1
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Maresca M, Liu NQ, de Wit E. Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome. Methods Mol Biol 2022; 2532:311-331. [PMID: 35867256 DOI: 10.1007/978-1-0716-2497-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The organization of the genome inside the nucleus facilitates many nuclear processes. Because the nuclear genome is highly dynamic and often regulated by essential proteins, rapid depletion strategies are necessary to perform loss-of-function analyses. Fortunately, in recent years, various methods have been developed to manipulate the cellular levels of a protein directly and acutely. Here, we describe different methods that have been developed to rapidly deplete proteins from cells, with a focus on auxin inducible degron and dTAG methods, as these are most commonly used in 3D genome organization studies. We outline best practices for designing a knockin strategy, as well as generation and validation of knockin cell lines. Acute depletion strategies have been transformative for the study of the 3D genome and will be important tools for delineating the processes and factors that determine organization of the genome inside the nucleus.
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Affiliation(s)
- Michela Maresca
- Division Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ning Qing Liu
- Division Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elzo de Wit
- Division Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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2
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Krstic A, Konietzny A, Halasz M, Cain P, Oppermann U, Kolch W, Duffy DJ. A Chemo-Genomic Approach Identifies Diverse Epigenetic Therapeutic Vulnerabilities in MYCN-Amplified Neuroblastoma. Front Cell Dev Biol 2021; 9:612518. [PMID: 33968920 PMCID: PMC8097097 DOI: 10.3389/fcell.2021.612518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
Although a rare disease, neuroblastoma accounts for the highest proportion of childhood cancer deaths. There is a lack of recurrent somatic mutations in neuroblastoma embryonal tumours, suggesting a possible role for epigenetic alterations in driving this cancer. While an increasing number of reports suggest an association of MYCN with epigenetic machinery, the mechanisms of these interactions are poorly understood in the neuroblastoma setting. Utilising chemo-genomic approaches we revealed global MYCN-epigenetic interactions and identified numerous epigenetic proteins as MYCN targets. The epigenetic regulators HDAC2, CBX8 and CBP (CREBBP) were all MYCN target genes and also putative MYCN interactors. MYCN-related epigenetic genes included SMARCs, HDACs, SMYDs, BRDs and CREBBP. Expression levels of the majority of MYCN-related epigenetic genes showed predictive ability for neuroblastoma patient outcome. Furthermore, a compound library screen targeting epigenetic proteins revealed broad susceptibility of neuroblastoma cells to all classes of epigenetic regulators, belonging to families of bromodomains, HDACs, HATs, histone methyltransferases, DNA methyltransferases and lysin demethylases. Ninety-six percent of the compounds reduced MYCN-amplified neuroblastoma cell viability. We show that the C646 (CBP-bromodomain targeting compound) exhibits switch-like temporal and dose response behaviour and is effective at reducing neuroblastoma viability. Responsiveness correlates with MYCN expression, with MYCN-amplified cells being more susceptible to C646 treatment. Thus, exploiting the broad vulnerability of neuroblastoma cells to epigenetic targeting compounds represents an exciting strategy in neuroblastoma treatment, particularly for high-risk MYCN-amplified tumours.
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Affiliation(s)
- Aleksandar Krstic
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Anja Konietzny
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Molecular Neurobiology Hamburg (ZMNH), Emmy-Noether Group "Neuronal Protein Transport", University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Melinda Halasz
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Peter Cain
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Institute of Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Institute of Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Walter Kolch
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - David J Duffy
- Systems Biology Ireland and Precision Oncology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, United States.,Department of Biology, University of Florida, Gainesville, FL, United States
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3
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Zhang Z, Zhou L, Xie N, Nice EC, Zhang T, Cui Y, Huang C. Overcoming cancer therapeutic bottleneck by drug repurposing. Signal Transduct Target Ther 2020; 5:113. [PMID: 32616710 PMCID: PMC7331117 DOI: 10.1038/s41392-020-00213-8] [Citation(s) in RCA: 260] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Ever present hurdles for the discovery of new drugs for cancer therapy have necessitated the development of the alternative strategy of drug repurposing, the development of old drugs for new therapeutic purposes. This strategy with a cost-effective way offers a rare opportunity for the treatment of human neoplastic disease, facilitating rapid clinical translation. With an increased understanding of the hallmarks of cancer and the development of various data-driven approaches, drug repurposing further promotes the holistic productivity of drug discovery and reasonably focuses on target-defined antineoplastic compounds. The "treasure trove" of non-oncology drugs should not be ignored since they could target not only known but also hitherto unknown vulnerabilities of cancer. Indeed, different from targeted drugs, these old generic drugs, usually used in a multi-target strategy may bring benefit to patients. In this review, aiming to demonstrate the full potential of drug repurposing, we present various promising repurposed non-oncology drugs for clinical cancer management and classify these candidates into their proposed administration for either mono- or drug combination therapy. We also summarize approaches used for drug repurposing and discuss the main barriers to its uptake.
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Affiliation(s)
- Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, China
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, China
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Tao Zhang
- The School of Biological Science and Technology, Chengdu Medical College, 610083, Chengdu, China.
- Department of Oncology, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, 610051, Sichuan, China.
| | - Yongping Cui
- Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, and Cancer Institute, Shenzhen Bay Laboratory Shenzhen, 518035, Shenzhen, China.
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, China.
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China.
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4
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Ma CP, Liu H, Yi-Feng Chang I, Wang WC, Chen YT, Wu SM, Chen HW, Kuo YP, Shih CT, Li CY, Tan BCM. ADAR1 promotes robust hypoxia signaling via distinct regulation of multiple HIF-1α-inhibiting factors. EMBO Rep 2019; 20:e47107. [PMID: 30948460 PMCID: PMC6500999 DOI: 10.15252/embr.201847107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/15/2022] Open
Abstract
Adenosine deaminase acting on RNA (ADAR)-catalyzed adenosine-to-inosine RNA editing is potentially dysregulated in neoplastic progression. However, how this transcriptome recoding process is functionally correlated with tumorigenesis remains largely elusive. Our analyses of RNA editome datasets identify hypoxia-related genes as A-to-I editing targets. In particular, two negative regulators of HIF-1A-the natural antisense transcript HIF1A-AS2 and the ubiquitin ligase scaffold LIMD1-are directly but differentially modulated by ADAR1. We show that HIF1A-AS2 antagonizes the expression of HIF-1A in the immediate-early phase of hypoxic challenge, likely through a convergent transcription competition in cis ADAR1 in turn suppresses transcriptional progression of the antisense gene. In contrast, ADAR1 affects LIMD1 expression post-transcriptionally, by interfering with the cytoplasmic translocation of LIMD1 mRNA and thus protein translation. This multi-tier regulation coordinated by ADAR1 promotes robust and timely accumulation of HIF-1α upon oxygen depletion and reinforces target gene induction and downstream angiogenesis. Our results pinpoint ADAR1-HIF-1α axis as a hitherto unrecognized key regulator in hypoxia.
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Affiliation(s)
- Chung-Pei Ma
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsuan Liu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Colon and Rectal Surgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Cheng Wang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Tung Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shao-Min Wu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hui-Wen Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Ping Kuo
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chieh-Tien Shih
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chuan-Yun Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Bertrand Chin-Ming Tan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
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5
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Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1513. [PMID: 30370679 DOI: 10.1002/wrna.1513] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Cellular RNA levels are the result of a juggling act between RNA transcription, processing, and degradation. By tuning one or more of these parameters, cells can rapidly alter the available pool of transcripts in response to stimuli. While RNA sequencing (RNA-seq) is a vital method to quantify RNA levels genome-wide, it is unable to capture the dynamics of different RNA populations at steady-state or distinguish between different mechanisms that induce changes to the steady-state (i.e., altered rate of transcription vs. degradation). The dynamics of different RNA populations can be studied by targeted incorporation of noncanonical nucleosides. 4-Thiouridine (s4 U) is a commonly used and versatile RNA metabolic label that allows the study of many properties of RNA metabolism from synthesis to degradation. Numerous experimental strategies have been developed that leverage the power of s4 U to label newly transcribed RNA in whole cells, followed by enrichment with activated disulfides or chemistry to induce C mutations at sites of s4 U during sequencing. This review presents existing methods to study RNA population dynamics genome-wide using s4 U metabolic labeling, as well as a discussion of considerations and challenges when designing s4 U metabolic labeling experiments. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Jeremy A Schofield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
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6
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Duffy DJ, Konietzny A, Krstic A, Mehta JP, Halasz M, Kolch W. Identification of a MYCN and Wnt-related VANGL2-ITLN1 fusion gene in neuroblastoma. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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7
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Duffy DJ, Krstic A, Schwarzl T, Halasz M, Iljin K, Fey D, Haley B, Whilde J, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. Wnt signalling is a bi-directional vulnerability of cancer cells. Oncotarget 2018; 7:60310-60331. [PMID: 27531891 PMCID: PMC5312386 DOI: 10.18632/oncotarget.11203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 07/26/2016] [Indexed: 12/30/2022] Open
Abstract
Wnt signalling is involved in the formation, metastasis and relapse of a wide array of cancers. However, there is ongoing debate as to whether activation or inhibition of the pathway holds the most promise as a therapeutic treatment for cancer, with conflicting evidence from a variety of tumour types. We show that Wnt/β-catenin signalling is a bi-directional vulnerability of neuroblastoma, malignant melanoma and colorectal cancer, with hyper-activation or repression of the pathway both representing a promising therapeutic strategy, even within the same cancer type. Hyper-activation directs cancer cells to undergo apoptosis, even in cells oncogenically driven by β-catenin. Wnt inhibition blocks proliferation of cancer cells and promotes neuroblastoma differentiation. Wnt and retinoic acid co-treatments synergise, representing a promising combination treatment for MYCN-amplified neuroblastoma. Additionally, we report novel cross-talks between MYCN and β-catenin signalling, which repress normal β-catenin mediated transcriptional regulation. A β-catenin target gene signature could predict patient outcome, as could the expression level of its DNA binding partners, the TCF/LEFs. This β-catenin signature provides a tool to identify neuroblastoma patients likely to benefit from Wnt-directed therapy. Taken together, we show that Wnt/β-catenin signalling is a bi-directional vulnerability of a number of cancer entities, and potentially a more broadly conserved feature of malignant cells.
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Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Bridget Haley
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Jenny Whilde
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Vidal Fey
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matthias Fischer
- Department of Paediatric Haematology and Oncology and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Frank Westermann
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Bannert
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
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8
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Metabolic labeling and recovery of nascent RNA to accurately quantify mRNA stability. Methods 2017; 120:39-48. [PMID: 28219744 DOI: 10.1016/j.ymeth.2017.02.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022] Open
Abstract
Changes in the rate of mRNA decay are closely coordinated with transcriptional changes and together these events have profound effects on gene expression during development and disease. Traditional approaches to assess mRNA decay have relied on inhibition of transcription, which can alter mRNA decay rates and confound interpretation. More recently, metabolic labeling combined with chemical modification and fractionation of labeled RNAs has allowed the isolation of nascent transcripts and the subsequent calculation of mRNA decay rates. This approach has been widely adopted for measuring mRNA half-lives on a global scale, but has proven challenging to use for analysis of single genes. We present a series of normalization and quality assurance steps to be used in combination with 4-thiouridine pulse labeling of cultured eukaryotic cells. Importantly, we demonstrate how the relative amount of 4sU-labeled nascent RNA influences accurate quantification. The approach described facilitates reproducible measurement of individual mRNA half-lives using 4-thiouridine and could be adapted for use with other nucleoside analogs.
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9
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Duffy DJ, Krstic A, Halasz M, Schwarzl T, Konietzny A, Iljin K, Higgins DG, Kolch W. Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance. Genome Med 2017; 9:15. [PMID: 28187790 PMCID: PMC5303304 DOI: 10.1186/s13073-017-0407-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/20/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance. METHODS We applied RNA sequencing (RNA-seq) and interaction proteomics coupled with network-based systems level analysis to identify targetable vulnerabilities of MYCN-mediated retinoid resistance. We altered MYCN expression levels in a MYCN-inducible neuroblastoma cell line to facilitate or block retinoic acid (RA)-mediated neuronal differentiation. The relevance of differentially expressed genes and transcriptional regulators for neuroblastoma outcome were then confirmed using existing patient microarray datasets. RESULTS We determined the signalling networks through which RA mediates neuroblastoma differentiation and the inhibitory perturbations to these networks upon MYCN overexpression. We revealed opposing regulation of RA and MYCN on a number of differentiation-relevant genes, including LMO4, CYP26A1, ASCL1, RET, FZD7 and DKK1. Furthermore, we revealed a broad network of transcriptional regulators involved in regulating retinoid responsiveness, such as Neurotrophin, PI3K, Wnt and MAPK, and epigenetic signalling. Of these regulators, we functionally confirmed that MYCN-driven inhibition of transforming growth factor beta (TGF-β) signalling is a vulnerable node of the MYCN network and that multiple levels of cross-talk exist between MYCN and TGF-β. Co-targeting of the retinoic acid and TGF-β pathways, through RA and kartogenin (KGN; a TGF-β signalling activating small molecule) combination treatment, induced the loss of viability of MYCN-amplified retinoid-resistant neuroblastoma cells. CONCLUSIONS Our approach provides a powerful precision oncology tool for identifying the driving signalling networks for malignancies not primarily driven by somatic mutations, such as paediatric cancers. By applying global omics approaches to the signalling networks regulating neuroblastoma differentiation and stemness, we have determined the pathways involved in the MYCN-mediated retinoid resistance, with TGF-β signalling being a key regulator. These findings revealed a number of combination treatments likely to improve clinical response to retinoid therapy, including co-treatment with retinoids and KGN, which may prove valuable in the treatment of high-risk MYCN-amplified neuroblastoma.
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Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, Florida, 32080, USA.
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Anja Konietzny
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Present address: Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kristiina Iljin
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02044 VTT, Espoo, Finland
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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10
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Duffy DJ, Krstic A, Halasz M, Schwarzl T, Fey D, Iljin K, Mehta JP, Killick K, Whilde J, Turriziani B, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma. Oncotarget 2016; 6:43182-201. [PMID: 26673823 PMCID: PMC4791225 DOI: 10.18632/oncotarget.6568] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-druggable oncogene. We used systems medicine based computational network reconstruction and analysis to integrate a range of omic techniques: sequencing-based transcriptomics, genome-wide chromatin immunoprecipitation, siRNA screening and interaction proteomics, revealing that MYCN controls highly connected networks, with MYCN primarily supressing the activity of network components. MYCN's oncogenic functions are likely independent of its classical heterodimerisation partner, MAX. In particular, MYCN controls its own protein interaction network by transcriptionally regulating its binding partners. Our network-based approach identified vulnerable therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma. These were validated by siRNA knockdown screens, functional studies and patient data. We identified β-estradiol and MAPK/ERK as having functional cross-talk with MYCN and being novel targetable vulnerabilities of MYCN-amplified neuroblastoma. These results reveal surprising differences between the functioning of endogenous, overexpressed and amplified MYCN, and rationalise how different MYCN dosages can orchestrate cell fate decisions and cancerous outcomes. Importantly, this work describes a systems-level approach to systematically uncovering network based vulnerabilities and therapeutic targets for multifactorial diseases by integrating disparate omic data types.
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Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,European Molecular Biology Laboratory (EMBL), Meyerhofstraße, Heidelberg, Germany
| | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Jai Prakash Mehta
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Kate Killick
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Jenny Whilde
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | | | - Vidal Fey
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matthias Fischer
- Department of Paediatric Haematology and Oncology and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Frank Westermann
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Bannert
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
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Ostankovitch M, Stagljar I. Omics Approaches Deciphering Molecular Function in Large Biological Systems. J Mol Biol 2015; 427:3351-5. [DOI: 10.1016/j.jmb.2015.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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