1
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Lu X, Yin P, Li H, Gao W, Jia H, Ma W. Transcriptome Analysis of Key Genes Involved in the Initiation of Spermatogonial Stem Cell Differentiation. Genes (Basel) 2024; 15:141. [PMID: 38397131 PMCID: PMC10888189 DOI: 10.3390/genes15020141] [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: 11/25/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
PURPOSE The purpose of this study was to screen the genes and pathways that are involved in spermatogonia stem cell (SSC) differentiation regulation during the transition from Aundiff to A1. Methods: RNA sequencing was performed to screen differentially expressed genes at 1 d and 2 d after SSC differentiation culture. KEGG pathway enrichment and GO function analysis were performed to reveal the genes and pathways related to the initiation of early SSC differentiation. RESULTS The GO analysis showed that Rpl21, which regulates cell differentiation initiation, significantly increased after 1 day of SSC differentiation. The expressions of Fn1, Cd9, Fgf2, Itgb1, Epha2, Ctgf, Cttn, Timp2 and Fgfr1, which are related to promoting differentiation, were up-regulated after 2 days of SSC differentiation. The analysis of the KEGG pathway revealed that RNA transport is the most enriched pathway 1 day after SSC differentiation. Hspa2, which promotes the differentiation of male reproductive cells, and Cdkn2a, which participates in the cell cycle, were significantly up-regulated. The p53 pathway and MAPK pathway were the most enriched pathways 2 days after SSC differentiation. Cdkn1a, Hmga2, Thbs1 and Cdkn2a, microRNAs that promote cell differentiation, were also significantly up-regulated. CONCLUSIONS RNA transport, the MAPK pathway and the p53 pathway may play vital roles in early SSC differentiation, and Rpl21, Fn1, Cd9, Fgf2, Itgb1, Epha2, Ctgf, Cttn, Timp2, Fgfr1, Hspa2, Cdkn2a, Cdkn1a, Hmga2 and Thbs1 are involved in the initiation of SSC differentiation. The findings of this study provide a reference for further revelations of the regulatory mechanism of SSC differentiation.
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Affiliation(s)
| | | | | | | | | | - Wenzhi Ma
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Key Laboratory of Reproduction and Genetics of Ningxia Hui Autonomous Region, School of Basic Medical Science, Ningxia Medical University, Yinchuan 750004, China; (X.L.); (P.Y.); (H.L.); (W.G.); (H.J.)
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2
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Zhang Y, Wang J, Ruan Y, Yang Y, Cheng Y, Wang F, Zhang C, Xu Y, Liu L, Yu M, Ren B, Wang J, Zhao B, Yang R, Xiong J, Wang J, Zhang J, Jian R, Liu Y, Tian Y. Genome-wide CRISPR screen identifies Puf60 as a novel stemness gene of mouse Embryonic Stem Cells. Stem Cells Dev 2022; 31:132-142. [PMID: 35019759 DOI: 10.1089/scd.2021.0309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mechanisms underlying self-renewal of embryonic stem cells (ESCs) hold great value in the clinical translation of stem cell biology and regenerative medicine research. To study the mechanisms in ESC self-renewal, screening and identification of key genes maintaining ESC self-renewal were performed by a genome-wide CRISPR-Cas9 knockout virus library. The mouse ESC R1 were infected with CRISPR-Cas9 knockout virus library and cultured for 14 days. The variation of sgRNA ratio was analyzed by high-throughput sequencing, followed by bioinformatics analysis to profile the altered genes. Our results showed 1375 genes with increased sgRNA ratio were found to be mainly involved in signal transduction, cell differentiation and cell apoptosis; 2929 genes with decreased sgRNA ratio were mainly involved in cell cycle regulation, RNA splicing, and biological metabolic processes. We further confirmed our screen specificity by confirming Puf60, U2af2, Wdr75 and Usp16 as novel positive regulators in mESC self-renewal. Meanwhile, further analysis showed the relevance between Puf60 expression and tumor. In conclusion, our study screened key genes maintaining ESC self-renewal and successful identified Puf60, U2af2, Wdr75 and Usp16 as novel positive regulators in mESC self-renewal, which provided theoretical basis and research clues for a better understanding of ESC self-renewal regulation.
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Affiliation(s)
- Yue Zhang
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, 30# Gaotanyan St., Shapingba District, Chongqing 400038, China, Chongqing, China, 400038;
| | - Jiaqi Wang
- Army Medical University, 12525, Institude of Immunulogy PLA & Department of Immunology, Army Medical University, Chongqing 400038, China, Chongqing, China;
| | - Yan Ruan
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Yi Yang
- Army Medical University, 12525, Experimental Center of Basic Medicine, College of Basic Medical Sciences, Chongqing, China;
| | - Yuda Cheng
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Fengsheng Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Chen Zhang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Yixiao Xu
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China;
| | - Lianlian Liu
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Meng Yu
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Bangqi Ren
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China;
| | - Jiangjun Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Binyu Zhao
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Ran Yang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Jiaxiang Xiong
- Army Medical University, 12525, Experimental Center of Basic Medicine, College of Basic Medical Sciences, Chongqing, China;
| | - Jiali Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, China;
| | - Junlei Zhang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, China;
| | - Rui Jian
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology,, Chongqing, China;
| | - Yong Liu
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China;
| | - Yanping Tian
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology,, Chongqing, China;
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3
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Lakpour N, Saliminejad K, Ghods R, Reza Sadeghi M, Pilatz A, Khosravi F, Madjd Z. Potential biomarkers for testicular germ cell tumour: Risk assessment, diagnostic, prognostic and monitoring of recurrence. Andrologia 2021; 53:e13998. [PMID: 33534171 DOI: 10.1111/and.13998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/01/2021] [Accepted: 01/12/2021] [Indexed: 12/17/2022] Open
Abstract
Testicular germ cell tumour (TGCT) is considered a relatively rare malignancy usually occurring in young men between 15 and 35 years of age, and both genetic and environmental factors contribute to its development. The majority of patients are diagnosed in an early-stage of TGCTs with an elevated 5-year survival rate after therapy. However, approximately 25% of patients show an incomplete response to chemotherapy or tumours relapse. The current therapies are accompanied by several adverse effects, including infertility. Aside from classical serum biomarker, many studies reported novel biomarkers for TGCTs, but without proper validation. Cancer cells share many similarities with embryonic stem cells (ESCs), and since ESC genes are not transcribed in most adult tissues, they could be considered ideal candidate targets for cancer-specific diagnosis and treatment. Added to this, several microRNAs (miRNA) including miRNA-371-3p can be further investigated as a molecular biomarker for diagnosis and monitoring of TGCTs. In this review, we will illustrate the findings of recent investigations in novel TGCTs biomarkers applicable for risk assessment, screening, diagnosis, prognosis, prediction and monitoring of the relapse.
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Affiliation(s)
- Niknam Lakpour
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Kioomars Saliminejad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Roya Ghods
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Sadeghi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Adrian Pilatz
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Farhad Khosravi
- Department of Physiology, Faculty of Medicine, Justus Liebig University, Giessen, Germany
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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4
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Mair B, Tomic J, Masud SN, Tonge P, Weiss A, Usaj M, Tong AHY, Kwan JJ, Brown KR, Titus E, Atkins M, Chan KSK, Munsie L, Habsid A, Han H, Kennedy M, Cohen B, Keller G, Moffat J. Essential Gene Profiles for Human Pluripotent Stem Cells Identify Uncharacterized Genes and Substrate Dependencies. Cell Rep 2020; 27:599-615.e12. [PMID: 30970261 DOI: 10.1016/j.celrep.2019.02.041] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/24/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold promise for regenerative medicine. For understanding pluripotency and lineage differentiation mechanisms, a critical first step involves systematically cataloging essential genes (EGs) that are indispensable for hPSC fitness, defined as cell reproduction in this study. To map essential genetic determinants of hPSC fitness, we performed genome-scale loss-of-function screens in an inducible Cas9 H1 hPSC line cultured on feeder cells and laminin to identify EGs. Among these, we found FOXH1 and VENTX, genes that encode transcription factors previously implicated in stem cell biology, as well as an uncharacterized gene, C22orf43/DRICH1. hPSC EGs are substantially different from other human model cell lines, and EGs in hPSCs are highly context dependent with respect to different growth substrates. Our CRISPR screens establish parameters for genome-wide screens in hPSCs, which will facilitate the characterization of unappreciated genetic regulators of hPSC biology.
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Affiliation(s)
- Barbara Mair
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jelena Tomic
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sanna N Masud
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Tonge
- Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
| | | | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Jamie J Kwan
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Emily Titus
- Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
| | - Michael Atkins
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Lise Munsie
- Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Marion Kennedy
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Brenda Cohen
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Gordon Keller
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Canadian Institute for Advanced Research, Toronto, ON, Canada; Institute for Biomaterials and BioMedical Engineering, University of Toronto, ON, Canada.
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5
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Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J. Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2. EMBO J 2020; 39:e102591. [PMID: 31782544 PMCID: PMC6960450 DOI: 10.15252/embj.2019102591] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
Developmental cell fate specification is a unidirectional process that can be reverted in response to injury or experimental reprogramming. Whether differentiation and de-differentiation trajectories intersect mechanistically is unclear. Here, we performed comparative screening in lineage-related mouse naïve embryonic stem cells (ESCs) and primed epiblast stem cells (EpiSCs), and identified the constitutively expressed zinc finger transcription factor (TF) Zfp281 as a bidirectional regulator of cell state interconversion. We showed that subtle chromatin binding changes in differentiated cells translate into activation of the histone H3 lysine 9 (H3K9) methyltransferase Ehmt1 and stabilization of the zinc finger TF Zic2 at enhancers and promoters. Genetic gain-of-function and loss-of-function experiments confirmed a critical role of Ehmt1 and Zic2 downstream of Zfp281 both in driving exit from the ESC state and in restricting reprogramming of EpiSCs. Our study reveals that cell type-invariant chromatin association of Zfp281 provides an interaction platform for remodeling the cis-regulatory network underlying cellular plasticity.
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Affiliation(s)
- Daniela Mayer
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Melanie Rittirsch
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Ilya Lukonin
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Maria Winzi
- Medical Systems BiologyUCC, Medical Faculty Carl Gustav CarusTU DresdenDresdenGermany
| | - Austin Smith
- Wellcome‐MRC Cambridge Stem Cell Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Frank Buchholz
- Medical Systems BiologyUCC, Medical Faculty Carl Gustav CarusTU DresdenDresdenGermany
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
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6
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Zaballos MA, Acuña-Ruiz A, Morante M, Crespo P, Santisteban P. Regulators of the RAS-ERK pathway as therapeutic targets in thyroid cancer. Endocr Relat Cancer 2019; 26:R319-R344. [PMID: 30978703 DOI: 10.1530/erc-19-0098] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/30/2022]
Abstract
Thyroid cancer is mostly an ERK-driven carcinoma, as up to 70% of thyroid carcinomas are caused by mutations that activate the RAS/ERK mitogenic signaling pathway. The incidence of thyroid cancer has been steadily increasing for the last four decades; yet, there is still no effective treatment for advanced thyroid carcinomas. Current research efforts are focused on impairing ERK signaling with small-molecule inhibitors, mainly at the level of BRAF and MEK. However, despite initial promising results in animal models, the clinical success of these inhibitors has been limited by the emergence of tumor resistance and relapse. The RAS/ERK pathway is an extremely complex signaling cascade with multiple points of control, offering many potential therapeutic targets: from the modulatory proteins regulating the activation state of RAS proteins to the scaffolding proteins of the pathway that provide spatial specificity to the signals, and finally, the negative feedbacks and phosphatases responsible for inactivating the pathway. The aim of this review is to give an overview of the biology of RAS/ERK regulators in human cancer highlighting relevant information on thyroid cancer and future areas of research.
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Affiliation(s)
- Miguel A Zaballos
- Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Adrián Acuña-Ruiz
- Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Morante
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Cantabria, Santander, Spain
| | - Piero Crespo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Cantabria, Santander, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
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7
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Pettitt SJ, Krastev DB, Pemberton HN, Fontebasso Y, Frankum J, Rehman FL, Brough R, Song F, Bajrami I, Rafiq R, Wallberg F, Kozarewa I, Fenwick K, Armisen-Garrido J, Swain A, Gulati A, Campbell J, Ashworth A, Lord CJ. Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells. Sci Data 2017; 4:170020. [PMID: 28248920 PMCID: PMC5332012 DOI: 10.1038/sdata.2017.20] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022] Open
Abstract
We describe a screen for cellular response to drugs that makes use of haploid embryonic stem cells. We generated ten libraries of mutants with piggyBac gene trap transposon integrations, totalling approximately 100,000 mutant clones. Random barcode sequences were inserted into the transposon vector to allow the number of cells bearing each insertion to be measured by amplifying and sequencing the barcodes. These barcodes were associated with their integration sites by inverse PCR. We exposed these libraries to commonly used cancer drugs and profiled changes in barcode abundance by Ion Torrent sequencing in order to identify mutations that conferred sensitivity. Drugs tested included conventional chemotherapeutics as well as targeted inhibitors of topoisomerases, poly(ADP-ribose) polymerase (PARP), Hsp90 and WEE1.
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Affiliation(s)
- Stephen J. Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Dragomir B. Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Helen N. Pemberton
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Yari Fontebasso
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Farah L. Rehman
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Feifei Song
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Fredrik Wallberg
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Iwanka Kozarewa
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Javier Armisen-Garrido
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Amanda Swain
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Aditi Gulati
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Alan Ashworth
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
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8
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Identifying survival-associated modules from the dysregulated triplet network in glioblastoma multiforme. J Cancer Res Clin Oncol 2017; 143:661-671. [DOI: 10.1007/s00432-016-2332-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/23/2016] [Indexed: 12/25/2022]
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9
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Choi YJ, Lin CP, Risso D, Chen S, Kim TA, Tan MH, Li JB, Wu Y, Chen C, Xuan Z, Macfarlan T, Peng W, Lloyd KCK, Kim SY, Speed TP, He L. Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells. Science 2017; 355:science.aag1927. [PMID: 28082412 DOI: 10.1126/science.aag1927] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022]
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) efficiently generate all embryonic cell lineages but rarely generate extraembryonic cell types. We found that microRNA miR-34a deficiency expands the developmental potential of mouse pluripotent stem cells, yielding both embryonic and extraembryonic lineages and strongly inducing MuERV-L (MERVL) endogenous retroviruses, similar to what is seen with features of totipotent two-cell blastomeres. miR-34a restricts the acquisition of expanded cell fate potential in pluripotent stem cells, and it represses MERVL expression through transcriptional regulation, at least in part by targeting the transcription factor Gata2. Our studies reveal a complex molecular network that defines and restricts pluripotent developmental potential in cultured ESCs and iPSCs.
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Affiliation(s)
- Yong Jin Choi
- Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94705, USA
| | - Chao-Po Lin
- Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94705, USA.
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Sean Chen
- Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94705, USA
| | - Thomas Aquinas Kim
- Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94705, USA
| | - Meng How Tan
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yalei Wu
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Caifu Chen
- Integrated DNA Technologies, 200 Chesapeake Drive, Redwood City, CA 94063, USA
| | - Zhenyu Xuan
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Todd Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Weiqun Peng
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA 95616, USA
| | - Sang Yong Kim
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010, Australia.,Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Lin He
- Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94705, USA.
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10
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Betschinger J. Charting Developmental Dissolution of Pluripotency. J Mol Biol 2016; 429:1441-1458. [PMID: 28013029 DOI: 10.1016/j.jmb.2016.12.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 12/14/2016] [Indexed: 02/06/2023]
Abstract
The formation of tissues and organs during metazoan development begs fundamental questions of cellular plasticity: How can the very same genome program have diverse cell types? How do cell identity programs unfold during development in space and time? How can defects in these mechanisms cause disease and also provide opportunities for therapeutic intervention? And ultimately, can developmental programs be exploited for bioengineering tissues and organs? Understanding principle designs of cellular identity and developmental progression is crucial for providing answers. Here, I will discuss how the capture of embryonic pluripotency in murine embryonic stem cells (ESCs) in vitro has allowed fundamental insights into the molecular underpinnings of a developmental cell state and how its ordered disassembly during differentiation prepares for lineage specification.
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Affiliation(s)
- Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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11
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Tan BSN, Kwek J, Wong CKE, Saner NJ, Yap C, Felquer F, Morris MB, Gardner DK, Rathjen PD, Rathjen J. Src Family Kinases and p38 Mitogen-Activated Protein Kinases Regulate Pluripotent Cell Differentiation in Culture. PLoS One 2016; 11:e0163244. [PMID: 27723793 PMCID: PMC5056717 DOI: 10.1371/journal.pone.0163244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 09/05/2016] [Indexed: 02/04/2023] Open
Abstract
Multiple pluripotent cell populations, which together comprise the pluripotent cell lineage, have been identified. The mechanisms that control the progression between these populations are still poorly understood. The formation of early primitive ectoderm-like (EPL) cells from mouse embryonic stem (mES) cells provides a model to understand how one such transition is regulated. EPL cells form from mES cells in response to l-proline uptake through the transporter Slc38a2. Using inhibitors of cell signaling we have shown that Src family kinases, p38 MAPK, ERK1/2 and GSK3β are required for the transition between mES and EPL cells. ERK1/2, c-Src and GSK3β are likely to be enforcing a receptive, primed state in mES cells, while Src family kinases and p38 MAPK are involved in the establishment of EPL cells. Inhibition of these pathways prevented the acquisition of most, but not all, features of EPL cells, suggesting that other pathways are required. L-proline activation of differentiation is mediated through metabolism and changes to intracellular metabolite levels, specifically reactive oxygen species. The implication of multiple signaling pathways in the process suggests a model in which the context of Src family kinase activation determines the outcomes of pluripotent cell differentiation.
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Affiliation(s)
- Boon Siang Nicholas Tan
- School of BioSciences, University of Melbourne, Parkville, Australia
- Stem Cells Australia, The University of Melbourne, Parkville, Australia
| | - Joly Kwek
- School of BioSciences, University of Melbourne, Parkville, Australia
- Australian Stem Cell Centre, Monash University, Clayton, Australia
| | - Chong Kum Edwin Wong
- School of BioSciences, University of Melbourne, Parkville, Australia
- Australian Stem Cell Centre, Monash University, Clayton, Australia
| | - Nicholas J. Saner
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
| | - Charlotte Yap
- School of BioSciences, University of Melbourne, Parkville, Australia
| | - Fernando Felquer
- Stem Cells Australia, The University of Melbourne, Parkville, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Michael B. Morris
- Australian Stem Cell Centre, Monash University, Clayton, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - David K. Gardner
- School of BioSciences, University of Melbourne, Parkville, Australia
- Stem Cells Australia, The University of Melbourne, Parkville, Australia
| | - Peter D. Rathjen
- School of BioSciences, University of Melbourne, Parkville, Australia
- Australian Stem Cell Centre, Monash University, Clayton, Australia
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Joy Rathjen
- School of BioSciences, University of Melbourne, Parkville, Australia
- Stem Cells Australia, The University of Melbourne, Parkville, Australia
- Australian Stem Cell Centre, Monash University, Clayton, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
- School of Medicine, University of Tasmania, Hobart, Australia
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12
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Yamakawa T, Sato Y, Matsumura Y, Kobayashi Y, Kawamura Y, Goshima N, Yamanaka S, Okita K. Screening of Human cDNA Library Reveals Two differentiation-Related Genes, HHEX and HLX, as Promoters of Early Phase Reprogramming toward Pluripotency. Stem Cells 2016; 34:2661-2669. [PMID: 27335261 DOI: 10.1002/stem.2436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/09/2016] [Accepted: 05/30/2016] [Indexed: 11/09/2022]
Abstract
Gene screenings have identified a number of reprogramming factors that induce pluripotency from somatic cells. However, the screening methods have mostly considered only factors that maintain pluripotency in embryonic stem cells, ignoring a potentially long list of other contributing factors involved. To expand the search, we developed a new screening method that examined 2,008 human genes in the generation of human induced pluripotent stem cells (iPSCs), including not only pluripotent genes but also differentiation-related genes that suppress pluripotency. We found the top 100 genes that increased reprogramming efficiency and discovered they contained many differentiation-related genes and homeobox genes. We selected two, HHEX and HLX, for further analysis. These genes enhanced the appearance of premature reprograming cells in the early phase of human iPSC induction, but had inhibitory effect on the late phase. In addition, when expressed in human iPSCs, HHEX and HLX interfered with the pluripotent state, indicating inverse effects on somatic reprograming and pluripotent maintenance. These results demonstrate that our screening is useful for identifying differentiation-related genes in somatic reprograming. Stem Cells 2016;34:2661-2669.
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Affiliation(s)
- Tatsuya Yamakawa
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yoshiko Sato
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yasuko Matsumura
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yukiko Kobayashi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | | | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.,Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
| | - Keisuke Okita
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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13
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Gonzales KAU, Ng HH. Biological Networks Governing the Acquisition, Maintenance, and Dissolution of Pluripotency: Insights from Functional Genomics Approaches. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:189-98. [PMID: 26582790 DOI: 10.1101/sqb.2015.80.027326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The repertoire of transcripts encoded by the genome contributes to the diversity of cellular states. Functional genomics aims to comprehensively uncover the roles of these transcripts to reconstruct biological networks and transform this information into useful knowledge. High-throughput functional screening has served as a powerful genetic discovery tool by enabling massively parallel implementation of biological assays. In recent years, high-throughput screening has unearthed crucial players in the regulation of different aspects of pluripotency, which is a unique property that enables a cell to differentiate into multiple cell types of the three major lineages. Pluripotency thus represents an interesting biological paradigm for studying the acquisition, maintenance, and dissolution of cellular states. In this review, we highlight the major findings of high-throughput studies to dissect these three aspects of pluripotency for the mouse and human systems. Collectively, they provide new insights into cell fate maintenance and transition. In addition, we also discuss the opportunities and challenges awaiting high-throughput screening in the future.
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Affiliation(s)
| | - Huck-Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore 138672, Singapore Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore Department of Biological Sciences, National University of Singapore, Singapore 117597, Singapore School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
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14
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Gingold JA, Coakley ES, Su J, Lee DF, Lau Z, Zhou H, Felsenfeld DP, Schaniel C, Lemischka IR. Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen. BMC Bioinformatics 2015. [PMID: 26198214 PMCID: PMC4511455 DOI: 10.1186/s12859-015-0636-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Chemical or small interfering (si) RNA screens measure the effects of many independent experimental conditions, each applied to a population of cells (e.g., all of the cells in a well). High-content screens permit a readout (e.g., fluorescence, luminescence, cell morphology) from each cell in the population. Most analysis approaches compare the average effect on each population, precluding identification of outliers that affect the distribution of the reporter in the population but not its average. Other approaches only measure changes to the distribution with a single parameter, precluding accurate distinction and clustering of interesting outlier distributions. Results We describe a methodology to identify outlier conditions by considering the cell-level measurements from each condition as a sample of an underlying distribution. With appropriate selection of a distance metric, all effects can be embedded in a fixed-dimensionality Euclidean basis, facilitating identification and clustering of biologically interesting outliers. We demonstrate that measurement of distances with the Hellinger distance metric offers substantial computational efficiencies over alternative metrics. We validate this methodology using an RNA interference (RNAi) screen in mouse embryonic stem cells (ESC) with a Nanog reporter. The methodology clusters effects of multiple control siRNAs into their true identities better than conventional approaches describing the median cell fluorescence or the commonly used Kolmogorov-Smirnov distance between the observed fluorescence distribution and the null distribution. It identifies outlier genes with effects on the reporter distribution that would have been missed by other methods. Among them, siRNA targeting Chek1 leads to a wider Nanog reporter fluorescence distribution. Similarly, siRNA targeting Med14 or Med27 leads to a narrower Nanog reporter fluorescence distribution. We confirm the roles of these three genes in regulating pluripotency by mRNA expression and alkaline phosphatase staining using independent short hairpin (sh) RNAs. Conclusions Using our methodology, we describe each experimental condition by a probability distribution. Measuring distances between probability distributions permits a multivariate rather than univariate readout. Clustering points derived from these distances allows us to obtain greater biological insight than methods based solely on single parameters. We find several outliers from a mouse ESC RNAi screen that we confirm to be pluripotency regulators. Many of these outliers would have been missed by other analysis methods. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0636-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julian A Gingold
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Ed S Coakley
- Program in Applied Mathematics, Yale University, New Haven, CT, 06511, USA.
| | - Jie Su
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Dung-Fang Lee
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Zerlina Lau
- Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Hongwei Zhou
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Dan P Felsenfeld
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Christoph Schaniel
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Ihor R Lemischka
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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15
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Yeung ATY, Hale C, Xia J, Tate PH, Goulding D, Keane JA, Mukhopadhyay S, Forrester L, Billker O, Skarnes WC, Hancock REW, Dougan G. Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function. Sci Rep 2015; 5:8908. [PMID: 25752829 PMCID: PMC4354151 DOI: 10.1038/srep08908] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/10/2015] [Indexed: 11/09/2022] Open
Abstract
The ability to differentiate genetically modified mouse embryonic stem (ES) cells into functional macrophages provides a potentially attractive resource to study host-pathogen interactions without the need for animal experimentation. This is particularly useful in instances where the gene of interest is essential and a knockout mouse is not available. Here we differentiated mouse ES cells into macrophages in vitro and showed, through a combination of flow cytometry, microscopic imaging, and RNA-Seq, that ES cell-derived macrophages responded to S. Typhimurium, in a comparable manner to mouse bone marrow derived macrophages. We constructed a homozygous mutant mouse ES cell line in the Traf2 gene that is known to play a role in tumour necrosis factor-α signalling but has not been studied for its role in infections or response to Toll-like receptor agonists. Interestingly, traf2-deficient macrophages produced reduced levels of inflammatory cytokines in response to lipopolysaccharide (LPS) or flagellin stimulation and exhibited increased susceptibility to S. Typhimurium infection.
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Affiliation(s)
- A. T. Y. Yeung
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - C. Hale
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - J. Xia
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - P. H. Tate
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - D. Goulding
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - J. A. Keane
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - S. Mukhopadhyay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - L. Forrester
- University of Edinburgh/MRC Centre for Regenerative Medicine, Edinburgh, United Kingdom
| | - O. Billker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - W. C. Skarnes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - R. E. W. Hancock
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - G. Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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16
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Atlasi Y, Looijenga L, Fodde R. Cancer stem cells, pluripotency, and cellular heterogeneity: a WNTer perspective. Curr Top Dev Biol 2014; 107:373-404. [PMID: 24439813 DOI: 10.1016/b978-0-12-416022-4.00013-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer stem cells (CSCs) are thought to represent the "beating heart" of malignant growth as they continuously fuel tumors through their ability to self-renew and differentiate. Moreover, they are also believed to underlie malignant behavior, local invasion, and metastasis in distal organ sites upon reversible epithelial-to-mesenchymal transitions (EMTs). Nevertheless, the CSC concept has been the object of controversy, mainly due to the absence of robust operational definitions and to the lack of consistency in the use of the often incorrect nomenclature employed to refer to these cells. Notwithstanding the controversies, it is now generally accepted that primary cancers are organized in hierarchical fashion with neoplastic stem-like cells able to give rise to new CSCs and to more committed malignant cells. Notably, these hierarchical structures are not unidirectional, but are rather characterized by a more dynamic equilibrium where stem-like and more committed cancer cells transit from one meta-state to the other partly because of cues from the microenvironment (niche), but also because of intrinsic and yet incompletely understood characteristics in the activation/silencing of specific signal transduction pathways. Here, we will focus on the Wnt/β-catenin signaling pathway as one of the major regulator of stemness in homeostasis and cancer, and on germ cell tumors as the type of malignancy that most closely mimics normal embryonic development and as such serve as a unique model to study the role of stem cells in neoplasia.
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Affiliation(s)
- Yaser Atlasi
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Leendert Looijenga
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Riccardo Fodde
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, Rotterdam, The Netherlands.
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17
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Kapoor S, Berishvili E, Bandi S, Gupta S. Ischemic preconditioning affects long-term cell fate through DNA damage-related molecular signaling and altered proliferation. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:2779-90. [PMID: 25128377 DOI: 10.1016/j.ajpath.2014.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/11/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022]
Abstract
Despite the potential of ischemic preconditioning for organ protection, long-term effects in terms of molecular processes and cell fates are ill defined. We determined consequences of hepatic ischemic preconditioning in rats, including cell transplantation assays. Ischemic preconditioning induced persistent alterations; for example, after 5 days liver histology was normal, but γ-glutamyl transpeptidase expression was observed, with altered antioxidant enzyme content, lipid peroxidation, and oxidative DNA adducts. Nonetheless, ischemic preconditioning partially protected from toxic liver injury. Similarly, primary hepatocytes from donor livers preconditioned with ischemia exhibited undesirably altered antioxidant enzyme content and lipid peroxidation, but better withstood insults. However, donor hepatocytes from livers preconditioned with ischemia did not engraft better than hepatocytes from control livers. Moreover, proliferation of hepatocytes from donor livers preconditioned with ischemia decreased under liver repopulation conditions. Hepatocytes from donor livers preconditioned with ischemia showed oxidative DNA damage with expression of genes involved in MAPK signaling that impose G1/S and G2/M checkpoint restrictions, including p38 MAPK-regulated or ERK-1/2-regulated cell-cycle genes such as FOS, MAPK8, MYC, various cyclins, CDKN2A, CDKN2B, TP53, and RB1. Thus, although ischemic preconditioning allowed hepatocytes to better withstand secondary insults, accompanying DNA damage and molecular events simultaneously impaired their proliferation capacity over the long term. Mitigation of ischemic preconditioning-induced DNA damage and deleterious molecular perturbations holds promise for advancing clinical applications.
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Affiliation(s)
- Sorabh Kapoor
- Department of Medicine and Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Ekaterine Berishvili
- Department of Medicine and Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Sriram Bandi
- Department of Medicine and Pathology, Albert Einstein College of Medicine, Bronx, New York; Department of Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, New York
| | - Sanjeev Gupta
- Department of Medicine and Pathology, Albert Einstein College of Medicine, Bronx, New York; Department of Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, New York; Department of Diabetes Center, Albert Einstein College of Medicine, Bronx, New York; Department of Cancer Center, Albert Einstein College of Medicine, Bronx, New York; Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York; Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, New York.
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18
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Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 2014; 158:673-88. [PMID: 25083876 PMCID: PMC4137894 DOI: 10.1016/j.cell.2014.06.027] [Citation(s) in RCA: 348] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 04/03/2014] [Accepted: 06/10/2014] [Indexed: 12/15/2022]
Abstract
Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type. Using the broadest H3K4me3 domains as a discovery tool in neural progenitor cells, we identify novel regulators of these cells. Machine learning models reveal that the broadest H3K4me3 domains represent a distinct entity, characterized by increased marks of elongation. The broadest H3K4me3 domains also have more paused polymerase at their promoters, suggesting a unique transcriptional output. Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [corrected] increased transcriptional levels, and perturbation of H3K4me3 breadth leads to changes in transcriptional consistency. Thus, H3K4me3 breadth contains information that could ensure transcriptional precision at key cell identity/function genes.
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Affiliation(s)
- Bérénice A Benayoun
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA
| | - Duygu Ucar
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Salah Mahmoudi
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Edith D Wong
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | | | | | - Anshul B Kundaje
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Elena Mancini
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Rakhi Gupta
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Thomas A Rando
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford CA 94305, USA; RR&D REAP, VA Palo Alto Health Care Systems, Palo Alto, CA 94304,USA
| | - Julie C Baker
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA.
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19
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Testicular cancer: biology and biomarkers. Virchows Arch 2014; 464:301-13. [DOI: 10.1007/s00428-013-1522-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 11/25/2013] [Indexed: 12/13/2022]
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20
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Betschinger J, Nichols J, Dietmann S, Corrin P, Paddison P, Smith A. Exit from pluripotency is gated by intracellular redistribution of the bHLH transcription factor Tfe3. Cell 2013; 153:335-47. [PMID: 23582324 PMCID: PMC3661979 DOI: 10.1016/j.cell.2013.03.012] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 01/14/2013] [Accepted: 03/07/2013] [Indexed: 02/02/2023]
Abstract
Factors that sustain self-renewal of mouse embryonic stem cells (ESCs) are well described. In contrast, the machinery regulating exit from pluripotency is ill defined. In a large-scale small interfering RNA (siRNA) screen, we found that knockdown of the tumor suppressors Folliculin (Flcn) and Tsc2 prevent ESC commitment. Tsc2 lies upstream of mammalian target of rapamycin (mTOR), whereas Flcn acts downstream and in parallel. Flcn with its interaction partners Fnip1 and Fnip2 drives differentiation by restricting nuclear localization and activity of the bHLH transcription factor Tfe3. Conversely, enforced nuclear Tfe3 enables ESCs to withstand differentiation conditions. Genome-wide location and functional analyses showed that Tfe3 directly integrates into the pluripotency circuitry through transcriptional regulation of Esrrb. These findings identify a cell-intrinsic rheostat for destabilizing ground-state pluripotency to allow lineage commitment. Congruently, stage-specific subcellular relocalization of Tfe3 suggests that Flcn-Fnip1/2 contributes to developmental progression of the pluripotent epiblast in vivo.
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Affiliation(s)
- Joerg Betschinger
- Wellcome Trust—Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, UK
| | - Jennifer Nichols
- Wellcome Trust—Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 1QR, UK
| | - Sabine Dietmann
- Wellcome Trust—Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Philip D. Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Centre, Seattle, WA 98109, USA
| | - Patrick J. Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Centre, Seattle, WA 98109, USA
| | - Austin Smith
- Wellcome Trust—Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, UK
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Yang SH, Kalkan T, Morrisroe C, Smith A, Sharrocks AD. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation. PLoS Genet 2012; 8:e1003112. [PMID: 23271975 PMCID: PMC3521700 DOI: 10.1371/journal.pgen.1003112] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 10/08/2012] [Indexed: 01/13/2023] Open
Abstract
Embryonic stem cells and induced pluripotent stem cells represent potentially important therapeutic agents in regenerative medicine. Complex interlinked transcriptional and signaling networks control the fate of these cells towards maintenance of pluripotency or differentiation. In this study we have focused on how mouse embryonic stem cells begin to differentiate and lose pluripotency and, in particular, the role that the ERK MAP kinase and GSK3 signaling pathways play in this process. Through a genome-wide siRNA screen we have identified more than 400 genes involved in loss of pluripotency and promoting the onset of differentiation. These genes were functionally associated with the ERK and/or GSK3 pathways, providing an important resource for studying the roles of these pathways in controlling escape from the pluripotent ground state. More detailed analysis identified MAP kinase phosphatases as a focal point of regulation and demonstrated an important role for these enzymes in controlling ERK activation kinetics and subsequently determining early embryonic stem cell fate decisions.
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Affiliation(s)
- Shen-Hsi Yang
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Tuzer Kalkan
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Claire Morrisroe
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Austin Smith
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D. Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Khromov T, Dressel R, Siamishi I, Nolte J, Opitz L, Engel W, Pantakani DVK. Apoptosis-related gene expression profiles of mouse ESCs and maGSCs: role of Fgf4 and Mnda in pluripotent cell responses to genotoxicity. PLoS One 2012; 7:e48869. [PMID: 23145002 PMCID: PMC3492253 DOI: 10.1371/journal.pone.0048869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 10/02/2012] [Indexed: 01/27/2023] Open
Abstract
Stem cells in the developing embryo proliferate and differentiate while maintaining genomic integrity, failure of which may lead to accumulation of mutations and subsequent damage to the embryo. Embryonic stem cells (ESCs), the in vitro counterpart of embryo stem cells are highly sensitive to genotoxic stress. Defective ESCs undergo either efficient DNA damage repair or apoptosis, thus maintaining genomic integrity. However, the genotoxicity- and apoptosis-related processes in germ-line derived pluripotent cells, multipotent adult germ-line stem cells (maGSCs), are currently unknown. Here, we analyzed the expression of apoptosis-related genes using OligoGEArray in undifferentiated maGSCs and ESCs and identified a similar set of genes expressed in both cell types. We detected the expression of intrinsic, but not extrinsic, apoptotic pathway genes in both cell types. Further, we found that apoptosis-related gene expression patterns of differentiated ESCs and maGSCs are identical to each other. Comparative analysis revealed that several pro- and anti-apoptotic genes are expressed specifically in pluripotent cells, but markedly downregulated in the differentiated counterparts of these cells. Activation of the intrinsic apoptotic pathway cause approximately ∼35% of both ESCs and maGSCs to adopt an early-apoptotic phenotype. Moreover, we performed transcriptome studies using early-apoptotic cells to identify novel pluripotency- and apoptosis-related genes. From these transcriptome studies, we selected Fgf4 (Fibroblast growth factor 4) and Mnda (Myeloid cell nuclear differentiating antigen), which are highly downregulated in early-apoptotic cells, as novel candidates and analyzed their roles in apoptosis and genotoxicity responses in ESCs. Collectively, our results show the existence of common molecular mechanisms for maintaining the pristine stem cell pool of both ESCs and maGSCs.
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Affiliation(s)
- Tatjana Khromov
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Ralf Dressel
- Department of Cellular and Molecular Immunology, University of Goettingen, Goettingen, Germany
| | - Iliana Siamishi
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Jessica Nolte
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Lennart Opitz
- DNA Microarray Facility, University of Goettingen, Goettingen, Germany
| | - Wolfgang Engel
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
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