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Zhu C, Soto-Feliciano YM, Morris JP, Huang CH, Koche RP, Ho YJ, Banito A, Chen CWD, Shroff A, Tian S, Livshits G, Chen CC, Fennell M, Armstrong SA, Allis CD, Tschaharganeh DF, Lowe SW. MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer. eLife 2023; 12:80854. [PMID: 37261974 DOI: 10.7554/elife.80854] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Mutations in genes encoding components of chromatin modifying and remodeling complexes are among the most frequently observed somatic events in human cancers. For example, missense and nonsense mutations targeting the mixed lineage leukemia family member 3 (MLL3, encoded by KMT2C) histone methyltransferase occur in a range of solid tumors, and heterozygous deletions encompassing KMT2C occur in a subset of aggressive leukemias. Although MLL3 loss can promote tumorigenesis in mice, the molecular targets and biological processes by which MLL3 suppresses tumorigenesis remain poorly characterized. Here we combined genetic, epigenomic, and animal modeling approaches to demonstrate that one of the mechanisms by which MLL3 links chromatin remodeling to tumor suppression is by co-activating the Cdkn2a tumor suppressor locus. Disruption of Kmt2c cooperates with Myc overexpression in the development of murine hepatocellular carcinoma (HCC), in which MLL3 binding to the Cdkn2a locus is blunted, resulting in reduced H3K4 methylation and low expression levels of the locus-encoded tumor suppressors p16/Ink4a and p19/Arf. Conversely, elevated KMT2C expression increases its binding to the CDKN2A locus and co-activates gene transcription. Endogenous Kmt2c restoration reverses these chromatin and transcriptional effects and triggers Ink4a/Arf-dependent apoptosis. Underscoring the human relevance of this epistasis, we found that genomic alterations in KMT2C and CDKN2A were associated with similar transcriptional profiles in human HCC samples. These results collectively point to a new mechanism for disrupting CDKN2A activity during cancer development and, in doing so, link MLL3 to an established tumor suppressor network.
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Affiliation(s)
- Changyu Zhu
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Yadira M Soto-Feliciano
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - John P Morris
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Yu-Jui Ho
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Ana Banito
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chun-Wei David Chen
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Aditya Shroff
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sha Tian
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chi-Chao Chen
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Myles Fennell
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, United States
| | | | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
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2
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Revia S, Seretny A, Wendler L, Banito A, Eckert C, Breuer K, Mayakonda A, Lutsik P, Evert M, Ribback S, Gallage S, Chikh Bakri I, Breuhahn K, Schirmacher P, Heinrich S, Gaida MM, Heikenwälder M, Calvisi DF, Plass C, Lowe SW, Tschaharganeh DF. Histone H3K27 demethylase KDM6A is an epigenetic gatekeeper of mTORC1 signalling in cancer. Gut 2022; 71:1613-1628. [PMID: 34509979 PMCID: PMC9279849 DOI: 10.1136/gutjnl-2021-325405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/31/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Large-scale genome sequencing efforts of human tumours identified epigenetic modifiers as one of the most frequently mutated gene class in human cancer. However, how these mutations drive tumour development and tumour progression are largely unknown. Here, we investigated the function of the histone demethylase KDM6A in gastrointestinal cancers, such as liver cancer and pancreatic cancer. DESIGN Genetic alterations as well as expression analyses of KDM6A were performed in patients with liver cancer. Genetic mouse models of liver and pancreatic cancer coupled with Kdm6a-deficiency were investigated, transcriptomic and epigenetic profiling was performed, and in vivo and in vitro drug treatments were conducted. RESULTS KDM6A expression was lost in 30% of patients with liver cancer. Kdm6a deletion significantly accelerated tumour development in murine liver and pancreatic cancer models. Kdm6a-deficient tumours showed hyperactivation of mTORC1 signalling, whereas endogenous Kdm6a re-expression by inducible RNA-interference in established Kdm6a-deficient tumours diminished mTORC1 activity resulting in attenuated tumour progression. Genome-wide transcriptional and epigenetic profiling revealed direct binding of Kdm6a to crucial negative regulators of mTORC1, such as Deptor, and subsequent transcriptional activation by epigenetic remodelling. Moreover, in vitro and in vivo genetic epistasis experiments illustrated a crucial function of Deptor and mTORC1 in Kdm6a-dependent tumour suppression. Importantly, KDM6A expression in human tumours correlates with mTORC1 activity and KDM6A-deficient tumours exhibit increased sensitivity to mTORC1 inhibition. CONCLUSION KDM6A is an important tumour suppressor in gastrointestinal cancers and acts as an epigenetic toggle for mTORC1 signalling. Patients with KDM6A-deficient tumours could benefit of targeted therapy focusing on mTORC1 inhibition.
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Affiliation(s)
- Steffie Revia
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Agnieszka Seretny
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Lena Wendler
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Ana Banito
- Pediatric Soft Tissue Sarcoma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Eckert
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Kersten Breuer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anand Mayakonda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Silvia Ribback
- Institute of Pathology, University Hospital Greifswald, Greifswald, Germany
| | - Suchira Gallage
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Heinrich
- Department of Surgery, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | - Matthias M Gaida
- Institute of Pathology, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
- Joint Unit Immunopathology, Institute of Pathology, University Medical Center, JGU-Mainz, Mainz, Germany
- TRON, Translational Oncology, University Medical Center, JGU-Mainz, Mainz, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diego F Calvisi
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology, University Hospital, Heidelberg, Germany
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3
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Li X, Huang CH, Sánchez-Rivera FJ, Kennedy MC, Tschaharganeh DF, Morris JP, Montinaro A, O'Rourke KP, Banito A, Wilkinson JE, Chen CC, Ho YJ, Dow LE, Tian S, Luan W, de Stanchina E, Zhang T, Gray NS, Walczak H, Lowe SW. A preclinical platform for assessing antitumor effects and systemic toxicities of cancer drug targets. Proc Natl Acad Sci U S A 2022; 119:e2110557119. [PMID: 35442775 PMCID: PMC9169916 DOI: 10.1073/pnas.2110557119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
Anticancer drug development campaigns often fail due to an incomplete understanding of the therapeutic index differentiating the efficacy of the agent against the cancer and its on-target toxicities to the host. To address this issue, we established a versatile preclinical platform in which genetically defined cancers are produced using somatic tissue engineering in transgenic mice harboring a doxycycline-inducible short hairpin RNA against the target of interest. In this system, target inhibition is achieved by the addition of doxycycline, enabling simultaneous assessment of efficacy and toxicity in the same animal. As proof of concept, we focused on CDK9—a cancer target whose clinical development has been hampered by compounds with poorly understood target specificity and unacceptable toxicities. We systematically compared phenotypes produced by genetic Cdk9 inhibition to those achieved using a recently developed highly specific small molecule CDK9 inhibitor and found that both perturbations led to robust antitumor responses. Remarkably, nontoxic levels of CDK9 inhibition could achieve significant treatment efficacy, and dose-dependent toxicities produced by prolonged CDK9 suppression were largely reversible upon Cdk9 restoration or drug withdrawal. Overall, these results establish a versatile in vivo target validation platform that can be employed for rapid triaging of therapeutic targets and lend support to efforts aimed at advancing CDK9 inhibitors for cancer therapy.
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Affiliation(s)
- Xiang Li
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
| | - Francisco J. Sánchez-Rivera
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Margaret C. Kennedy
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Darjus F. Tschaharganeh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - John P. Morris
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Antonella Montinaro
- Centre for Cell Death, Cancer, and Inflammation, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Kevin P. O'Rourke
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
- Weill Cornell Medicine/The Rockefeller University/Sloan Kettering Institute Tri-Institutional MD-PhD Program, New York, NY 10065
| | - Ana Banito
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - John E. Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109
| | - Chi-Chao Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Lukas E. Dow
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Sha Tian
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Wei Luan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Elisa de Stanchina
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
| | - Tinghu Zhang
- Innovative Medicines Accelerator, Stanford Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305
| | - Nathanael S. Gray
- Innovative Medicines Accelerator, Stanford Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305
| | - Henning Walczak
- Centre for Cell Death, Cancer, and Inflammation, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
- Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cluster of Excellence, University of Cologne, Cologne 50931, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY 10065
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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4
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Billon P, Nambiar TS, Hayward SB, Zafra MP, Schatoff EM, Oshima K, Dunbar A, Breinig M, Park YC, Ryu HS, Tschaharganeh DF, Levine RL, Baer R, Ferrando A, Dow LE, Ciccia A. Detection of Marker-Free Precision Genome Editing and Genetic Variation through the Capture of Genomic Signatures. Cell Rep 2020; 30:3280-3295.e6. [PMID: 32160537 PMCID: PMC7108696 DOI: 10.1016/j.celrep.2020.02.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/13/2020] [Accepted: 02/14/2020] [Indexed: 10/29/2022] Open
Abstract
Genome editing technologies have transformed our ability to engineer desired genomic changes within living systems. However, detecting precise genomic modifications often requires sophisticated, expensive, and time-consuming experimental approaches. Here, we describe DTECT (Dinucleotide signaTurE CapTure), a rapid and versatile detection method that relies on the capture of targeted dinucleotide signatures resulting from the digestion of genomic DNA amplicons by the type IIS restriction enzyme AcuI. DTECT enables the accurate quantification of marker-free precision genome editing events introduced by CRISPR-dependent homology-directed repair, base editing, or prime editing in various biological systems, such as mammalian cell lines, organoids, and tissues. Furthermore, DTECT allows the identification of oncogenic mutations in cancer mouse models, patient-derived xenografts, and human cancer patient samples. The ease, speed, and cost efficiency by which DTECT identifies genomic signatures should facilitate the generation of marker-free cellular and animal models of human disease and expedite the detection of human pathogenic variants.
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Affiliation(s)
- Pierre Billon
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Maria P Zafra
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Emma M Schatoff
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Koichi Oshima
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrew Dunbar
- Human Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marco Breinig
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, 69120 Heidelberg, Germany
| | - Young C Park
- Human Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Han S Ryu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, 69120 Heidelberg, Germany
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard Baer
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Adolfo Ferrando
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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5
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Moon SH, Huang CH, Houlihan SL, Regunath K, Freed-Pastor WA, Morris JP, Tschaharganeh DF, Kastenhuber ER, Barsotti AM, Culp-Hill R, Xue W, Ho YJ, Baslan T, Li X, Mayle A, de Stanchina E, Zender L, Tong DR, D'Alessandro A, Lowe SW, Prives C. p53 Represses the Mevalonate Pathway to Mediate Tumor Suppression. Cell 2018; 176:564-580.e19. [PMID: 30580964 DOI: 10.1016/j.cell.2018.11.011] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 08/24/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
Abstract
There are still gaps in our understanding of the complex processes by which p53 suppresses tumorigenesis. Here we describe a novel role for p53 in suppressing the mevalonate pathway, which is responsible for biosynthesis of cholesterol and nonsterol isoprenoids. p53 blocks activation of SREBP-2, the master transcriptional regulator of this pathway, by transcriptionally inducing the ABCA1 cholesterol transporter gene. A mouse model of liver cancer reveals that downregulation of mevalonate pathway gene expression by p53 occurs in premalignant hepatocytes, when p53 is needed to actively suppress tumorigenesis. Furthermore, pharmacological or RNAi inhibition of the mevalonate pathway restricts the development of murine hepatocellular carcinomas driven by p53 loss. Like p53 loss, ablation of ABCA1 promotes murine liver tumorigenesis and is associated with increased SREBP-2 maturation. Our findings demonstrate that repression of the mevalonate pathway is a crucial component of p53-mediated liver tumor suppression and outline the mechanism by which this occurs.
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Affiliation(s)
- Sung-Hwan Moon
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shauna L Houlihan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kausik Regunath
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - John P Morris
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Darjus F Tschaharganeh
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edward R Kastenhuber
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anthony M Barsotti
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Rachel Culp-Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Wen Xue
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiang Li
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Allison Mayle
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisa de Stanchina
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lars Zender
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David R Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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6
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Breinig M, Schweitzer AY, Herianto AM, Revia S, Schaefer L, Wendler L, Cobos Galvez A, Tschaharganeh DF. Multiplexed orthogonal genome editing and transcriptional activation by Cas12a. Nat Methods 2018; 16:51-54. [PMID: 30559432 DOI: 10.1038/s41592-018-0262-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/05/2018] [Indexed: 01/06/2023]
Abstract
CRISPR-Cas9-based combinatorial perturbation approaches for orthogonal knockout and gene activation have been impeded by complex vector designs and co-delivery of multiple constructs. Here, we demonstrate that catalytically active CRISPR-Cas12a fused to a transcriptional-activator domain enables flexible switching between genome editing and transcriptional activation by altering guide length. By leveraging Cas12a-mediated CRISPR-RNA array processing, we illustrate that Cas12a-VPR enables simplified multiplexed knockout and transcriptional activation in vitro and in vivo.
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Affiliation(s)
- Marco Breinig
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Anabel Y Schweitzer
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Anna M Herianto
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Steffie Revia
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Lisa Schaefer
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Lena Wendler
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Ana Cobos Galvez
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Darjus F Tschaharganeh
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany.
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7
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Banito A, Li X, Laporte AN, Roe JS, Sanchez-Vega F, Huang CH, Dancsok AR, Hatzi K, Chen CC, Tschaharganeh DF, Chandwani R, Tasdemir N, Jones KB, Capecchi MR, Vakoc CR, Schultz N, Ladanyi M, Nielsen TO, Lowe SW. The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma. Cancer Cell 2018; 34:346-348. [PMID: 30107180 PMCID: PMC6161360 DOI: 10.1016/j.ccell.2018.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Zafra MP, Schatoff EM, Katti A, Foronda M, Breinig M, Schweitzer AY, Simon A, Han T, Goswami S, Montgomery E, Thibado J, Kastenhuber ER, Sánchez-Rivera FJ, Shi J, Vakoc CR, Lowe SW, Tschaharganeh DF, Dow LE. Optimized base editors enable efficient editing in cells, organoids and mice. Nat Biotechnol 2018; 36:888-893. [PMID: 29969439 PMCID: PMC6130889 DOI: 10.1038/nbt.4194] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/21/2018] [Indexed: 12/24/2022]
Abstract
CRISPR base editing enables the creation of targeted single-base conversions without generating double stranded breaks. However, the efficiency of current base editors is very low in many cell types. We re-engineered the sequences of BE3, BE4Gam, and xBE3 by codon optimization and incorporation of additional nuclear localization sequences. Our collection of optimized constitutive and inducible base-editing vector systems dramatically improves the efficiency by which single nucleotide variants can be created. The re-engineered base editors enable target modification in a wide range of mouse and human cell lines, and intestinal organoids. We also show that the optimized base editors mediate efficient in vivo somatic editing in the liver of adult mice.
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Affiliation(s)
- Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Emma M Schatoff
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD program, New York, New York, USA
| | - Alyna Katti
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Miguel Foronda
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Marco Breinig
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Anabel Y Schweitzer
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Amber Simon
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Teng Han
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Sukanya Goswami
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Emma Montgomery
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jordana Thibado
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Edward R Kastenhuber
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | | | - Junwei Shi
- Cold Spring Harbor Laboratory, New York, New York, USA.,Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Scott W Lowe
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Darjus F Tschaharganeh
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA.,Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA
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9
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Shamay Y, Shah J, Işık M, Mizrachi A, Leibold J, Tschaharganeh DF, Roxbury D, Budhathoki-Uprety J, Nawaly K, Sugarman JL, Baut E, Neiman MR, Dacek M, Ganesh KS, Johnson DC, Sridharan R, Chu KL, Rajasekhar VK, Lowe SW, Chodera JD, Heller DA. Quantitative self-assembly prediction yields targeted nanomedicines. Nat Mater 2018; 17:361-368. [PMID: 29403054 PMCID: PMC5930166 DOI: 10.1038/s41563-017-0007-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 12/04/2017] [Indexed: 05/18/2023]
Abstract
Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.
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Affiliation(s)
- Yosi Shamay
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Faculty of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Janki Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mehtap Işık
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aviram Mizrachi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Otolaryngology Head and Neck Surgery, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Josef Leibold
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology University Hospital, Heidelberg, Germany
| | - Daniel Roxbury
- Department of Chemical Engineering, University of Rhode Island, Kingston, RI, 02881, USA
| | | | - Karla Nawaly
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Emily Baut
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | | | - Megan Dacek
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Kripa S Ganesh
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Darren C Johnson
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ramya Sridharan
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Karen L Chu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | | | - Scott W Lowe
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John D Chodera
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel A Heller
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, Cornell University, New York, NY, USA.
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10
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Banito A, Li X, Laporte AN, Roe JS, Sanchez-Vega F, Huang CH, Dancsok AR, Hatzi K, Chen CC, Tschaharganeh DF, Chandwani R, Tasdemir N, Jones KB, Capecchi MR, Vakoc CR, Schultz N, Ladanyi M, Nielsen TO, Lowe SW. The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma. Cancer Cell 2018; 33:527-541.e8. [PMID: 29502955 PMCID: PMC5881394 DOI: 10.1016/j.ccell.2018.01.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/14/2017] [Accepted: 01/27/2018] [Indexed: 12/25/2022]
Abstract
Synovial sarcoma is an aggressive cancer invariably associated with a chromosomal translocation involving genes encoding the SWI-SNF complex component SS18 and an SSX (SSX1 or SSX2) transcriptional repressor. Using functional genomics, we identify KDM2B, a histone demethylase and component of a non-canonical polycomb repressive complex 1 (PRC1.1), as selectively required for sustaining synovial sarcoma cell transformation. SS18-SSX1 physically interacts with PRC1.1 and co-associates with SWI/SNF and KDM2B complexes on unmethylated CpG islands. Via KDM2B, SS18-SSX1 binds and aberrantly activates expression of developmentally regulated genes otherwise targets of polycomb-mediated repression, which is restored upon KDM2B depletion, leading to irreversible mesenchymal differentiation. Thus, SS18-SSX1 deregulates developmental programs to drive transformation by hijacking a transcriptional repressive complex to aberrantly activate gene expression.
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Affiliation(s)
- Ana Banito
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Xiang Li
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Aimée N Laporte
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jae-Seok Roe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Francisco Sanchez-Vega
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Amanda R Dancsok
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Katerina Hatzi
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Chi-Chao Chen
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Darjus F Tschaharganeh
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Rohit Chandwani
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Nilgun Tasdemir
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Kevin B Jones
- Department of Orthopedics and Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84103, USA
| | - Mario R Capecchi
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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11
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González-Vallinas M, Rodríguez-Paredes M, Albrecht M, Sticht C, Stichel D, Gutekunst J, Pitea A, Sass S, Sánchez-Rivera FJ, Lorenzo-Bermejo J, Schmitt J, De La Torre C, Warth A, Theis FJ, Müller NS, Gretz N, Muley T, Meister M, Tschaharganeh DF, Schirmacher P, Matthäus F, Breuhahn K. Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients. Mol Cancer Res 2018; 16:390-402. [PMID: 29330288 DOI: 10.1158/1541-7786.mcr-17-0334] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/18/2017] [Accepted: 12/08/2017] [Indexed: 11/16/2022]
Abstract
Most lung cancer deaths are related to metastases, which indicates the necessity of detecting and inhibiting tumor cell dissemination. Here, we aimed to identify miRNAs involved in metastasis of lung adenocarcinoma as prognostic biomarkers and therapeutic targets. To that end, lymph node metastasis-associated miRNAs were identified in The Cancer Genome Atlas lung adenocarcinoma patient cohort (sequencing data; n = 449) and subsequently validated by qRT-PCR in an independent clinical cohort (n = 108). Overexpression of miRNAs located on chromosome 14q32 was associated with metastasis in lung adenocarcinoma patients. Importantly, Kaplan-Meier analysis and log-rank test revealed that higher expression levels of individual 14q32 miRNAs (mir-539, mir-323b, and mir-487a) associated with worse disease-free survival of never-smoker patients. Epigenetic analysis including DNA methylation microarray data and bisulfite sequencing validation demonstrated that the induction of 14q32 cluster correlated with genomic hypomethylation of the 14q32 locus. CRISPR activation technology, applied for the first time to functionally study the increase of clustered miRNA levels in a coordinated manner, showed that simultaneous overexpression of 14q32 miRNAs promoted tumor cell migratory and invasive properties. Analysis of individual miRNAs by mimic transfection further illustrated that miR-323b-3p, miR-487a-3p, and miR-539-5p significantly contributed to the invasive phenotype through the indirect regulation of different target genes. In conclusion, overexpression of 14q32 miRNAs, associated with the respective genomic hypomethylation, promotes metastasis and correlates with poor patient prognosis in lung adenocarcinoma.Implications: This study points to chromosome 14q32 miRNAs as promising targets to inhibit tumor cell dissemination and to predict patient prognosis in lung adenocarcinoma. Mol Cancer Res; 16(3); 390-402. ©2018 AACR.
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Affiliation(s)
- Margarita González-Vallinas
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Systems Biology of Signal Transduction, German Cancer Research Center, Heidelberg, Germany
| | | | - Marco Albrecht
- Center for Modeling and Simulation in the Biosciences (BIOMS), University of Heidelberg, Heidelberg, Germany.,Life Sciences Research Unit, University of Luxembourg, Luxembourg, Luxembourg
| | - Carsten Sticht
- Medical Research Centre, University of Heidelberg, Mannheim, Germany
| | - Damian Stichel
- Center for Modeling and Simulation in the Biosciences (BIOMS), University of Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Adriana Pitea
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Steffen Sass
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Justo Lorenzo-Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Jennifer Schmitt
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nikola S Müller
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Norbert Gretz
- Medical Research Centre, University of Heidelberg, Mannheim, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC-H), member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC-H), member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Darjus F Tschaharganeh
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Helmholtz University Group "Cell Plasticity and Epigenetic Remodeling," German Cancer Research Center, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Franziska Matthäus
- Center for Modeling and Simulation in the Biosciences (BIOMS), University of Heidelberg, Heidelberg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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12
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Méndez-Lucas A, Li X, Hu J, Che L, Song X, Jia J, Wang J, Xie C, Driscoll PC, Tschaharganeh DF, Calvisi DF, Yuneva M, Chen X. Glucose Catabolism in Liver Tumors Induced by c-MYC Can Be Sustained by Various PKM1/PKM2 Ratios and Pyruvate Kinase Activities. Cancer Res 2017; 77:4355-4364. [PMID: 28630053 PMCID: PMC5559320 DOI: 10.1158/0008-5472.can-17-0498] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/05/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022]
Abstract
Different pyruvate kinase isoforms are expressed in a tissue-specific manner, with pyruvate kinase M2 (PKM2) suggested to be the predominant isoform in proliferating cells and cancer cells. Because of differential regulation of enzymatic activities, PKM2, but not PKM1, has been thought to favor cell proliferation. However, the role of PKM2 in tumorigenesis has been recently challenged. Here we report that increased glucose catabolism through glycolysis and increased pyruvate kinase activity in c-MYC-driven liver tumors are associated with increased expression of both PKM1 and PKM2 isoforms and decreased expression of the liver-specific isoform of pyruvate kinase, PKL. Depletion of PKM2 at the time of c-MYC overexpression in murine livers did not affect c-MYC-induced tumorigenesis and resulted in liver tumor formation with decreased pyruvate kinase activity and decreased catabolism of glucose into alanine and the Krebs cycle. An increased PKM1/PKM2 ratio by ectopic PKM1 expression further decreased glucose flux into serine biosynthesis and increased flux into lactate and the Krebs cycle, resulting in reduced total levels of serine. However, these changes also did not affect c-MYC-induced liver tumor development. These results suggest that increased expression of PKM2 is not required to support c-MYC-induced tumorigenesis in the liver and that various PKM1/PKM2 ratios and pyruvate kinase activities can sustain glucose catabolism required for this process. Cancer Res; 77(16); 4355-64. ©2017 AACR.
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Affiliation(s)
| | - Xiaolei Li
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
- Department of Thyroid and Breast Surgery, Jinan Military General Hospital of PLA, Jinan, Shandong, P.R. China
| | - Junjie Hu
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, Hubei, P.R. China
| | - Li Che
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
| | - Xinhua Song
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
| | - Jiaoyuan Jia
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
- Department of Oncology and Hematology, The Second Hospital, Jilin University, Changchun, China
| | - Jingxiao Wang
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
| | - Chencheng Xie
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
- Department of Internal Medicine, University of South Dakota Sanford School of Medicine, Vermillion, South Dakota
| | | | - Darjus F Tschaharganeh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Helmholtz-Junior Research Group "Cell plasticity and Epigenetic Remodeling", German Cancer Research Center and Institute of Pathology at Heidelberg University, Heidelberg, Germany
| | - Diego F Calvisi
- Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - Mariia Yuneva
- The Francis Crick Institute, London, United Kingdom.
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California.
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, Hubei, P.R. China
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13
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Yuan D, Huang S, Berger E, Liu L, Gross N, Heinzmann F, Ringelhan M, Connor TO, Stadler M, Meister M, Weber J, Öllinger R, Simonavicius N, Reisinger F, Hartmann D, Meyer R, Reich M, Seehawer M, Leone V, Höchst B, Wohlleber D, Jörs S, Prinz M, Spalding D, Protzer U, Luedde T, Terracciano L, Matter M, Longerich T, Knolle P, Ried T, Keitel V, Geisler F, Unger K, Cinnamon E, Pikarsky E, Hüser N, Davis RJ, Tschaharganeh DF, Rad R, Weber A, Zender L, Haller D, Heikenwalder M. Kupffer Cell-Derived Tnf Triggers Cholangiocellular Tumorigenesis through JNK due to Chronic Mitochondrial Dysfunction and ROS. Cancer Cell 2017; 31:771-789.e6. [PMID: 28609656 PMCID: PMC7909318 DOI: 10.1016/j.ccell.2017.05.006] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/31/2017] [Accepted: 05/11/2017] [Indexed: 12/15/2022]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a highly malignant, heterogeneous cancer with poor treatment options. We found that mitochondrial dysfunction and oxidative stress trigger a niche favoring cholangiocellular overgrowth and tumorigenesis. Liver damage, reactive oxygen species (ROS) and paracrine tumor necrosis factor (Tnf) from Kupffer cells caused JNK-mediated cholangiocellular proliferation and oncogenic transformation. Anti-oxidant treatment, Kupffer cell depletion, Tnfr1 deletion, or JNK inhibition reduced cholangiocellular pre-neoplastic lesions. Liver-specific JNK1/2 deletion led to tumor reduction and enhanced survival in Akt/Notch- or p53/Kras-induced ICC models. In human ICC, high Tnf expression near ICC lesions, cholangiocellular JNK-phosphorylation, and ROS accumulation in surrounding hepatocytes are present. Thus, Kupffer cell-derived Tnf favors cholangiocellular proliferation/differentiation and carcinogenesis. Targeting the ROS/Tnf/JNK axis may provide opportunities for ICC therapy.
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Affiliation(s)
- Detian Yuan
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Shan Huang
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Emanuel Berger
- Chair of Nutrition and Immunology, Technische Universität München, Gregor-Mendel-Straße 2, 85350 Freising-Weihenstephan, Germany
| | - Lei Liu
- Department of Surgery, Technische Universität München, 81675 Munich, Germany
| | - Nina Gross
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Florian Heinzmann
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Marc Ringelhan
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Tracy O Connor
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mira Stadler
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Meister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Julia Weber
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Rupert Öllinger
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Nicole Simonavicius
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Florian Reisinger
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Daniel Hartmann
- Department of Surgery, Technische Universität München, 81675 Munich, Germany
| | - Rüdiger Meyer
- Genome Technology Branch, National Human Genome Research Institute, U.S. National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Reich
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine University, 40204 Düsseldorf, Germany
| | - Marco Seehawer
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Valentina Leone
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Bastian Höchst
- Institute of Molecular Immunology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Simone Jörs
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Marco Prinz
- Institute of Neuropathology, University of Freiburg, 79106 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79106 Freiburg, Germany
| | - Duncan Spalding
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Tom Luedde
- Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, RWTH Aachen University, 52074 Aachen, Germany
| | - Luigi Terracciano
- Institute of Pathology, University Hospital of Basel, 4003 Basel, Switzerland
| | - Matthias Matter
- Institute of Pathology, University Hospital of Basel, 4003 Basel, Switzerland
| | - Thomas Longerich
- Institute of Pathology, University Hospital RWTH, 52074 Aachen, Germany
| | - Percy Knolle
- Institute of Molecular Immunology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Thomas Ried
- Genome Technology Branch, National Human Genome Research Institute, U.S. National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine University, 40204 Düsseldorf, Germany
| | - Fabian Geisler
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Einat Cinnamon
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; Department of Pathology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Norbert Hüser
- Department of Surgery, Technische Universität München, 81675 Munich, Germany
| | - Roger J Davis
- Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology University Hospital, 69120 Heidelberg, Germany
| | - Roland Rad
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Lars Zender
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Translational Gastrointestinal Oncology Group within the German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Gregor-Mendel-Straße 2, 85350 Freising-Weihenstephan, Germany; ZIEL - Institute for Food & Health, Technische Universität München, 85350 Freising-Weihenstephan, Germany.
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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14
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Pelossof R, Fairchild L, Huang CH, Widmer C, Sreedharan VT, Sinha N, Lai DY, Guan Y, Premsrirut PK, Tschaharganeh DF, Hoffmann T, Thapar V, Xiang Q, Garippa RJ, Rätsch G, Zuber J, Lowe SW, Leslie CS, Fellmann C. Prediction of potent shRNAs with a sequential classification algorithm. Nat Biotechnol 2017; 35:350-353. [PMID: 28263295 PMCID: PMC5416823 DOI: 10.1038/nbt.3807] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/18/2017] [Indexed: 12/31/2022]
Abstract
We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with an optimized miR-E backbone, >90% of high-scoring SplashRNA predictions trigger >85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries.
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Affiliation(s)
- Raphael Pelossof
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lauren Fairchild
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Christian Widmer
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Machine Learning Group, Department of Computer Science, Berlin Institute of Technology, Berlin, Germany
| | - Vipin T Sreedharan
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | | | | | - Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Vishal Thapar
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Qing Xiang
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ralph J Garippa
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gunnar Rätsch
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York, USA.,Howard Hughes Medical Institute and Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christof Fellmann
- Mirimus Inc., Woodbury, New York, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
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15
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Manchado E, Huang CH, Tasdemir N, Tschaharganeh DF, Wilkinson JE, Lowe SW. A Pipeline for Drug Target Identification and Validation. Cold Spring Harb Symp Quant Biol 2017; 81:257-267. [PMID: 28057848 PMCID: PMC5469697 DOI: 10.1101/sqb.2016.81.031096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Rapid and affordable tumor profiling has led to an explosion of genomic data that is facilitating the development of new cancer therapies. The potential of therapeutic strategies aimed at inactivating the oncogenic lesions that contribute to the aberrant survival and proliferation of tumor cells has yielded remarkable success in some malignancies such as BRAF-mutant melanoma and BCR-ABL expressing chronic myeloid leukemia. However, the direct inhibition of several well-established oncoproteins in some of these cancers is not possible or produces only transient benefits. Functional genomics represents a powerful approach for the identification of vulnerabilities linked to specific genetic alterations and has provided substantial insights into cancer signaling networks. Still, as inhibition of gene function can have diverse effects on both tumor and normal tissues, information on the potency of target inhibition on tumor growth as well as the toxic side effects of target inhibition are also needed. Here, we discuss our RNA interference (RNAi) pipeline for cancer target discovery based on our optimized short-hairpin RNA (shRNA) tools for negative selection screens and inducible RNAi platform that, in combination with embryonic stem cell (ESC)-based genetically engineered mouse models (GEMMs), enable deep in vivo target validation.
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Affiliation(s)
- Eusebio Manchado
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065
| | - Nilgun Tasdemir
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - John E Wilkinson
- ULAM/Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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16
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Tschaharganeh DF, Lowe SW, Garippa RJ, Livshits G. Using CRISPR/Cas to study gene function and model disease in vivo. FEBS J 2016; 283:3194-203. [PMID: 27149548 DOI: 10.1111/febs.13750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 12/23/2022]
Abstract
The recent discovery of the CRISPR/Cas system and repurposing of this technology to edit a variety of different genomes have revolutionized an array of scientific fields, from genetics and translational research, to agriculture and bioproduction. In particular, the prospect of rapid and precise genome editing in laboratory animals by CRISPR/Cas has generated an immense interest in the scientific community. Here we review current in vivo applications of CRISPR/Cas and how this technology can improve our knowledge of gene function and our understanding of biological processes in animal models.
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Affiliation(s)
- Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA
| | - Ralph J Garippa
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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17
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Tschaharganeh DF, Xue W, Calvisi DF, Evert M, Michurina TV, Dow LE, Banito A, Katz SF, Kastenhuber ER, Weissmueller S, Huang CH, Lechel A, Andersen JB, Capper D, Zender L, Longerich T, Enikolopov G, Lowe SW. p53-Dependent Nestin Regulation Links Tumor Suppression to Cellular Plasticity in Liver Cancer. Cell 2016; 165:1546-1547. [PMID: 27259155 DOI: 10.1016/j.cell.2016.05.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Abstract
In this issue of Cancer Cell, Cai et al. use genome editing to study 8p deletions in a mammary epithelial cell model and show that 8p loss of heterozygosity (LOH) attenuates the action of several genes that collectively promote cell invasion and enhance cellular sensitivity to autophagy inhibitors.
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Affiliation(s)
- Darjus F Tschaharganeh
- Department of Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benedikt Bosbach
- Department of Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott W Lowe
- Department of Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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19
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Tasdemir N, Banito A, Roe JS, Alonso-Curbelo D, Camiolo M, Tschaharganeh DF, Huang CH, Aksoy O, Bolden JE, Chen CC, Fennell M, Thapar V, Chicas A, Vakoc CR, Lowe SW. BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance. Cancer Discov 2016; 6:612-29. [PMID: 27099234 DOI: 10.1158/2159-8290.cd-16-0217] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/14/2016] [Indexed: 12/15/2022]
Abstract
UNLABELLED Oncogene-induced senescence is a potent barrier to tumorigenesis that limits cellular expansion following certain oncogenic events. Senescent cells display a repressive chromatin configuration thought to stably silence proliferation-promoting genes while simultaneously activating an unusual form of immune surveillance involving a secretory program referred to as the senescence-associated secretory phenotype (SASP). Here, we demonstrate that senescence also involves a global remodeling of the enhancer landscape with recruitment of the chromatin reader BRD4 to newly activated super-enhancers adjacent to key SASP genes. Transcriptional profiling and functional studies indicate that BRD4 is required for the SASP and downstream paracrine signaling. Consequently, BRD4 inhibition disrupts immune cell-mediated targeting and elimination of premalignant senescent cells in vitro and in vivo Our results identify a critical role for BRD4-bound super-enhancers in senescence immune surveillance and in the proper execution of a tumor-suppressive program. SIGNIFICANCE This study reveals how cells undergoing oncogene-induced senescence acquire a distinctive enhancer landscape that includes formation of super-enhancers adjacent to immune-modulatory genes required for paracrine immune activation. This process links BRD4 and super-enhancers to a tumor-suppressive immune surveillance program that can be disrupted by small molecule inhibitors of the bromo and extra terminal domain family of proteins. Cancer Discov; 6(6); 612-29. ©2016 AACR.See related commentary by Vizioli and Adams, p. 576This article is highlighted in the In This Issue feature, p. 561.
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Affiliation(s)
- Nilgun Tasdemir
- Memorial Sloan Kettering Cancer Center, New York, New York. Watson School of Biological Sciences, Cold Spring Harbor, New York. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Ana Banito
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jae-Seok Roe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | | | - Matthew Camiolo
- Medical Scientist Training Program, Stony Brook University, Stony Brook, New York
| | | | - Chun-Hao Huang
- Memorial Sloan Kettering Cancer Center, New York, New York. Weill Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Ozlem Aksoy
- Memorial Sloan Kettering Cancer Center, New York, New York. Watson School of Biological Sciences, Cold Spring Harbor, New York. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | | | - Chi-Chao Chen
- Memorial Sloan Kettering Cancer Center, New York, New York. Weill Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Myles Fennell
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vishal Thapar
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agustin Chicas
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Scott W Lowe
- Memorial Sloan Kettering Cancer Center, New York, New York. Howard Hughes Medical Institute, New York, New York.
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20
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Dow LE, O'Rourke KP, Simon J, Tschaharganeh DF, van Es JH, Clevers H, Lowe SW. Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer. Cell 2015; 161:1539-1552. [PMID: 26091037 DOI: 10.1016/j.cell.2015.05.033] [Citation(s) in RCA: 374] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/27/2015] [Accepted: 04/10/2015] [Indexed: 12/15/2022]
Abstract
The adenomatous polyposis coli (APC) tumor suppressor is mutated in the vast majority of human colorectal cancers (CRC) and leads to deregulated Wnt signaling. To determine whether Apc disruption is required for tumor maintenance, we developed a mouse model of CRC whereby Apc can be conditionally suppressed using a doxycycline-regulated shRNA. Apc suppression produces adenomas in both the small intestine and colon that, in the presence of Kras and p53 mutations, can progress to invasive carcinoma. In established tumors, Apc restoration drives rapid and widespread tumor-cell differentiation and sustained regression without relapse. Tumor regression is accompanied by the re-establishment of normal crypt-villus homeostasis, such that once aberrantly proliferating cells reacquire self-renewal and multi-lineage differentiation capability. Our study reveals that CRC cells can revert to functioning normal cells given appropriate signals and provide compelling in vivo validation of the Wnt pathway as a therapeutic target for treatment of CRC.
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Affiliation(s)
- Lukas E Dow
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kevin P O'Rourke
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program
| | - Janelle Simon
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darjus F Tschaharganeh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Johan H van Es
- Hubrecht Institute for Developmental Biology and Stem Cell Research and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY
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21
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Huang CH, Lujambio A, Zuber J, Kitzing T, Tschaharganeh DF, Stanchina ED, Lowe SW. Abstract 2935: RNAi screen identifies therapeutic targets in hepatocellular carcinoma. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Liver cancer is the third leading cause of cancer related mortality worldwide. Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is a very aggressive type of cancer that lacks effective treatment, in part, due to the undruggable nature of its main genetic drivers, such as oncogene MYC amplification or loss of tumor suppressor TP53. The introduction of the multikinase inhibitor Sorafenib represents the biggest therapeutic advance in the past decade, though its activity only increases the life expectancy of liver cancer patients from 8 to 11 months. To identify new therapeutic targets for HCC, we employ RNA interference (RNAi) screens as a non-biased means to identify genes required for tumor maintenance in genetically defined tumors. In the current study, we applied an optimized shRNA platform to perform a negative selection screen in genetically-defined murine hepatocellular carcinoma cell in vitro. Specifically, we have designed a library that contains 2,245 shRNAs targeting 442 “drugged” genes, including genes encoding proteins targeted by FDA-approved drugs, small molecules in clinical trials, or compounds under preclinical development. Countersceening and validation was performed in normal murine cells and human HCC cell lines and xenograft using shRNAs and corresponding small molecular drugs. Pharmacological or shRNA-mediated inhibition of certain targets led to robust antitumor effects, both in vitro and in vivo, and suggest new strategies to inhibit Myc function therapeutically. Our results highlight the utility of RNAi screening for studying cancer vulnerabilities that can be exploited for direct pharmacological intervention.
Citation Format: Chun-Hao Huang, Amaia Lujambio, Johannes Zuber, Thomas Kitzing, Darjus F. Tschaharganeh, Elisa De Stanchina, Scott W. Lowe. RNAi screen identifies therapeutic targets in hepatocellular carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2935. doi:10.1158/1538-7445.AM2014-2935
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Affiliation(s)
- Chun-Hao Huang
- 1Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Amaia Lujambio
- 1Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Johannes Zuber
- 2Research Institute of Molecular Pathology, Vienna, Austria
| | - Thomas Kitzing
- 1Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Elisa D. Stanchina
- 3Antitumor Assessment Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Scott W. Lowe
- 4Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY
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22
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Huang CH, Lujambio A, Zuber J, Tschaharganeh DF, Doran MG, Evans MJ, Kitzing T, Zhu N, de Stanchina E, Sawyers CL, Armstrong SA, Lewis JS, Sherr CJ, Lowe SW. CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma. Genes Dev 2014; 28:1800-14. [PMID: 25128497 PMCID: PMC4197965 DOI: 10.1101/gad.244368.114] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One-year survival rates for newly diagnosed hepatocellular carcinoma (HCC) are <50%, and unresectable HCC carries a dismal prognosis owing to its aggressiveness and the undruggable nature of its main genetic drivers. By screening a custom library of shRNAs directed toward known drug targets in a genetically defined Myc-driven HCC model, we identified cyclin-dependent kinase 9 (Cdk9) as required for disease maintenance. Pharmacological or shRNA-mediated CDK9 inhibition led to robust anti-tumor effects that correlated with MYC expression levels and depended on the role that both CDK9 and MYC exert in transcription elongation. Our results establish CDK9 inhibition as a therapeutic strategy for MYC-overexpressing liver tumors and highlight the relevance of transcription elongation in the addiction of cancer cells to MYC.
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Affiliation(s)
- Chun-Hao Huang
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Amaia Lujambio
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Johannes Zuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | | | - Michael G Doran
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Michael J Evans
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Thomas Kitzing
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nan Zhu
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | | | - Charles L Sawyers
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Scott A Armstrong
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jason S Lewis
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Charles J Sherr
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Scott W Lowe
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA;
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23
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Tschaharganeh DF, Xue W, Calvisi DF, Evert M, Michurina TV, Dow LE, Banito A, Katz SF, Kastenhuber ER, Weissmueller S, Huang CH, Lechel A, Andersen JB, Capper D, Zender L, Longerich T, Enikolopov G, Lowe SW. p53-dependent Nestin regulation links tumor suppression to cellular plasticity in liver cancer. Cell 2014; 158:579-92. [PMID: 25083869 PMCID: PMC4221237 DOI: 10.1016/j.cell.2014.05.051] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 04/21/2014] [Accepted: 05/27/2014] [Indexed: 01/08/2023]
Abstract
The p53 tumor suppressor coordinates a series of antiproliferative responses that restrict the expansion of malignant cells, and as a consequence, p53 is lost or mutated in the majority of human cancers. Here, we show that p53 restricts expression of the stem and progenitor-cell-associated protein nestin in an Sp1/3 transcription-factor-dependent manner and that Nestin is required for tumor initiation in vivo. Moreover, loss of p53 facilitates dedifferentiation of mature hepatocytes into nestin-positive progenitor-like cells, which are poised to differentiate into hepatocellular carcinomas (HCCs) or cholangiocarcinomas (CCs) in response to lineage-specific mutations that target Wnt and Notch signaling, respectively. Many human HCCs and CCs show elevated nestin expression, which correlates with p53 loss of function and is associated with decreased patient survival. Therefore, transcriptional repression of Nestin by p53 restricts cellular plasticity and tumorigenesis in liver cancer.
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Affiliation(s)
- Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wen Xue
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Diego F Calvisi
- Institute of Pathology, University of Medicine, Greifswald 17487, Germany
| | - Matthias Evert
- Institute of Pathology, University of Medicine, Greifswald 17487, Germany
| | | | - Lukas E Dow
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ana Banito
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarah F Katz
- Department of Internal Medicine I, University of Ulm, Ulm 89070, Germany
| | - Edward R Kastenhuber
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Susann Weissmueller
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andre Lechel
- Department of Internal Medicine I, University of Ulm, Ulm 89070, Germany
| | - Jesper B Andersen
- Laboratory of Experimental Carcinogenesis, NCI/CCR, NIH, Bethesda, MD 20892, USA; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
| | - David Capper
- Institute of Pathology, University Hospital Heidelberg and Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Lars Zender
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | | | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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24
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Weissmueller S, Manchado E, Saborowski M, Morris JP, Wagenblast E, Davis CA, Moon SH, Pfister NT, Tschaharganeh DF, Kitzing T, Aust D, Markert EK, Wu J, Grimmond SM, Pilarsky C, Prives C, Biankin AV, Lowe SW. Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling. Cell 2014; 157:382-394. [PMID: 24725405 PMCID: PMC4001090 DOI: 10.1016/j.cell.2014.01.066] [Citation(s) in RCA: 385] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/17/2013] [Accepted: 01/23/2014] [Indexed: 12/14/2022]
Abstract
Missense mutations in the p53 tumor suppressor inactivate its antiproliferative properties but can also promote metastasis through a gain-of-function activity. We show that sustained expression of mutant p53 is required to maintain the prometastatic phenotype of a murine model of pancreatic cancer, a highly metastatic disease that frequently displays p53 mutations. Transcriptional profiling and functional screening identified the platelet-derived growth factor receptor b (PDGFRb) as both necessary and sufficient to mediate these effects. Mutant p53 induced PDGFRb through a cell-autonomous mechanism involving inhibition of a p73/NF-Y complex that represses PDGFRb expression in p53-deficient, noninvasive cells. Blocking PDGFRb signaling by RNA interference or by small molecule inhibitors prevented pancreatic cancer cell invasion in vitro and metastasis formation in vivo. Finally, high PDGFRb expression correlates with poor disease-free survival in pancreatic, colon, and ovarian cancer patients, implicating PDGFRb as a prognostic marker and possible target for attenuating metastasis in p53 mutant tumors.
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Affiliation(s)
- Susann Weissmueller
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eusebio Manchado
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Saborowski
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - John P Morris
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Elvin Wagenblast
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Carrie A Davis
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sung-Hwan Moon
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Neil T Pfister
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas Kitzing
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Daniela Aust
- Department of Visceral, Thoracic and Vascular Surgery, Technical University of Dresden, 01062 Dresden, Germany
| | - Elke K Markert
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA
| | - Jianmin Wu
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Sean M Grimmond
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Santa Lucia 4072, Australia; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland G61 1BD, UK
| | - Christian Pilarsky
- Department of Visceral, Thoracic and Vascular Surgery, Technical University of Dresden, 01062 Dresden, Germany
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Andrew V Biankin
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland G61 1BD, UK
| | - Scott W Lowe
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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25
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Gaida MM, Steffen TG, Günther F, Tschaharganeh DF, Felix K, Bergmann F, Schirmacher P, Hänsch GM. Polymorphonuclear neutrophils promote dyshesion of tumor cells and elastase-mediated degradation of E-cadherin in pancreatic tumors. Eur J Immunol 2012; 42:3369-80. [PMID: 23001948 DOI: 10.1002/eji.201242628] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 08/02/2012] [Accepted: 09/17/2012] [Indexed: 12/11/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) presenting with a micropapillary growth pattern is frequently associated with a prominent neutrophil infiltration into the tumor. The relevance of neutrophil infiltrates for tumor progression, however, is still debated. To gain insight into the role of polymorphonuclear neutrophils (PMNs) in PDAC, we assessed their effect on pancreatic tumor cells grown in vitro as monolayers. Time-lapse video microscopy showed a PMN-induced dyshesion of the tumor cells, and subsequent experiments revealed that this dyshesion was due to PMN elastase-mediated degradation of E-cadherin, an adhesion molecule that mediates the intercellular contact of the tumor cells. E-cadherin degradation by elastase or--(for comparison) down-modulation by specific siRNA, significantly increased the migratory capacity of the pancreatic tumor cells, leading to the hypothesis that PMNs could contribute to the invasive tumor growth. To address this issue, biopsies of patients with PDAC (n = 112) were analyzed. We found that E-cadherin expression correlated negatively with PMN infiltration, compatible with the notion that E-cadherin is cleaved by PMN-derived elastase, which in turn could result in the dispersal of the tumor cells, enhanced migratory capacity and thus invasive tumor growth.
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Affiliation(s)
- Matthias M Gaida
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
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Kaldenbach M, Giebeler A, Tschaharganeh DF, Erschfeld S, Wasmuth HE, Dolle L, Floege J, Trautwein C, Streetz KL. Hepatocyte growth factor/c-Met signalling is important for the selection of transplanted hepatocytes. Gut 2012; 61:1209-18. [PMID: 22287599 DOI: 10.1136/gutjnl-2011-301345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
BACKGROUND At present hepatocyte transplantation is a promising option for cellular therapy of end-stage liver diseases. However, the underlying molecular mechanisms need to be better defined in order to translate this technique into clinical use. This study investigated the cursiv relevance of hepatocyte growth factor (HGF)/c-Met signalling for hepatocyte repopulation after transplantion. METHODS Wild-type mice (c-Met(loxP/loxP)) and hepatocyte-specific conditional c-Met (HGF receptor) knockout (c-Met(Δhepa)) mice were used as donors and recipients for hepatocyte transplantation. RESULTS Transplantation experiments revealed two major findings. First it was demonstrated that c-Met is indispensable in donor cells, as c-Met(Δhepa) cells did not repopulate recipient livers after transplantation. Second, genetic deletion of c-Met in recipient hepatocytes resulted in enhanced expansion of unmodified donor cells in host livers (up to 250-fold after 12 weeks). The relevant mechanisms for this observation in c-Met(Δhepa) host hepatocytes could be defined. c-Met(Δhepa) hepatocytes showed enhanced apoptosis, reduced cellular proliferation and a lack of AKT-kinase and STAT3 activation. In addition, tissue remodelling was changed in c-Met(Δhepa) recipient livers. Therefore, the lack of pro-proliferative transcription factors, increased apoptosis and changes in matrix-remodelling inhibit host cell proliferation in c-Met(Δhepa) recipient livers and thus favour repopulation of transplanted hepatocytes. Therapeutically liver repopulation could be increased through adenoviral expression of NK-4--an inhibitor of HGF signalling--in host hepatocytes. CONCLUSION HGF/c-Met plays a crucial role in host and donor cells of the liver for the cursiv selection of transplanted hepatocytes. Modulating HGF-dependent signalling seems a promising therapeutic option to favour expansion of transplanted hepatocytes.
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Tschaharganeh DF, Chen XC, Latzko P, Malz M, Gaida M, Felix K, Singer S, Pinna F, Gretz N, Sticht C, Delogu S, Evert M, Biao F, Ribback S, Jiang L, Brozzetti S, Bergmann F, Dombrowski F, Schirmacher P, Calvisi DF, Breuhahn K. Abstract 984: High-level expression of YAP induces protumorigenic Notch signalling in human hepatocarcinogenesis. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The evolutionary conserved Hippo-pathway negatively regulates organ size control by phosphorylation and cytoplasmic retention of the transcriptional co-activator yes-associated protein (YAP). Recent studies demonstrated that deletion of essential Hippo-pathway constituents (e.g., Mst-1/2 and WW45) or overexpression of YAP lead to the development of liver cancer. However, the underlying molecular tumor-supporting mechanisms in carcinogenesis have not been defined so far. Overexpression and nuclear accumulation of YAP in nearly 70% of all human hepatocellular carcinomas (HCC) significantly correlated with tumor cell proliferation and dedifferentiation. In human HCC cell lines, siRNA-mediated inhibition of YAP significantly reduced tumor cell viability, and migration/invasion. Based on transcriptomic profiling approaches, the Notch ligand Jagged-1 (Jag-1) was identified as YAP-dependent target gene in HCC cells and in primary murine hepatocytes of transgenic animals expressing constitutively active YAPS127A. Inhibition of YAP reduced the protein levels of Jag-1, cleaved Notch receptor (NICD), and Hes-1, while YAP overexpression increased the amounts of all factors. As detected for YAP knock down, transfection of gene-specific siRNA targeting Jag-1 diminished HCC cell viability and migration. Overexpression and concomitant inhibition of Jag-1 abolished Hes-1 expression and YAP-induced HCC cell viability. By applying different mutant isoforms of YAP (e.g., YAPS127A and YAP5SA-delta-C - dominant negative isoform), TEAD4 but not TEAD1 was identified as the transcription factor required for YAP-dependent regulation of Jag-1 and Hes-1. Furthermore, the WNT/beta-catenin pathway, a putative inducer of Jag-1, did not influence the YAP-dependent modulation of Jag-1. Knock down experiments revealed Mst-2 and Lats-2 as negative regulators of YAP activity and Jag-1/Hes-1 expression. The amounts of YAP, Jag-1, and Hes-1 transcripts as well as proteins significantly correlated with each other in human HCC tissues. Most importantly, increased concentrations of all factors significantly associated with poor prognosis of HCC patients. These data demonstrate that high-level expression of YAP in HCC cells induces tumor growth and tumor cell dissemination in part through activation of the Jag-1/Notch pathway in a TEAD4-dependent and beta-catenin-independent manner. This regulatory cross-talk between Hippo- and Notch-signalling defines a group of HCC patients with poor overall survival.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 984. doi:1538-7445.AM2012-984
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Affiliation(s)
| | - Xin Chen Chen
- 2Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA
| | | | - Mona Malz
- 1University Hospital of Heidelberg, Heidelberg, Germany
| | | | - Klaus Felix
- 3Departement of Surgery Univerity Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Norbert Gretz
- 4Medical Research Center, Medical Faculty Mannheim, Mannheim, Germany
| | - Carsten Sticht
- 4Medical Research Center, Medical Faculty Mannheim, Mannheim, Germany
| | - Salvatore Delogu
- 5Institut of Pathologie, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Matthias Evert
- 5Institut of Pathologie, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Fan Biao
- 2Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA
| | - Silvia Ribback
- 5Institut of Pathologie, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Lijie Jiang
- 2Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA
| | - Stefania Brozzetti
- 6Department of Surgery “Pietro Valdoni,” University of Rome “La Sapienza,” Rome, Italy
| | | | - Frank Dombrowski
- 5Institut of Pathologie, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | | | - Diego F. Calvisi
- 5Institut of Pathologie, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Kai Breuhahn
- 1University Hospital of Heidelberg, Heidelberg, Germany
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Gaida MM, Welsch T, Herpel E, Tschaharganeh DF, Fischer L, Schirmacher P, Hänsch GM, Bergmann F. MHC class II expression in pancreatic tumors: a link to intratumoral inflammation. Virchows Arch 2011; 460:47-60. [PMID: 22120497 DOI: 10.1007/s00428-011-1175-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 10/28/2011] [Accepted: 11/09/2011] [Indexed: 12/22/2022]
Abstract
Major histocompatibility complex class II antigens (MHC class II) are constitutively expressed by professional antigen presenting cells and present antigenic peptides to specific CD4+ T lymphocytes. MHC class II expression, however, can also be induced on epithelial cells and in a variety of solid tumors. We tested MHC class II expression on tissue samples derived from patients with pancreatic ductal adenocarcinoma (PDAC) and pancreatic endocrine tumors (PET). Immunohistochemistry revealed MHC class II expression in 86 of 112 (76.8%) PDAC samples and in 30 of 43 (70.0%) PET samples. In PDAC and PET, MHC class II expression correlated significantly with severity and activity of intratumoral inflammation, as well as with the infiltration of CD4+ T lymphocytes. High MHC class II expression significantly correlated with a better histological grade of differentiation in PDAC. In vitro MHC class II expression could be induced on PDAC tumor cell lines by interferon-γ. These cells were then able to present the staphylococci enterotoxin B superantigen to T lymphocytes, which resulted in T cell proliferation. Our findings suggest that MHC class II expression on pancreatic tumor cells is induced by the intratumoral inflammatory reaction in pancreatic tumors.
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Affiliation(s)
- Matthias M Gaida
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 220, Heidelberg, Germany
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Gaida MM, Bach ST, Günther F, Baseras B, Tschaharganeh DF, Welsch T, Felix K, Bergmann F, Hänsch GM, Wente MN. Expression of galectin-3 in pancreatic ductal adenocarcinoma. Pathol Oncol Res 2011; 18:299-307. [PMID: 21910036 DOI: 10.1007/s12253-011-9444-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 08/01/2011] [Indexed: 12/11/2022]
Abstract
Galectin-3 influences neoangiogenesis, tumor cell adhesion, and tumor-immune-escape mechanisms. Hence, the expression of galectin-3 in pancreatic ductal adenocarcinoma (PDAC) was evaluated. Galectin-3 expression in PDAC cell lines was proven by the presence of intracellular protein and by release into the supernatant. Furthermore, galectin-3 was found in the majority of human tissue samples. Serum concentrations of galectin-3 in PDAC patients did not differ significantly from healthy donors and did not correlate with established tumor markers. In conclusion, galectin-3 is expressed in PDAC tissues suggesting a role in tumor development; however, no relationship between expression and clinical findings could be established.
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Affiliation(s)
- Matthias M Gaida
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
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30
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Gaida MM, Haag N, Günther F, Tschaharganeh DF, Schirmacher P, Friess H, Giese NA, Schmidt J, Wente MN. Expression of A disintegrin and metalloprotease 10 in pancreatic carcinoma. Int J Mol Med 2010; 26:281-8. [PMID: 20596609 DOI: 10.3892/ijmm_00000463] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The protease ADAM10 influences progression and metastasis of cancer cells and is overexpressed in various malignancies. Therefore, the aim of our study was to evaluate the expression and potential function of ADAM10 in the pathophysiology of pancreatic cancer (PDAC). ADAM10 expression in normal pancreatic (NP), chronic pancreatitis (CP), PDAC tissues, as well as PDAC cell lines was determined. To evaluate whether rhADAM10 or ADAM10 silencing influences cancer cell viability, MTT assay was used. Matrigel invasion and wound healing assays were performed to observe influence on invasion and migration. ADAM10 mRNA was expressed in all samples of NP, CP and PDAC tissue and cell lines. Western blotting and immunohistochemistry revealed stronger ADAM10 expression in PDAC than in NP. ADAM10 silencing or rhADAM10 had no effect on cell viability. ADAM10 silencing markedly reduced invasiveness and migration of cancer cells. These findings establish ADAM10 as a contributing factor in PDAC invasion and metastasis.
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Affiliation(s)
- Matthias M Gaida
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
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31
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Plum W, Tschaharganeh DF, Kroy DC, Corsten E, Erschfeld S, Dierssen U, Wasmuth H, Trautwein C, Streetz KL. Lack of glycoprotein 130/signal transducer and activator of transcription 3-mediated signaling in hepatocytes enhances chronic liver injury and fibrosis progression in a model of sclerosing cholangitis. Am J Pathol 2010; 176:2236-46. [PMID: 20382701 DOI: 10.2353/ajpath.2010.090469] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) model leads to chronic cholestatic liver injury and therefore resembles human diseases such as sclerosing cholangitis and forms of metabolic liver diseases. The role of the interleukin-6/glycoprotein 130 (gp130) system in this context is still undefined. Therefore, conditional gp130 knockout and knockin mice were used to achieve hepatocyte-specific deletions of gp130 (gp130(Deltahepa)), gp130-dependent ras (gp130(DeltahepaRas)), and signal transducer and activator of transcription (STAT) (gp130(DeltahepaSTAT)) activation. These mice were treated with a DDC-containing diet and analyzed over time. Mice deficient in hepatic gp130 and STAT signaling showed increased and earlier mortality than wild-type and gp130(DeltahepaRas) animals. Over time, significantly more apoptosis and cholestasis became evident in gp130(Deltahepa) and gp130(DeltahepaSTAT) mice. These mice also displayed increased tumor necrosis factor-alpha expression, a diminished acute-phase response (lack of STAT3 and serum amyloid A activation), and enhanced immune cell infiltration in the liver. These were associated with stronger periportal oval cell activation. In addition, DDC treatment in gp130(Deltahepa) and gp130(DeltahepaSTAT) mice resulted in significantly stronger hepatic stellate cell activation. Long-term analysis revealed the development of severe liver fibrosis in gp130(Deltahepa) and gp130(DeltahepaSTAT) animals, as evidenced by increased collagen accumulation. Here we demonstrate that gp130/STAT signaling in hepatocytes provides protection in a cholestatic hepatitis mouse model. STAT3-dependent signaling pathways in hepatocytes protect from apoptosis and tissue injury, which subsequently reduce oval cell activation and prevent fibrosis progression.
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Affiliation(s)
- Werner Plum
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
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Kroy DC, Beraza N, Tschaharganeh DF, Sander LE, Erschfeld S, Giebeler A, Liedtke C, Wasmuth HE, Trautwein C, Streetz KL. Lack of interleukin-6/glycoprotein 130/signal transducers and activators of transcription-3 signaling in hepatocytes predisposes to liver steatosis and injury in mice. Hepatology 2010; 51:463-73. [PMID: 19918973 DOI: 10.1002/hep.23322] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
UNLABELLED A deregulated cytokine balance is involved in triggering the sequence from steatosis to nonalcoholic steatohepatitis, ultimately leading to liver fibrosis and cancer. To better define the role of proinflammatory interleukin-6 (IL-6)-type cytokines in hepatocytes we investigated the role of IL-6 and its shared receptor, glycoprotein 130 (gp130), in a mouse model of steatohepatitis. IL-6(-/-) mice were fed a choline-deficient, ethionine-supplemented (CDE) diet. Conditional gp130 knockout and knockin mice were used to achieve hepatocyte-specific deletion of gp130 (gp130(Deltahepa)), gp130-dependent rat sarcoma (Ras)-(gp130(DeltahepaRas)), and signal transducers and activators of transcription (STAT)-(gp130(DeltahepaSTAT)) activation. CDE-treated IL-6(-/-) mice showed a significant hepatic steatosis at 2 weeks after feeding. The mice rapidly developed elevated fasting blood glucose, insulin serum levels, and transaminases. To better define IL-6-dependent intracellular pathways, specifically in hepatocytes, we next treated gp130(Deltahepa) mice with a CDE diet. These animals also developed a marked steatosis with hyperglycemia and displayed elevated insulin serum levels. Additionally, gp130(Deltahepa) animals showed an imbalanced inflammatory response with increased hepatic tumor necrosis factor-alpha and decreased adiponectin messenger RNA levels. Dissecting the hepatocyte-specific gp130-dependent pathways revealed a similar disease phenotype in gp130(DeltahepaSTAT) mice, whereas gp130(DeltahepaRas) animals were protected. In CDE-treated mice lack of gp130-STAT3 signaling was associated with immune-cell-infiltration, jun kinase-activation, a blunted acute-phase-response, and elevated transaminases. Furthermore, gp130(Deltahepa) and gp130(DeltahepaSTAT) mice showed beginning signs of liver fibrosis compared to gp130(DeltahepaRas) mice and controls. CONCLUSION During CDE treatment mice lacking IL-6 and gp130-STAT signaling in hepatocytes are prone to hepatic metabolic changes and inflammation. This ultimately leads to progressive steatohepatitis with signs of liver remodeling. Thus, the presented model allows one to further dissect the role of IL-6/gp130-type signaling in hepatocytes during fatty liver degeneration to define new therapeutic targets in metabolic liver diseases.
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Affiliation(s)
- Daniela C Kroy
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
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Tschaharganeh DF, Kaldenbach M, Erschfeld S, Tischendorf JJW, Trautwein C, Streetz KL. Glycoprotein 130-dependent pathways in host hepatocytes are important for liver repopulation in mice. Liver Transpl 2010; 16:23-32. [PMID: 20035522 DOI: 10.1002/lt.21962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatocyte transplantation (HT) is still restricted by the limited amount of transplantable cells. Therefore, a better understanding of the mechanisms involved in cellular engraftment, proliferation, and in vivo selection is important. Here we aimed to evaluate the role of the interleukin 6 (IL-6)/glycoprotein 130 (gp130) system for liver repopulation. Mice carrying a conditional hepatocyte-specific deletion of the common IL-6 signal transducer gp130 (gp130(Deltahepa)) were used for HT. First, we compared bone marrow transplantation (BMT), partial hepatectomy (PH), and retrorsine treatment of recipient mice to optimize the in vivo selection of transplanted hepatocytes. BMT combined with PH was sufficient to induce a 30-fold increase in the number of transplanted donor hepatocytes, whereas additional retrorsine pretreatment led to an up to 40-fold increase. Next, the influence of gp130 signaling in hepatocytes on cell selection was evaluated. Wild-type (WT) hepatocytes repopulated WT recipients at the same rate as gp130(Deltahepa) cells. In contrast, liver repopulation by transplanted cells was enhanced in gp130(Deltahepa) recipient mice. This was associated with higher proliferation of donor hepatocytes and enhanced apoptosis in gp130(Deltahepa) recipient livers. Additionally, the acute phase response was strongly induced after HT in WT recipients but blunted in gp130(Deltahepa) recipients. As a result, significantly more liver remodeling, evidenced by stronger hepatic stellate cell activation and collagen accumulation, was found in gp130(Deltahepa) mice after HT. In conclusion, the HT model established here can be efficiently applied to investigate cell-specific mechanisms in liver repopulation. Moreover, we have shown that gp130-dependent pathways in host hepatocytes are important for controlling liver repopulation.
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