation(s)
- Kyungmin Kang
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Youngjae Song
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Inho Kim
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Tae-Jung Kim
- Department of Hospital Pathology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea
- Correspondence: ; Tel.: +82-2-3779-2157
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128
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Hojo H, Saito T, He X, Guo Q, Onodera S, Azuma T, Koebis M, Nakao K, Aiba A, Seki M, Suzuki Y, Okada H, Tanaka S, Chung UI, McMahon AP, Ohba S. Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages. Cell Rep 2022; 40:111315. [PMID: 36070691 PMCID: PMC9510047 DOI: 10.1016/j.celrep.2022.111315] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/31/2022] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator Runx2 (runt-related transcription factor 2) has essential but distinct roles in osteoblasts and chondrocytes in skeletal development. However, Runx2-mediated regulatory mechanisms underlying the distinctive programming of osteoblasts and chondrocytes are not well understood. Here, we perform an integrative analysis to investigate Runx2-DNA binding and chromatin accessibility ex vivo using neonatal osteoblasts and chondrocytes. We find that Runx2 engages with cell-type-distinct chromatin-accessible regions, potentially interacting with different combinations of transcriptional regulators, forming cell-type-specific hotspots, and potentiating chromatin accessibility. Genetic analysis and direct cellular reprogramming studies suggest that Runx2 is essential for establishment of chromatin accessibility in osteoblasts. Functional enhancer studies identify an Sp7 distal enhancer driven by Runx2-dependent binding and osteoblast-specific chromatin accessibility, contributing to normal osteoblast differentiation. Our findings provide a framework for understanding the regulatory landscape encompassing Runx2-mediated and cell-type-distinct enhancer networks that underlie the specification of osteoblasts. Hojo et al. investigate the gene-regulatory landscape underlying specification of skeletal cell types in neonatal mice. Runx2, an osteoblast determinant, engages with cell-type-distinct chromatin-accessible regions and is essential for establishment of chromatin accessibility in osteoblasts. The study provides insights into enhancer networks in skeletal development.
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Affiliation(s)
- Hironori Hojo
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Taku Saito
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Xinjun He
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shoko Onodera
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hiroyuki Okada
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Sakae Tanaka
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ung-Il Chung
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shinsuke Ohba
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan; Department of Oral Anatomy and Developmental Biology, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan.
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129
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Gupta S, Dovey OM, Domingues AF, Cyran OW, Cash CM, Giotopoulos G, Rak J, Cooper J, Gozdecka M, Dijkhuis L, Asby RJ, Al-Jabery N, Hernandez-Hernandez V, Prabakaran S, Huntly BJ, Vassiliou GS, Pina C. Transcriptional variability accelerates preleukemia by cell diversification and perturbation of protein synthesis. SCIENCE ADVANCES 2022; 8:eabn4886. [PMID: 35921412 PMCID: PMC9348803 DOI: 10.1126/sciadv.abn4886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Transcriptional variability facilitates stochastic cell diversification and can in turn underpin adaptation to stress or injury. We hypothesize that it may analogously facilitate progression of premalignancy to cancer. To investigate this, we initiated preleukemia in mouse cells with enhanced transcriptional variability due to conditional disruption of the histone lysine acetyltransferase gene Kat2a. By combining single-cell RNA sequencing of preleukemia with functional analysis of transformation, we show that Kat2a loss results in global variegation of cell identity and accumulation of preleukemic cells. Leukemia progression is subsequently facilitated by destabilization of ribosome biogenesis and protein synthesis, which confer a transient transformation advantage. The contribution of transcriptional variability to early cancer evolution reflects a generic role in promoting cell fate transitions, which, in the case of well-adapted malignancies, contrastingly differentiates and depletes cancer stem cells. That is, transcriptional variability confers forward momentum to cell fate systems, with differential multistage impact throughout cancer evolution.
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Affiliation(s)
- Shikha Gupta
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Oliver M. Dovey
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ana Filipa Domingues
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Oliwia W. Cyran
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Caitlin M. Cash
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
| | - George Giotopoulos
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jonathan Cooper
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Liza Dijkhuis
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
| | - Ryan J. Asby
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Noor Al-Jabery
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
| | - Victor Hernandez-Hernandez
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
- Centre for Genome Engineering and Maintenance, Brunel University London, Uxbridge, UB8 3PH, UK
| | | | - Brian J. Huntly
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - George S. Vassiliou
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Cristina Pina
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
- Centre for Genome Engineering and Maintenance, Brunel University London, Uxbridge, UB8 3PH, UK
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130
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Álvarez MM, Biayna J, Supek F. TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening. Nat Commun 2022; 13:4520. [PMID: 35927263 PMCID: PMC9352712 DOI: 10.1038/s41467-022-32285-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/26/2022] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas9 gene editing can inactivate genes in a precise manner. This process involves DNA double-strand breaks (DSB), which may incur a loss of cell fitness. We hypothesize that DSB toxicity may be variable depending on the chromatin environment in the targeted locus. Here, by analyzing isogenic cell line pair CRISPR experiments jointly with previous screening data from across ~900 cell lines, we show that TP53-associated break toxicity is higher in genomic regions that harbor active chromatin, such as gene regulatory elements or transcription elongation histone marks. DSB repair pathway choice and DNA sequence context also associate with toxicity. We also show that, due to noise introduced by differential toxicity of sgRNA-targeted sites, the power of genetic screens to detect conditional essentiality is reduced in TP53 wild-type cells. Understanding the determinants of Cas9 cut toxicity will help improve design of CRISPR reagents to avoid incidental selection of TP53-deficient and/or DNA repair deficient cells.
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Affiliation(s)
- Miguel M Álvarez
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona institute for Science and Technology, Barcelona, Spain
| | - Josep Biayna
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona institute for Science and Technology, Barcelona, Spain
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Würzburg, Germany
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona institute for Science and Technology, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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131
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BRD4 Inhibitor GNE-987 Exerts Anticancer Effects by Targeting Super-Enhancer-Related Gene LYL1 in Acute Myeloid Leukemia. J Immunol Res 2022; 2022:7912484. [PMID: 35958877 PMCID: PMC9359861 DOI: 10.1155/2022/7912484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/17/2022] [Accepted: 07/06/2022] [Indexed: 12/13/2022] Open
Abstract
Background. AML (acute myeloid leukemia) is a common hematological malignancy in children with poor treatment effects and poor prognosis. Recent studies have shown that as a novel BRD4 (bromodomain containing 4) PROTACs (proteolysis targeting chimeras) degrader, GNE-987 can slow down the growth of various tumors and increase apoptosis, with promising clinical prospects. However, the function and molecular mechanism of GNE-987 in AML remain unclear. This study is aimed at investigating the therapeutic effect of GNE-987 on AML and its underlying mechanism. Methods. The association between BRD4 and AML was assessed by studying public databases. After GNE-987 was added to AML cells, cell proliferation slowed down, the cycle was disturbed, and apoptosis increased. Western blotting was used to detect BRD2 (bromodomain containing 2), BRD3 (bromodomain containing 3), BRD4, and PARP (poly ADP-ribose polymerase) proteins. The effect of GNE-987 on AML cells was analyzed in vivo. RNA-seq (RNA sequencing) and ChIP-seq (chromatin immunoprecipitation sequencing) validated the function and molecular pathways of GNE-987 in processing AML. Results. BRD4 expression was significantly elevated in pediatric AML samples compared with healthy donors. GNE-987 inhibited AML cell proliferation by inhibiting the cell cycle and inducing apoptosis. BRD2, BRD3, and BRD4 were consistent with decreased VHL (Von Hippel Lindau) expression in AML cells. In an AML xenograft model, GNE-987 significantly reduced the hepatosplenic infiltration of leukemia cells and increased the mouse survival time. Based on analysis of RNA-seq and ChIP-seq analyses, GNE-987 could target multiple SE- (super-enhancer-) related genes, including LYL1 (lymphoblastic leukemia 1), to inhibit AML. Conclusions. GNE-987 had strong antitumor activity in AML. GNE-987 could effectively inhibit the expression of SE-related oncogenes including LYL1 in AML. Our results suggested that GNE-987 had broad prospects in the treatment of AML.
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De Kesel J, Fijalkowski I, Taylor J, Ntziachristos P. Splicing dysregulation in human hematologic malignancies: beyond splicing mutations. Trends Immunol 2022; 43:674-686. [PMID: 35850914 DOI: 10.1016/j.it.2022.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Splicing is a fundamental process in pre-mRNA maturation. Whereas alternative splicing (AS) enriches the diversity of the proteome, its aberrant regulation can drive oncogenesis. So far, most attention has been given to spliceosome mutations (SMs) in the context of splicing dysregulation in hematologic diseases. However, in recent years, post-translational modifications (PTMs) and transcriptional alterations of splicing factors (SFs), just as epigenetic signatures, have all been shown to contribute to global splicing dysregulation as well. In addition, the contribution of aberrant splicing to the neoantigen repertoire of cancers has been recognized. With the pressing need for novel therapeutics to combat blood cancers, this article provides an overview of emerging mechanisms that contribute to aberrant splicing, as well as their clinical potential.
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Affiliation(s)
- Jonas De Kesel
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Igor Fijalkowski
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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133
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Vinceti A, Perron U, Trastulla L, Iorio F. Reduced gene templates for supervised analysis of scale-limited CRISPR-Cas9 fitness screens. Cell Rep 2022; 40:111145. [PMID: 35905712 DOI: 10.1016/j.celrep.2022.111145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/26/2022] [Accepted: 07/07/2022] [Indexed: 12/21/2022] Open
Abstract
Pooled genome-wide CRISPR-Cas9 screens are furthering our mechanistic understanding of human biology and have allowed us to identify new oncology therapeutic targets. Scale-limited CRISPR-Cas9 screens-typically employing guide RNA libraries targeting subsets of functionally related genes, biological pathways, or portions of the druggable genome-constitute an optimal setting for investigating narrow hypotheses and are easier to execute on complex models, such as organoids and in vivo models. Different supervised methods are used for computational analysis of genome-wide CRISPR-Cas9 screens; most are not well suited for scale-limited screens, as they require large sets of positive/negative control genes (gene templates) to be included among the screened ones. Here, we develop a computational framework identifying optimal subsets of known essential and nonessential genes (at different subsampling percentages) that can be used as templates for supervised analyses of scale-limited CRISPR-Cas9 screens, while having a reduced impact on the size of the employed library.
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Affiliation(s)
- Alessandro Vinceti
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Umberto Perron
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Lucia Trastulla
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Francesco Iorio
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy; Cancer Dependency Map Analytics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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134
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Abdelhalim H, Berber A, Lodi M, Jain R, Nair A, Pappu A, Patel K, Venkat V, Venkatesan C, Wable R, Dinatale M, Fu A, Iyer V, Kalove I, Kleyman M, Koutsoutis J, Menna D, Paliwal M, Patel N, Patel T, Rafique Z, Samadi R, Varadhan R, Bolla S, Vadapalli S, Ahmed Z. Artificial Intelligence, Healthcare, Clinical Genomics, and Pharmacogenomics Approaches in Precision Medicine. Front Genet 2022; 13:929736. [PMID: 35873469 PMCID: PMC9299079 DOI: 10.3389/fgene.2022.929736] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Precision medicine has greatly aided in improving health outcomes using earlier diagnosis and better prognosis for chronic diseases. It makes use of clinical data associated with the patient as well as their multi-omics/genomic data to reach a conclusion regarding how a physician should proceed with a specific treatment. Compared to the symptom-driven approach in medicine, precision medicine considers the critical fact that all patients do not react to the same treatment or medication in the same way. When considering the intersection of traditionally distinct arenas of medicine, that is, artificial intelligence, healthcare, clinical genomics, and pharmacogenomics—what ties them together is their impact on the development of precision medicine as a field and how they each contribute to patient-specific, rather than symptom-specific patient outcomes. This study discusses the impact and integration of these different fields in the scope of precision medicine and how they can be used in preventing and predicting acute or chronic diseases. Additionally, this study also discusses the advantages as well as the current challenges associated with artificial intelligence, healthcare, clinical genomics, and pharmacogenomics.
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Affiliation(s)
- Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Asude Berber
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Mudassir Lodi
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Rihi Jain
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Achuth Nair
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Anirudh Pappu
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Kush Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Vignesh Venkat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Cynthia Venkatesan
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Raghu Wable
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Matthew Dinatale
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Allyson Fu
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Vikram Iyer
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Ishan Kalove
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Marc Kleyman
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Joseph Koutsoutis
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - David Menna
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Mayank Paliwal
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Nishi Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Thirth Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Zara Rafique
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Rothela Samadi
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Roshan Varadhan
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Shreyas Bolla
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Sreya Vadapalli
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, New Brunswick, NJ, United States
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135
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Ancos-Pintado R, Bragado-García I, Morales ML, García-Vicente R, Arroyo-Barea A, Rodríguez-García A, Martínez-López J, Linares M, Hernández-Sánchez M. High-Throughput CRISPR Screening in Hematological Neoplasms. Cancers (Basel) 2022; 14:3612. [PMID: 35892871 PMCID: PMC9329962 DOI: 10.3390/cancers14153612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
CRISPR is becoming an indispensable tool in biological research, revolutionizing diverse fields of medical research and biotechnology. In the last few years, several CRISPR-based genome-targeting tools have been translated for the study of hematological neoplasms. However, there is a lack of reviews focused on the wide uses of this technology in hematology. Therefore, in this review, we summarize the main CRISPR-based approaches of high throughput screenings applied to this field. Here we explain several libraries and algorithms for analysis of CRISPR screens used in hematology, accompanied by the most relevant databases. Moreover, we focus on (1) the identification of novel modulator genes of drug resistance and efficacy, which could anticipate relapses in patients and (2) new therapeutic targets and synthetic lethal interactions. We also discuss the approaches to uncover novel biomarkers of malignant transformations and immune evasion mechanisms. We explain the current literature in the most common lymphoid and myeloid neoplasms using this tool. Then, we conclude with future directions, highlighting the importance of further gene candidate validation and the integration and harmonization of the data from CRISPR screening approaches.
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Affiliation(s)
- Raquel Ancos-Pintado
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Irene Bragado-García
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Andrés Arroyo-Barea
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
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136
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In vivo genome-wide CRISPR screening in murine acute myeloid leukemia uncovers microenvironmental dependencies. Blood Adv 2022; 6:5072-5084. [PMID: 35793392 PMCID: PMC9631646 DOI: 10.1182/bloodadvances.2022007250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/26/2022] [Indexed: 11/20/2022] Open
Abstract
In vivo CRISPR screens in AML define key interactors of the microenvironment, including integrins, immune modulators, and glycosylation. Eight in vivo–specific hits are recurrently associated with adverse prognosis: BTBD6, FERMT3, ILK, SLC19A1, TAP2, TLN1, TPST2, and TRMT12.
Genome-wide CRISPR screens have been extremely useful in identifying therapeutic targets in diverse cancers by defining genes that are essential for malignant growth. However, most CRISPR screens were performed in vitro and thus cannot identify genes that are essential for interactions with the microenvironment in vivo. Here, we report genome-wide CRISPR screens in 2 in vivo murine models of acute myeloid leukemia (AML) driven by the KMT2A/MLLT3 fusion or by the constitutive coexpression of Hoxa9 and Meis1. Secondary validation using a focused library identified 72 genes specifically essential for leukemic growth in vivo, including components of the major histocompatibility complex class I complex, Cd47, complement receptor Cr1l, and the β-4-galactosylation pathway. Importantly, several of these in vivo–specific hits have a prognostic effect or are inferred to be master regulators of protein activity in human AML cases. For instance, we identified Fermt3, a master regulator of integrin signaling, as having in vivo–specific dependency with high prognostic relevance. Overall, we show an experimental and computational pipeline for genome-wide functional screens in vivo in AML and provide a genome-wide resource of essential drivers of leukemic growth in vivo.
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137
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Ellegast JM, Alexe G, Hamze A, Lin S, Uckelmann HJ, Rauch PJ, Pimkin M, Ross LS, Dharia NV, Robichaud AL, Conway AS, Khalid D, Perry JA, Wunderlich M, Benajiba L, Pikman Y, Nabet B, Gray NS, Orkin SH, Stegmaier K. Unleashing Cell-Intrinsic Inflammation as a Strategy to Kill AML Blasts. Cancer Discov 2022; 12:1760-1781. [PMID: 35405016 PMCID: PMC9308469 DOI: 10.1158/2159-8290.cd-21-0956] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 01/09/2023]
Abstract
Leukemic blasts are immune cells gone awry. We hypothesized that dysregulation of inflammatory pathways contributes to the maintenance of their leukemic state and can be exploited as cell-intrinsic, self-directed immunotherapy. To this end, we applied genome-wide screens to discover genetic vulnerabilities in acute myeloid leukemia (AML) cells implicated in inflammatory pathways. We identified the immune modulator IRF2BP2 as a selective AML dependency. We validated AML cell dependency on IRF2BP2 with genetic and protein degradation approaches in vitro and genetically in vivo. Chromatin and global gene-expression studies demonstrated that IRF2BP2 represses IL1β/TNFα signaling via NFκB, and IRF2BP2 perturbation results in an acute inflammatory state leading to AML cell death. These findings elucidate a hitherto unexplored AML dependency, reveal cell-intrinsic inflammatory signaling as a mechanism priming leukemic blasts for regulated cell death, and establish IRF2BP2-mediated transcriptional repression as a mechanism for blast survival. SIGNIFICANCE This study exploits inflammatory programs inherent to AML blasts to identify genetic vulnerabilities in this disease. In doing so, we determined that AML cells are dependent on the transcriptional repressive activity of IRF2BP2 for their survival, revealing cell-intrinsic inflammation as a mechanism priming leukemic blasts for regulated cell death. See related commentary by Puissant and Medyouf, p. 1617. This article is highlighted in the In This Issue feature, p. 1599.
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Affiliation(s)
- Jana M Ellegast
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Amanda Hamze
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hannah J Uckelmann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Philipp J Rauch
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Maxim Pimkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Linda S Ross
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amanda L Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Delan Khalid
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Lina Benajiba
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.,Université de Paris, INSERM U944 and CNRS 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, Paris, France
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Corresponding author: Dr. Kimberly Stegmaier (), Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston MA, 02215. Phone: 617-632-4438
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138
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Shin S, Kim SH, Park JH, Lee JS, Lee GM. Recombinase-mediated cassette exchange-based screening of a CRISPR/Cas9 library for enhanced recombinant protein production in human embryonic kidney cells: Improving resistance to hyperosmotic stress. Metab Eng 2022; 72:247-258. [DOI: 10.1016/j.ymben.2022.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
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139
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Trastulla L, Noorbakhsh J, Vazquez F, McFarland J, Iorio F. Computational estimation of quality and clinical relevance of cancer cell lines. Mol Syst Biol 2022; 18:e11017. [PMID: 35822563 PMCID: PMC9277610 DOI: 10.15252/msb.202211017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/12/2022] Open
Abstract
Immortal cancer cell lines (CCLs) are the most widely used system for investigating cancer biology and for the preclinical development of oncology therapies. Pharmacogenomic and genome-wide editing screenings have facilitated the discovery of clinically relevant gene-drug interactions and novel therapeutic targets via large panels of extensively characterised CCLs. However, tailoring pharmacological strategies in a precision medicine context requires bridging the existing gaps between tumours and in vitro models. Indeed, intrinsic limitations of CCLs such as misidentification, the absence of tumour microenvironment and genetic drift have highlighted the need to identify the most faithful CCLs for each primary tumour while addressing their heterogeneity, with the development of new models where necessary. Here, we discuss the most significant limitations of CCLs in representing patient features, and we review computational methods aiming at systematically evaluating the suitability of CCLs as tumour proxies and identifying the best patient representative in vitro models. Additionally, we provide an overview of the applications of these methods to more complex models and discuss future machine-learning-based directions that could resolve some of the arising discrepancies.
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Affiliation(s)
| | - Javad Noorbakhsh
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Present address:
Kojin TherapeuticsBostonMAUSA
| | - Francisca Vazquez
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMAUSA
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140
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Salame N, Fooks K, El-Hachem N, Bikorimana JP, Mercier FE, Rafei M. Recent Advances in Cancer Drug Discovery Through the Use of Phenotypic Reporter Systems, Connectivity Mapping, and Pooled CRISPR Screening. Front Pharmacol 2022; 13:852143. [PMID: 35795568 PMCID: PMC9250974 DOI: 10.3389/fphar.2022.852143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Multi-omic approaches offer an unprecedented overview of the development, plasticity, and resistance of cancer. However, the translation from anti-cancer compounds identified in vitro to clinically active drugs have a notoriously low success rate. Here, we review how technical advances in cell culture, robotics, computational biology, and development of reporter systems have transformed drug discovery, enabling screening approaches tailored to clinically relevant functional readouts (e.g., bypassing drug resistance). Illustrating with selected examples of “success stories,” we describe the process of phenotype-based high-throughput drug screening to target malignant cells or the immune system. Second, we describe computational approaches that link transcriptomic profiling of cancers with existing pharmaceutical compounds to accelerate drug repurposing. Finally, we review how CRISPR-based screening can be applied for the discovery of mechanisms of drug resistance and sensitization. Overall, we explore how the complementary strengths of each of these approaches allow them to transform the paradigm of pre-clinical drug development.
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Affiliation(s)
- Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada
| | - Katharine Fooks
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - François E. Mercier
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
| | - Moutih Rafei
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
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141
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Alford JS, Lampe JW, Brach D, Chesworth R, Cosmopoulos K, Duncan KW, Eckley ST, Kutok JL, Raimondi A, Riera TV, Shook B, Tang C, Totman J, Farrow NA. Conformational-Design-Driven Discovery of EZM0414: A Selective, Potent SETD2 Inhibitor for Clinical Studies. ACS Med Chem Lett 2022; 13:1137-1143. [PMID: 35859865 PMCID: PMC9290024 DOI: 10.1021/acsmedchemlett.2c00167] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
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SETD2, a lysine N-methyltransferase, is a histone
methyltransferase that plays an important role in various cellular
processes and was identified as a target of interest in multiple myeloma
that features a t(4,14) translocation. We recently reported the discovery
of a novel small-molecule SETD2 inhibitor tool compound that is suitable
for preclinical studies. Herein we describe the conformational-design-driven
evolution of the advanced chemistry lead, which resulted in compounds
appropriate for clinical evaluation. Further optimization of this
chemical series led to the discovery of EZM0414, which is a potent,
selective, and orally bioavailable inhibitor of SETD2 with good pharmacokinetic
properties and robust pharmacodynamic activity in a mouse xenograft
model.
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Affiliation(s)
- Joshua S. Alford
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - John W. Lampe
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Dorothy Brach
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Richard Chesworth
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Kat Cosmopoulos
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Kenneth W. Duncan
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Sean T. Eckley
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Jeffrey L. Kutok
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Alejandra Raimondi
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Thomas V. Riera
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Brian Shook
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Cuyue Tang
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Jennifer Totman
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Neil A. Farrow
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
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142
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Wang Q, Li J, Zhu J, Mao J, Duan C, Liang X, Zhu L, Zhu M, Zhang Z, Lin F, Guo R. Genome-wide CRISPR/Cas9 screening for therapeutic targets in NSCLC carrying wild-type TP53 and receptor tyrosine kinase genes. Clin Transl Med 2022; 12:e882. [PMID: 35692096 PMCID: PMC9189421 DOI: 10.1002/ctm2.882] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/21/2022] [Accepted: 05/03/2022] [Indexed: 11/25/2022] Open
Abstract
Background Targeted drugs have greatly improved the therapeutic outcome of non‐small cell lung cancer (NSCLC) patients compared with conventional chemotherapy, whereas about one‐third of patients are so far not suitable for targeted therapy due to lack of known driver oncogenes such as a mutated receptor tyrosine kinase (RTK) genes. In this study, we aimed to identify therapeutic targets for this subgroup of NSCLC patients. Methods We performed genome‐wide CRISPR/Cas9 screens in two NSCLC cell lines carrying wild‐type TP53 and receptor tyrosine kinase (wtTP53‐RTK) genes using a GeCKO v2.0 lentiviral library (containing 123411 sgRNAs and targeting 19050 genes). MAGeCKFlute was used to analyse and identify candidate genes. Genetic perturbation and pharmacological inhibition were used to validate the result in vitro and in vivo. Results The Genome‐wide CRISPR/Cas9 screening identified MDM2 as a potential therapeutic target for wtTP53‐RTK NSCLC. Genetic and pharmacological inhibition of MDM2 reduced cell proliferation and impaired tumour growth in the xenograft model, thus confirming the finding of the CRISPR/Cas9 screening. Moreover, treatment by a selective MDM2 inhibitor RG7388 triggered both cell cycle arrest and apoptosis in several NSCLC cell lines. Additionally, RG7388 and pemetrexed synergistically blocked the cell proliferation and growth of wtTP53‐RTK tumours but had limited effects for other genotypes. Conclusions We identified MDM2 as an essential gene and a potential therapeutic target in wtTP53‐RTK NSCLC via a genome‐wide CRISPR/Cas9 screening. For this subgroup, treatment by RG7388 alone or by its combination with pemetrexed resulted in significant tumour inhibition.
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Affiliation(s)
- Qianqian Wang
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jun Li
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jing Zhu
- Department of Oncologythe Affiliated Jiangning Hospital of Nanjing Medical UniversityNanjingChina
| | - Jiaqi Mao
- Department of Cell BiologySchool of Basic Medical SciencesInstitute for Brain Tumors & Key Laboratory of Rare Metabolic DiseasesNanjing Medical UniversityNanjingChina
| | - Chao Duan
- Department of Cell BiologySchool of Basic Medical SciencesInstitute for Brain Tumors & Key Laboratory of Rare Metabolic DiseasesNanjing Medical UniversityNanjingChina
| | - Xiao Liang
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lingyun Zhu
- Department of Cell BiologySchool of Basic Medical SciencesInstitute for Brain Tumors & Key Laboratory of Rare Metabolic DiseasesNanjing Medical UniversityNanjingChina
| | - Mengyan Zhu
- Department of BioinformaticsNanjing Medical UniversityNanjingChina
| | - Zhihong Zhang
- Department of Pathologythe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Fan Lin
- Department of Cell BiologySchool of Basic Medical SciencesInstitute for Brain Tumors & Key Laboratory of Rare Metabolic DiseasesNanjing Medical UniversityNanjingChina
| | - Renhua Guo
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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143
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Fowler FC, Chen BR, Zolnerowich N, Wu W, Pavani R, Paiano J, Peart C, Chen Z, Nussenzweig A, Sleckman BP, Tyler JK. DNA-PK promotes DNA end resection at DNA double strand breaks in G 0 cells. eLife 2022; 11:e74700. [PMID: 35575473 PMCID: PMC9122494 DOI: 10.7554/elife.74700] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/06/2022] [Indexed: 11/16/2022] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs are predominately repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 murine and human cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in proliferating cells at the G1 or G2 phase of the cell cycle was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, which has important implications for DNA DSB repair in quiescent cells.
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Affiliation(s)
- Faith C Fowler
- Weill Cornell Medicine Pharmacology Graduate ProgramNew YorkUnited States
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Bo-Ruei Chen
- Department of Medicine, Division of Hematology and Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | | | - Wei Wu
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Chelsea Peart
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Zulong Chen
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Barry P Sleckman
- Department of Medicine, Division of Hematology and Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jessica K Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
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144
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Ito R, Kitamura K, Inohara H, Yusa K, Kaneda Y, Nimura K. Peroxisomal Membrane Protein PMP34 Is Involved in the Human Papillomavirus Infection Pathway. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.870922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Infection with high-risk human papillomavirus (HPV) types is linked to the onset of several cancers. The mechanism of HPV infection, however, has not yet been fully elucidated. Here, using the newly developed HPV infectious pseudovirion (HPV PsV) and a genome-wide clustered regularly interspaced short palindromic repeat (CRISPR) screening system, we established an experimental system and searched for genes involved in HPV infection. The HPV PsV has the truncated herpes simplex virus thymidine kinase (dTK) to kill PsV-infected cells when combined with ganciclovir. The five rounds of selection of 293FT cells by infection with HPV PsVs identified two candidate genes involved in the HPV infection pathway. The validation experiments showed that SLC25A17, which encodes the peroxisomal membrane protein PMP34, was involved in the HPV infection pathway. The gRNAs against SLC25A17 attenuated the efficiency of HPV PsV infection in 293FT and HeLa cells. Although further experiments are required to determine whether PMP34 acts as the HPV infection pathway, these results indicate that our screening system is useful for identification of the genes involved in the HPV infection pathway.
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145
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A loss-of-adhesion CRISPR-Cas9 screening platform to identify cell adhesion-regulatory proteins and signaling pathways. Nat Commun 2022; 13:2136. [PMID: 35440579 PMCID: PMC9018714 DOI: 10.1038/s41467-022-29835-y] [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: 03/26/2020] [Accepted: 04/04/2022] [Indexed: 11/09/2022] Open
Abstract
The clinical introduction of the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib, which targets B-cell antigen-receptor (BCR)-controlled integrin-mediated retention of malignant B cells in their growth-supportive lymphoid organ microenvironment, provided a major breakthrough in lymphoma and leukemia treatment. Unfortunately, a significant subset of patients is intrinsically resistant or acquires resistance against ibrutinib. Here, to discover novel therapeutic targets, we present an unbiased loss-of-adhesion CRISPR-Cas9 knockout screening method to identify proteins involved in BCR-controlled integrin-mediated adhesion. Illustrating the validity of our approach, several kinases with an established role in BCR-controlled adhesion, including BTK and PI3K, both targets for clinically applied inhibitors, are among the top hits of our screen. We anticipate that pharmacological inhibitors of the identified targets, e.g. PAK2 and PTK2B/PYK2, may have great clinical potential as therapy for lymphoma and leukemia patients. Furthermore, this screening platform is highly flexible and can be easily adapted to identify cell adhesion-regulatory proteins and signaling pathways for other stimuli, adhesion molecules, and cell types. Targeting integrin-mediated retention of malignant B cells in their protective microenvironment is an efficacious treatment for lymphoma and leukemia. Here, the authors present an unbiased loss-of-adhesion CRISPR screening method, identifying therapeutic targets for these B-cell malignancies.
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146
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Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
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Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
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147
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Elmas E, Saljoughian N, de Souza Fernandes Pereira M, Tullius BP, Sorathia K, Nakkula RJ, Lee DA, Naeimi Kararoudi M. CRISPR Gene Editing of Human Primary NK and T Cells for Cancer Immunotherapy. Front Oncol 2022; 12:834002. [PMID: 35449580 PMCID: PMC9016158 DOI: 10.3389/fonc.2022.834002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Antitumor activity of immune cells such as T cells and NK cells has made them auspicious therapeutic regimens for adaptive cancer immunotherapy. Enhancing their cytotoxic effects against malignancies and overcoming their suppression in tumor microenvironment (TME) may improve their efficacy to treat cancers. Clustered, regularly interspaced short palindromic repeats (CRISPR) genome editing has become one of the most popular tools to enhance immune cell antitumor activity. In this review we highlight applications and practicability of CRISPR/Cas9 gene editing and engineering strategies for cancer immunotherapy. In addition, we have reviewed several approaches to study CRISPR off-target effects.
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Affiliation(s)
- Ezgi Elmas
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, United States
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Noushin Saljoughian
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- CRISPR/Gene Editing Core, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Marcelo de Souza Fernandes Pereira
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Brian P. Tullius
- Pediatric Cellular Therapy, AdventHealth for Children, Orlando, FL, United States
| | - Kinnari Sorathia
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Robin J. Nakkula
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Dean A. Lee
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Meisam Naeimi Kararoudi
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- CRISPR/Gene Editing Core, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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148
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Price S, Bhosle S, Gonçalves E, Li X, McClurg DP, Barthorpe S, Beck A, Hall C, Lightfoot H, Farrow L, Ansari R, Jackson DA, Allen L, Roberts K, Beaver C, Francies HE, Garnett MJ. A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens. Sci Rep 2022; 12:5571. [PMID: 35368031 PMCID: PMC8976852 DOI: 10.1038/s41598-022-09508-y] [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: 08/19/2021] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
Organoid cell culture methodologies are enabling the generation of cell models from healthy and diseased tissue. Patient-derived cancer organoids that recapitulate the genetic and histopathological diversity of patient tumours are being systematically generated, providing an opportunity to investigate new cancer biology and therapeutic approaches. The use of organoid cultures for many applications, including genetic and chemical perturbation screens, is limited due to the technical demands and cost associated with their handling and propagation. Here we report and benchmark a suspension culture technique for cancer organoids which allows for the expansion of models to tens of millions of cells with increased efficiency in comparison to standard organoid culturing protocols. Using whole-genome DNA and RNA sequencing analyses, as well as medium-throughput drug sensitivity testing and genome-wide CRISPR-Cas9 screening, we demonstrate that cancer organoids grown as a suspension culture are genetically and phenotypically similar to their counterparts grown in standard conditions. This culture technique simplifies organoid cell culture and extends the range of organoid applications, including for routine use in large-scale perturbation screens.
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149
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Grinkevitch V, Wappett M, Crawford N, Price S, Lees A, McCann C, McAllister K, Prehn J, Young J, Bateson J, Gallagher L, Michaut M, Iyer V, Chatzipli A, Barthorpe S, Ciznadija D, Sloma I, Wesa A, Tice DA, Wessels L, Garnett M, Longley DB, McDermott U, McDade SS. Functional Genomic Identification of Predictors of Sensitivity and Mechanisms of Resistance to Multivalent Second-Generation TRAIL-R2 Agonists. Mol Cancer Ther 2022; 21:594-606. [PMID: 35086954 PMCID: PMC7612587 DOI: 10.1158/1535-7163.mct-21-0532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 11/16/2022]
Abstract
Multivalent second-generation TRAIL-R2 agonists are currently in late preclinical development and early clinical trials. Herein, we use a representative second-generation agent, MEDI3039, to address two major clinical challenges facing these agents: lack of predictive biomarkers to enable patient selection and emergence of resistance. Genome-wide CRISPR knockout screens were notable for the lack of resistance mechanisms beyond the canonical TRAIL-R2 pathway (caspase-8, FADD, BID) as well as p53 and BAX in TP53 wild-type models, whereas a CRISPR activatory screen identified cell death inhibitors MCL-1 and BCL-XL as mechanisms to suppress MEDI3039-induced cell death. High-throughput drug screening failed to identify genomic alterations associated with response to MEDI3039; however, transcriptomics analysis revealed striking association between MEDI3039 sensitivity and expression of core components of the extrinsic apoptotic pathway, most notably its main apoptotic effector caspase-8 in solid tumor cell lines. Further analyses of colorectal cell lines and patient-derived xenografts identified caspase-8 expression ratio to its endogenous regulator FLIP(L) as predictive of sensitivity to MEDI3039 in several major solid tumor types and a further subset indicated by caspase-8:MCL-1 ratio. Subsequent MEDI3039 combination screening of TRAIL-R2, caspase-8, FADD, and BID knockout models with 60 compounds with varying mechanisms of action identified two inhibitor of apoptosis proteins (IAP) that exhibited strong synergy with MEDI3039 that could reverse resistance only in BID-deleted models. In summary, we identify the ratios of caspase-8:FLIP(L) and caspase-8:MCL-1 as potential predictive biomarkers for second-generation TRAIL-R2 agonists and loss of key effectors such as FADD and caspase-8 as likely drivers of clinical resistance in solid tumors.
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Affiliation(s)
| | - Mark Wappett
- Patrick G. Johnston Centre for Cancer Research, Queen's University, Belfast, United Kingdom
| | - Nyree Crawford
- Patrick G. Johnston Centre for Cancer Research, Queen's University, Belfast, United Kingdom
| | - Stacey Price
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Andrea Lees
- Patrick G. Johnston Centre for Cancer Research, Queen's University, Belfast, United Kingdom
| | - Christopher McCann
- Patrick G. Johnston Centre for Cancer Research, Queen's University, Belfast, United Kingdom
| | - Katherine McAllister
- Patrick G. Johnston Centre for Cancer Research, Queen's University, Belfast, United Kingdom
| | - Jochen Prehn
- Royal College of Surgeons Ireland, Dublin, Ireland
| | - Jamie Young
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Jess Bateson
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Lewis Gallagher
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Magali Michaut
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Vivek Iyer
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Syd Barthorpe
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Ido Sloma
- Champions Oncology Inc., Rockville, Maryland
| | - Amy Wesa
- Champions Oncology Inc., Rockville, Maryland
| | | | - Lodewyk Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, TU Delft, Delft, the Netherlands
| | - Mathew Garnett
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Daniel B. Longley
- Patrick G. Johnston Centre for Cancer Research, Queen's University, Belfast, United Kingdom
| | - Ultan McDermott
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Simon S. McDade
- Patrick G. Johnston Centre for Cancer Research, Queen's University, Belfast, United Kingdom
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150
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Gogleva A, Polychronopoulos D, Pfeifer M, Poroshin V, Ughetto M, Martin MJ, Thorpe H, Bornot A, Smith PD, Sidders B, Dry JR, Ahdesmäki M, McDermott U, Papa E, Bulusu KC. Knowledge graph-based recommendation framework identifies drivers of resistance in EGFR mutant non-small cell lung cancer. Nat Commun 2022; 13:1667. [PMID: 35351890 PMCID: PMC8964738 DOI: 10.1038/s41467-022-29292-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022] Open
Abstract
Resistance to EGFR inhibitors (EGFRi) presents a major obstacle in treating non-small cell lung cancer (NSCLC). One of the most exciting new ways to find potential resistance markers involves running functional genetic screens, such as CRISPR, followed by manual triage of significantly enriched genes. This triage process to identify 'high value' hits resulting from the CRISPR screen involves manual curation that requires specialized knowledge and can take even experts several months to comprehensively complete. To find key drivers of resistance faster we build a recommendation system on top of a heterogeneous biomedical knowledge graph integrating pre-clinical, clinical, and literature evidence. The recommender system ranks genes based on trade-offs between diverse types of evidence linking them to potential mechanisms of EGFRi resistance. This unbiased approach identifies 57 resistance markers from >3,000 genes, reducing hit identification time from months to minutes. In addition to reproducing known resistance markers, our method identifies previously unexplored resistance mechanisms that we prospectively validate.
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Affiliation(s)
- Anna Gogleva
- Biological Insight Knowledge Graph (BIKG), AI Engineering, R&D IT, AstraZeneca, Cambridge, UK
| | - Dimitris Polychronopoulos
- Early Computational Oncology, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Matthias Pfeifer
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Michaël Ughetto
- Biological Insight Knowledge Graph (BIKG), AI Engineering, R&D IT, AstraZeneca, Gothenburg, Sweden
| | - Matthew J Martin
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Hannah Thorpe
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Aurelie Bornot
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Paul D Smith
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Ben Sidders
- Early Computational Oncology, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jonathan R Dry
- Early Computational Oncology, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, MA, USA
| | - Miika Ahdesmäki
- Early Computational Oncology, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Ultan McDermott
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Eliseo Papa
- Biological Insight Knowledge Graph (BIKG), AI Engineering, R&D IT, AstraZeneca, Cambridge, UK.
| | - Krishna C Bulusu
- Early Computational Oncology, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
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