1
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House IG, Derrick EB, Sek K, Chen AXY, Li J, Lai J, Todd KL, Munoz I, Michie J, Chan CW, Huang YK, Chan JD, Petley EV, Tong J, Nguyen D, Engel S, Savas P, Hogg SJ, Vervoort SJ, Kearney CJ, Burr ML, Lam EYN, Gilan O, Bedoui S, Johnstone RW, Dawson MA, Loi S, Darcy PK, Beavis PA. CRISPR-Cas9 screening identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and antitumor immunity. Cell Rep 2024; 43:113793. [PMID: 38324452 DOI: 10.1016/j.celrep.2024.113793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
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2
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Gilan O, Talarmain L, Bell CC, Neville D, Knezevic K, Ferguson DT, Boudes M, Chan YC, Davidovich C, Lam EYN, Dawson MA. CRISPR-ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia. Nat Struct Mol Biol 2023; 30:1592-1606. [PMID: 37679565 DOI: 10.1038/s41594-023-01087-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 01/03/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023]
Abstract
Chromatin regulation involves the selective recruitment of chromatin factors to facilitate DNA repair, replication and transcription. Here we demonstrate the utility of coupling unbiased functional genomics with chromatin immunoprecipitation (CRISPR-ChIP) to identify the factors associated with active chromatin modifications in mammalian cells. Specifically, an integrated reporter containing a cis-regulatory element of interest and a single guide RNA provide a chromatinized template for a direct readout for regulators of histone modifications associated with actively transcribed genes such as H3K4me3 and H3K79me2. With CRISPR-ChIP, we identify all the nonredundant COMPASS complex members required for H3K4me3 and demonstrate that RNA polymerase II is dispensable for the maintenance of H3K4me3. As H3K79me2 has a putative oncogenic function in leukemia cells driven by MLL translocations, using CRISPR-ChIP we reveal a functional partitioning of H3K79 methylation into two distinct regulatory units: an oncogenic DOT1L complex directed by the MLL fusion protein in a Menin-dependent manner and a separate endogenous DOT1L complex, where catalytic activity is directed by MLLT10. Overall, CRISPR-ChIP provides a powerful tool for the unbiased interrogation of the mechanisms underpinning chromatin regulation.
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Affiliation(s)
- Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia.
| | - Laure Talarmain
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Neville
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel T Ferguson
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- EMBL-Australia, Clayton, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Clinical Haematology, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
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3
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House IG, Derrick EB, Sek K, Chen AXY, Li J, Lai J, Todd KL, Munoz I, Michie J, Chan CW, Huang YK, Chan JD, Petley EV, Tong J, Nguyen D, Engel S, Savas P, Hogg SJ, Vervoort SJ, Kearney CJ, Burr ML, Lam EYN, Gilan O, Bedoui S, Johnstone RW, Dawson MA, Loi S, Darcy PK, Beavis PA. CRISPR-Cas9 screening identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and antitumor immunity. Cell Rep 2023; 42:113014. [PMID: 37605534 DOI: 10.1016/j.celrep.2023.113014] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 06/13/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023] Open
Abstract
CXCL9 expression is a strong predictor of response to immune checkpoint blockade therapy. Accordingly, we sought to develop therapeutic strategies to enhance the expression of CXCL9 and augment antitumor immunity. To perform whole-genome CRISPR-Cas9 screening for regulators of CXCL9 expression, a CXCL9-GFP reporter line is generated using a CRISPR knockin strategy. This approach finds that IRF1 limits CXCL9 expression in both tumor cells and primary myeloid cells through induction of SOCS1, which subsequently limits STAT1 signaling. Thus, we identify a subset of STAT1-dependent genes that do not require IRF1 for their transcription, including CXCL9. Targeting of either IRF1 or SOCS1 potently enhances CXCL9 expression by intratumoral macrophages, which is further enhanced in the context of immune checkpoint blockade therapy. We hence show a non-canonical role for IRF1 in limiting the expression of a subset of STAT1-dependent genes through induction of SOCS1.
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Affiliation(s)
- Imran G House
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Emily B Derrick
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kevin Sek
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Amanda X Y Chen
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jasmine Li
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Junyun Lai
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kirsten L Todd
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Isabelle Munoz
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jessica Michie
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Cheok Weng Chan
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Yu-Kuan Huang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jack D Chan
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Emma V Petley
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Junming Tong
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - DatMinh Nguyen
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sven Engel
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Peter Savas
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Simon J Hogg
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Stephin J Vervoort
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Conor J Kearney
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Marian L Burr
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; Department of Anatomical Pathology, The Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Enid Y N Lam
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Omer Gilan
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Ricky W Johnstone
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia; Department of Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; Centre for Cancer Research, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Sherene Loi
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Phillip K Darcy
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Immunology, Monash University, Clayton, VIC, Australia.
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia.
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4
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Sparbier CE, Gillespie A, Gomez J, Kumari N, Motazedian A, Chan KL, Bell CC, Gilan O, Chan YC, Popp S, Gough DJ, Eckersley-Maslin MA, Dawson SJ, Lehner PJ, Sutherland KD, Ernst P, McGeehan GM, Lam EYN, Burr ML, Dawson MA. Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes. Nat Cell Biol 2023; 25:258-272. [PMID: 36635503 PMCID: PMC7614190 DOI: 10.1038/s41556-022-01056-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2022] [Indexed: 01/14/2023]
Abstract
Precise control of activating H3K4me3 and repressive H3K27me3 histone modifications at bivalent promoters is essential for normal development and frequently corrupted in cancer. By coupling a cell surface readout of bivalent MHC class I gene expression with whole-genome CRISPR-Cas9 screens, we identify specific roles for MTF2-PRC2.1, PCGF1-PRC1.1 and Menin-KMT2A/B complexes in maintaining bivalency. Genetic loss or pharmacological inhibition of Menin unexpectedly phenocopies the effects of polycomb disruption, resulting in derepression of bivalent genes in both cancer cells and pluripotent stem cells. While Menin and KMT2A/B contribute to H3K4me3 at active genes, a separate Menin-independent function of KMT2A/B maintains H3K4me3 and opposes polycomb-mediated repression at bivalent genes. Release of KMT2A from active genes following Menin targeting alters the balance of polycomb and KMT2A at bivalent genes, facilitating gene activation. This functional partitioning of Menin-KMT2A/B complex components reveals therapeutic opportunities that can be leveraged through inhibition of Menin.
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Affiliation(s)
- Christina E Sparbier
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrea Gillespie
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Juliana Gomez
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Nishi Kumari
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ali Motazedian
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kah Lok Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sarah Popp
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Daniel J Gough
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Melanie A Eckersley-Maslin
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kate D Sutherland
- ACRF Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Patricia Ernst
- Section of Hematology, Oncology and Bone Marrow Transplant, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marian L Burr
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
- Department of Anatomical Pathology, ACT Pathology, Canberra Health Services, Canberra, Australian Capital Territory, Australia.
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
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5
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He MY, Halford MM, Liu R, Roy JP, Grant ZL, Coultas L, Thio N, Gilan O, Chan YC, Dawson MA, Achen MG, Stacker SA. Three-dimensional CRISPR screening reveals epigenetic interaction with anti-angiogenic therapy. Commun Biol 2021; 4:878. [PMID: 34267311 PMCID: PMC8282794 DOI: 10.1038/s42003-021-02397-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/14/2020] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
Angiogenesis underlies development, physiology and pathogenesis of cancer, eye and cardiovascular diseases. Inhibiting aberrant angiogenesis using anti-angiogenic therapy (AAT) has been successful in the clinical treatment of cancer and eye diseases. However, resistance to AAT inevitably occurs and its molecular basis remains poorly understood. Here, we uncover molecular modifiers of the blood endothelial cell (EC) response to a widely used AAT bevacizumab by performing a pooled genetic screen using three-dimensional microcarrier-based cell culture and CRISPR–Cas9. Functional inhibition of the epigenetic reader BET family of proteins BRD2/3/4 shows unexpected mitigating effects on EC survival and/or proliferation upon VEGFA blockade. Moreover, transcriptomic and pathway analyses reveal an interaction between epigenetic regulation and anti-angiogenesis, which may affect chromosomal structure and activity in ECs via the cell cycle regulator CDC25B phosphatase. Collectively, our findings provide insight into epigenetic regulation of the EC response to VEGFA blockade and may facilitate development of quality biomarkers and strategies for overcoming resistance to AAT. Through three-dimensional CRISPR screening, He et al. report that functional inhibition of BET family of proteins BRD2/3/4 shows mitigating effects on blood endothelial cell (EC) survival and/or proliferation upon VEGFA blockade. An interaction between epigenetic regulation and anti-angiogenesis, which may affect chromosomal structure and activity in ECs through CDC25B phosphatase, is potentially involved with EC resistance to anti-angiogenic therapy.
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Affiliation(s)
- Michael Y He
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael M Halford
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ruofei Liu
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - James P Roy
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Zoe L Grant
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Gladstone Institutes, San Francisco, CA, USA
| | - Leigh Coultas
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Niko Thio
- Bioinformatics Core, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Omer Gilan
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Yih-Chih Chan
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Centre for Cancer Research, The University of Melbourne, Parkville, VIC, Australia.,Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Marc G Achen
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.,St Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Steven A Stacker
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. .,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.
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6
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Watt AC, Cejas P, DeCristo MJ, Metzger-Filho O, Lam EYN, Qiu X, BrinJones H, Kesten N, Coulson R, Font-Tello A, Lim K, Vadhi R, Daniels VW, Montero J, Taing L, Meyer CA, Gilan O, Bell CC, Korthauer KD, Giambartolomei C, Pasaniuc B, Seo JH, Freedman ML, Ma C, Ellis MJ, Krop I, Winer E, Letai A, Brown M, Dawson MA, Long HW, Zhao JJ, Goel S. CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity. Nat Cancer 2021; 2:34-48. [PMID: 33997789 PMCID: PMC8115221 DOI: 10.1038/s43018-020-00135-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023]
Abstract
Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) were designed to induce cancer cell cycle arrest. Recent studies have suggested that these agents also exert other effects, influencing cancer cell immunogenicity, apoptotic responses, and differentiation. Using cell-based and mouse models of breast cancer together with clinical specimens, we show that CDK4/6 inhibitors induce remodeling of cancer cell chromatin characterized by widespread enhancer activation, and that this explains many of these effects. The newly activated enhancers include classical super-enhancers that drive luminal differentiation and apoptotic evasion, as well as a set of enhancers overlying endogenous retroviral elements that is enriched for proximity to interferon-driven genes. Mechanistically, CDK4/6 inhibition increases the level of several Activator Protein-1 (AP-1) transcription factor proteins, which are in turn implicated in the activity of many of the new enhancers. Our findings offer insights into CDK4/6 pathway biology and should inform the future development of CDK4/6 inhibitors.
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Affiliation(s)
- April C Watt
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- CIBERONC CB16/12/00398, La Paz University Hospital, Madrid, Spain
| | - Molly J DeCristo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Otto Metzger-Filho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Haley BrinJones
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikolas Kesten
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rhiannon Coulson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Raga Vadhi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Veerle W Daniels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joan Montero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute for Bioengineering of Catalonia, Barcelona, Spain
| | - Len Taing
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Keegan D Korthauer
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cynthia Ma
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Ian Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eric Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Parkville, Victoria, Australia
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Jean J Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Shom Goel
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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7
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Gilan O, Rioja I, Knezevic K, Bell MJ, Yeung MM, Harker NR, Lam EYN, Chung CW, Bamborough P, Petretich M, Urh M, Atkinson SJ, Bassil AK, Roberts EJ, Vassiliadis D, Burr ML, Preston AGS, Wellaway C, Werner T, Gray JR, Michon AM, Gobbetti T, Kumar V, Soden PE, Haynes A, Vappiani J, Tough DF, Taylor S, Dawson SJ, Bantscheff M, Lindon M, Drewes G, Demont EH, Daniels DL, Grandi P, Prinjha RK, Dawson MA. Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation. Science 2020; 368:387-394. [PMID: 32193360 PMCID: PMC7610820 DOI: 10.1126/science.aaz8455] [Citation(s) in RCA: 234] [Impact Index Per Article: 58.5] [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: 10/23/2019] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
The two tandem bromodomains of the BET (bromodomain and extraterminal domain) proteins enable chromatin binding to facilitate transcription. Drugs that inhibit both bromodomains equally have shown efficacy in certain malignant and inflammatory conditions. To explore the individual functional contributions of the first (BD1) and second (BD2) bromodomains in biology and therapy, we developed selective BD1 and BD2 inhibitors. We found that steady-state gene expression primarily requires BD1, whereas the rapid increase of gene expression induced by inflammatory stimuli requires both BD1 and BD2 of all BET proteins. BD1 inhibitors phenocopied the effects of pan-BET inhibitors in cancer models, whereas BD2 inhibitors were predominantly effective in models of inflammatory and autoimmune disease. These insights into the differential requirement of BD1 and BD2 for the maintenance and induction of gene expression may guide future BET-targeted therapies.
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Affiliation(s)
- Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Inmaculada Rioja
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Matthew J Bell
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Miriam M Yeung
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Nicola R Harker
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Chun-Wa Chung
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Paul Bamborough
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Massimo Petretich
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | | | - Stephen J Atkinson
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Anna K Bassil
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Emma J Roberts
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Marian L Burr
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Alex G S Preston
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | | | - Thilo Werner
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - James R Gray
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Anne-Marie Michon
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Thomas Gobbetti
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Vinod Kumar
- Computational Biology, GlaxoSmithKline, Collegeville, PA, USA
| | - Peter E Soden
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Andrea Haynes
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Johanna Vappiani
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - David F Tough
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Simon Taylor
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Marcus Bantscheff
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Matthew Lindon
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Gerard Drewes
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Emmanuel H Demont
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | | | - Paola Grandi
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Rab K Prinjha
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK.
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
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8
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Abstract
As well as undergoing genetic evolution, cancer cells can alter their epigenetic state to adapt and resist treatment. This non-genetic evolution is emerging as a major component of cancer resistance. Only now are we beginning to acquire the necessary data and tools to establish some of the underlying principles and mechanisms that define when, why and how non-genetic resistance occurs. Preliminary studies suggest that it can exist in a number of forms, including drug persistence, unstable non-genetic resistance and, most intriguingly, stable non-genetic resistance. Exactly how they each arise remains unclear; however, epigenetic heterogeneity and plasticity appear to be important variables. In this review, we provide an overview of these different forms of non-genetic resistance, before exploring how epigenetic heterogeneity and plasticity influence their emergence. We highlight the distinction between non-genetic Darwinian selection and Lamarckian induction and discuss how each is capable of generating resistance. Finally, we discuss the potential interaction between genetic and non-genetic adaptation and propose the idea of ‘the path of most resistance’, which outlines the variables that dictate whether cancers adapt through genetic and/or epigenetic means. Through these discussions, we hope to provide a conceptual framework that focuses future studies, whose insights might help prevent or overcome non-genetic resistance.
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Affiliation(s)
- Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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9
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Burr ML, Sparbier CE, Chan KL, Chan YC, Kersbergen A, Lam EYN, Azidis-Yates E, Vassiliadis D, Bell CC, Gilan O, Jackson S, Tan L, Wong SQ, Hollizeck S, Michalak EM, Siddle HV, McCabe MT, Prinjha RK, Guerra GR, Solomon BJ, Sandhu S, Dawson SJ, Beavis PA, Tothill RW, Cullinane C, Lehner PJ, Sutherland KD, Dawson MA. An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer. Cancer Cell 2019; 36:385-401.e8. [PMID: 31564637 PMCID: PMC6876280 DOI: 10.1016/j.ccell.2019.08.008] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/26/2019] [Accepted: 08/24/2019] [Indexed: 12/21/2022]
Abstract
Loss of MHC class I (MHC-I) antigen presentation in cancer cells can elicit immunotherapy resistance. A genome-wide CRISPR/Cas9 screen identified an evolutionarily conserved function of polycomb repressive complex 2 (PRC2) that mediates coordinated transcriptional silencing of the MHC-I antigen processing pathway (MHC-I APP), promoting evasion of T cell-mediated immunity. MHC-I APP gene promoters in MHC-I low cancers harbor bivalent activating H3K4me3 and repressive H3K27me3 histone modifications, silencing basal MHC-I expression and restricting cytokine-induced upregulation. Bivalent chromatin at MHC-I APP genes is a normal developmental process active in embryonic stem cells and maintained during neural progenitor differentiation. This physiological MHC-I silencing highlights a conserved mechanism by which cancers arising from these primitive tissues exploit PRC2 activity to enable immune evasion.
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Affiliation(s)
- Marian L Burr
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| | - Christina E Sparbier
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Kah Lok Chan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Ariena Kersbergen
- ACRF Cancer Biology and Stem Cell Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | | | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Omer Gilan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Susan Jackson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Lavinia Tan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sebastian Hollizeck
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Ewa M Michalak
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Hannah V Siddle
- Department of Biological Sciences, University of Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Michael T McCabe
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Rab K Prinjha
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA; Epigenetics Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Glen R Guerra
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Benjamin J Solomon
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia
| | - Paul A Beavis
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Richard W Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Carleen Cullinane
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kate D Sutherland
- ACRF Cancer Biology and Stem Cell Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia.
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10
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Bell CC, Fennell KA, Chan YC, Rambow F, Yeung MM, Vassiliadis D, Lara L, Yeh P, Martelotto LG, Rogiers A, Kremer BE, Barbash O, Mohammad HP, Johanson TM, Burr ML, Dhar A, Karpinich N, Tian L, Tyler DS, MacPherson L, Shi J, Pinnawala N, Yew Fong C, Papenfuss AT, Grimmond SM, Dawson SJ, Allan RS, Kruger RG, Vakoc CR, Goode DL, Naik SH, Gilan O, Lam EYN, Marine JC, Prinjha RK, Dawson MA. Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia. Nat Commun 2019; 10:2723. [PMID: 31222014 PMCID: PMC6586637 DOI: 10.1038/s41467-019-10652-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [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: 03/13/2019] [Accepted: 05/21/2019] [Indexed: 12/16/2022] Open
Abstract
Non-genetic drug resistance is increasingly recognised in various cancers. Molecular insights into this process are lacking and it is unknown whether stable non-genetic resistance can be overcome. Using single cell RNA-sequencing of paired drug naïve and resistant AML patient samples and cellular barcoding in a unique mouse model of non-genetic resistance, here we demonstrate that transcriptional plasticity drives stable epigenetic resistance. With a CRISPR-Cas9 screen we identify regulators of enhancer function as important modulators of the resistant cell state. We show that inhibition of Lsd1 (Kdm1a) is able to overcome stable epigenetic resistance by facilitating the binding of the pioneer factor, Pu.1 and cofactor, Irf8, to nucleate new enhancers that regulate the expression of key survival genes. This enhancer switching results in the re-distribution of transcriptional co-activators, including Brd4, and provides the opportunity to disable their activity and overcome epigenetic resistance. Together these findings highlight key principles to help counteract non-genetic drug resistance.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Bone Marrow/pathology
- CRISPR-Cas Systems/genetics
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Epigenesis, Genetic/drug effects
- Female
- Gene Expression Regulation, Leukemic/drug effects
- HEK293 Cells
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Sequence Analysis, RNA
- Single-Cell Analysis
- Trans-Activators/antagonists & inhibitors
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription, Genetic/drug effects
- Treatment Outcome
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Katie A Fennell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
| | - Miriam M Yeung
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Dane Vassiliadis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Luis Lara
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Paul Yeh
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Aljosja Rogiers
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Brandon E Kremer
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Helai P Mohammad
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marian L Burr
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Arindam Dhar
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Luyi Tian
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Dean S Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathan Pinnawala
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Chun Yew Fong
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Sean M Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Ryan G Kruger
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - David L Goode
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Shalin H Naik
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Rab K Prinjha
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia.
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11
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Agarwal R, Chan YC, Tam CS, Hunter T, Vassiliadis D, Teh CE, Thijssen R, Yeh P, Wong SQ, Ftouni S, Lam EYN, Anderson MA, Pott C, Gilan O, Bell CC, Knezevic K, Blombery P, Rayeroux K, Zordan A, Li J, Huang DCS, Wall M, Seymour JF, Gray DHD, Roberts AW, Dawson MA, Dawson SJ. Dynamic molecular monitoring reveals that SWI–SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma. Nat Med 2018; 25:119-129. [DOI: 10.1038/s41591-018-0243-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/21/2018] [Indexed: 11/09/2022]
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12
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Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M. Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis. Cell 2018; 173:260-274.e25. [PMID: 29551266 PMCID: PMC5871718 DOI: 10.1016/j.cell.2018.02.030] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 12/01/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023]
Abstract
Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking. We developed “multiplexed proteome dynamics profiling” (mPDP), a mass-spectrometry-based approach combining dynamic-SILAC labeling with isobaric mass tagging for multiplexed analysis of protein degradation and synthesis. In three proof-of-concept studies, we uncover different responses induced by the bromodomain inhibitor JQ1 versus a JQ1 proteolysis targeting chimera; we elucidate distinct modes of action of estrogen receptor modulators; and we comprehensively classify HSP90 clients based on their requirement for HSP90 constitutively or during synthesis, demonstrating that constitutive HSP90 clients have lower thermal stability than non-clients, have higher affinity for the chaperone, vary between cell types, and change upon external stimuli. These findings highlight the potential of mPDP to identify dynamically controlled degradation mechanisms in cellular systems. Multiplexed proteome dynamics profiling, mPDP, measures changes in proteostasis JQ1-PROTAC degrades a key mRNA export factor and blocks protein synthesis Raloxifene induces TMEM97 degradation dysregulating cholesterol homeostasis Characterization of proteins dependent on HSP90 constitutively or during synthesis
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Affiliation(s)
- Mikhail M Savitski
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Nico Zinn
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Daniel Poeckel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anne J Wagner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Katrin Strohmer
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephanie Melchert
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Massimo Petretich
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anna Rutkowska
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Johanna Vappiani
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Michael Steidel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gavain M Sweetman
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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13
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Burr ML, Sparbier CE, Chan YC, Williamson JC, Woods K, Beavis PA, Lam EYN, Henderson MA, Bell CC, Stolzenburg S, Gilan O, Bloor S, Noori T, Morgens DW, Bassik MC, Neeson PJ, Behren A, Darcy PK, Dawson SJ, Voskoboinik I, Trapani JA, Cebon J, Lehner PJ, Dawson MA. CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity. Nature 2017; 549:101-105. [PMID: 28813417 PMCID: PMC5706633 DOI: 10.1038/nature23643] [Citation(s) in RCA: 559] [Impact Index Per Article: 79.9] [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: 01/18/2017] [Accepted: 07/17/2017] [Indexed: 12/13/2022]
Abstract
Cancer cells exploit the expression of the programmed death-1 (PD-1) ligand 1 (PD-L1) to subvert T-cell-mediated immunosurveillance. The success of therapies that disrupt PD-L1-mediated tumour tolerance has highlighted the need to understand the molecular regulation of PD-L1 expression. Here we identify the uncharacterized protein CMTM6 as a critical regulator of PD-L1 in a broad range of cancer cells, by using a genome-wide CRISPR-Cas9 screen. CMTM6 is a ubiquitously expressed protein that binds PD-L1 and maintains its cell surface expression. CMTM6 is not required for PD-L1 maturation but co-localizes with PD-L1 at the plasma membrane and in recycling endosomes, where it prevents PD-L1 from being targeted for lysosome-mediated degradation. Using a quantitative approach to profile the entire plasma membrane proteome, we find that CMTM6 displays specificity for PD-L1. Notably, CMTM6 depletion decreases PD-L1 without compromising cell surface expression of MHC class I. CMTM6 depletion, via the reduction of PD-L1, significantly alleviates the suppression of tumour-specific T cell activity in vitro and in vivo. These findings provide insights into the biology of PD-L1 regulation, identify a previously unrecognized master regulator of this critical immune checkpoint and highlight a potential therapeutic target to overcome immune evasion by tumour cells.
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Affiliation(s)
- Marian L. Burr
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Rd, Cambridge CB2 0XY, UK
| | - Christina E. Sparbier
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
| | - James C. Williamson
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Rd, Cambridge CB2 0XY, UK
| | - Katherine Woods
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria 3086, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
| | - Paul A. Beavis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Enid Y. N. Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Melissa A. Henderson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Charles C. Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Sabine Stolzenburg
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Stuart Bloor
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Rd, Cambridge CB2 0XY, UK
| | - Tahereh Noori
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
| | - David W. Morgens
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Paul J. Neeson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Andreas Behren
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria 3086, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
| | - Phillip K. Darcy
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Ilia Voskoboinik
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Joseph A. Trapani
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
| | - Jonathan Cebon
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria 3086, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Rd, Cambridge CB2 0XY, UK
| | - Mark A. Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3052, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Australia
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14
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House IG, House CM, Brennan AJ, Gilan O, Dawson MA, Whisstock JC, Law RH, Trapani JA, Voskoboinik I. Regulation of perforin activation and pre-synaptic toxicity through C-terminal glycosylation. EMBO Rep 2017; 18:1775-1785. [PMID: 28808112 DOI: 10.15252/embr.201744351] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 04/11/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 11/09/2022] Open
Abstract
Perforin is a highly cytotoxic pore-forming protein essential for immune surveillance by cytotoxic lymphocytes. Prior to delivery to target cells by exocytosis, perforin is stored in acidic secretory granules where it remains functionally inert. However, how cytotoxic lymphocytes remain protected from their own perforin prior to its export to secretory granules, particularly in the Ca2+-rich endoplasmic reticulum, remains unknown. Here, we show that N-linked glycosylation of the perforin C-terminus at Asn549 within the endoplasmic reticulum inhibits oligomerisation of perforin monomers and thus protects the host cell from premature pore formation. Subsequent removal of this glycan occurs through proteolytic processing of the C-terminus within secretory granules and is imperative for perforin activation prior to secretion. Despite evolutionary conservation of the C-terminus, we found that processing is carried out by multiple proteases, which we attribute to the unstructured and exposed nature of the region. In sum, our studies reveal a post-translational regulatory mechanism essential for maintaining perforin in an inactive state until its secretion from the inhibitory acidic environment of the secretory granule.
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Affiliation(s)
- Imran G House
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Colin M House
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia
| | - Amelia J Brennan
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Omer Gilan
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Centre for Cancer Research, University of Melbourne, Melbourne, Vic., Australia.,Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic., Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Vic., Australia
| | - Ruby Hp Law
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic., Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Vic., Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Ilia Voskoboinik
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
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15
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Tyler DS, Vappiani J, Cañeque T, Lam EYN, Ward A, Gilan O, Chan YC, Hienzsch A, Rutkowska A, Werner T, Wagner AJ, Lugo D, Gregory R, Ramirez Molina C, Garton N, Wellaway CR, Jackson S, MacPherson L, Figueiredo M, Stolzenburg S, Bell CC, House C, Dawson SJ, Hawkins ED, Drewes G, Prinjha RK, Rodriguez R, Grandi P, Dawson MA. Click chemistry enables preclinical evaluation of targeted epigenetic therapies. Science 2017; 356:1397-1401. [PMID: 28619718 DOI: 10.1126/science.aal2066] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 06/01/2017] [Indexed: 12/12/2022]
Abstract
The success of new therapies hinges on our ability to understand their molecular and cellular mechanisms of action. We modified BET bromodomain inhibitors, an epigenetic-based therapy, to create functionally conserved compounds that are amenable to click chemistry and can be used as molecular probes in vitro and in vivo. We used click proteomics and click sequencing to explore the gene regulatory function of BRD4 (bromodomain containing protein 4) and the transcriptional changes induced by BET inhibitors. In our studies of mouse models of acute leukemia, we used high-resolution microscopy and flow cytometry to highlight the heterogeneity of drug activity within tumor cells located in different tissue compartments. We also demonstrate the differential distribution and effects of BET inhibitors in normal and malignant cells in vivo. This study provides a potential framework for the preclinical assessment of a wide range of drugs.
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Affiliation(s)
- Dean S Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Johanna Vappiani
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Tatiana Cañeque
- Chemical Cell Biology Group, Institut Curie, Paris Sciences et Lettres Research University, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.,CNRS UMR3666, 75005 Paris, France.,INSERM U1143, 75005 Paris, France
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Aoife Ward
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Antje Hienzsch
- Chemical Cell Biology Group, Institut Curie, Paris Sciences et Lettres Research University, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.,CNRS UMR3666, 75005 Paris, France.,INSERM U1143, 75005 Paris, France
| | - Anna Rutkowska
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Anne J Wagner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Dave Lugo
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Richard Gregory
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Cesar Ramirez Molina
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Neil Garton
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Christopher R Wellaway
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Susan Jackson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Margarida Figueiredo
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sabine Stolzenburg
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Colin House
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Edwin D Hawkins
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Gerard Drewes
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Rab K Prinjha
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Raphaël Rodriguez
- Chemical Cell Biology Group, Institut Curie, Paris Sciences et Lettres Research University, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.,CNRS UMR3666, 75005 Paris, France.,INSERM U1143, 75005 Paris, France
| | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany.
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.,Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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16
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Ghisi M, Kats L, Masson F, Li J, Kratina T, Vidacs E, Gilan O, Doyle MA, Newbold A, Bolden JE, Fairfax KA, de Graaf CA, Firth M, Zuber J, Dickins RA, Corcoran LM, Dawson MA, Belz GT, Johnstone RW. Id2 and E Proteins Orchestrate the Initiation and Maintenance of MLL-Rearranged Acute Myeloid Leukemia. Cancer Cell 2016; 30:59-74. [PMID: 27374225 DOI: 10.1016/j.ccell.2016.05.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 02/29/2016] [Accepted: 05/31/2016] [Indexed: 12/19/2022]
Abstract
E proteins and their antagonists, the Id proteins, are transcriptional regulators important for normal hematopoiesis. We found that Id2 acts as a key regulator of leukemia stem cell (LSC) potential in MLL-rearranged acute myeloid leukemia (AML). Low endogenous Id2 expression is associated with LSC enrichment while Id2 overexpression impairs MLL-AF9-leukemia initiation and growth. Importantly, MLL-AF9 itself controls the E-protein pathway by suppressing Id2 while directly activating E2-2 expression, and E2-2 depletion phenocopies Id2 overexpression in MLL-AF9-AML cells. Remarkably, Id2 tumor-suppressive function is conserved in t(8;21) AML. Low expression of Id2 and its associated gene signature are associated with poor prognosis in MLL-rearranged and t(8;21) AML patients, identifying the Id2/E-protein axis as a promising new therapeutic target in AML.
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MESH Headings
- Animals
- Cell Proliferation
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 8/genetics
- Gene Expression Regulation, Leukemic
- Humans
- Inhibitor of Differentiation Protein 2/genetics
- Inhibitor of Differentiation Protein 2/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Neoplasms, Experimental
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Prognosis
- Stem Cells/cytology
- Stem Cells/metabolism
- Survival Analysis
- Transcription Factor 7-Like 2 Protein/genetics
- Transcription Factor 7-Like 2 Protein/metabolism
- Translocation, Genetic
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Affiliation(s)
- Margherita Ghisi
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia; Australian Centre for Blood Diseases, Monash University, Melbourne, 3004 VIC, Australia.
| | - Lev Kats
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3010 VIC, Australia
| | - Frederick Masson
- Cancer Inflammation Laboratory, Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, 3084 VIC, Australia; Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Jason Li
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3010 VIC, Australia; Bioinformatics Core, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia
| | - Tobias Kratina
- Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Eva Vidacs
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia
| | - Omer Gilan
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3010 VIC, Australia
| | - Maria A Doyle
- Research Computing Facility, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia
| | - Andrea Newbold
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3010 VIC, Australia
| | - Jessica E Bolden
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia; Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC, Australia
| | - Kirsten A Fairfax
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia; Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC, Australia
| | - Carolyn A de Graaf
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia; Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC, Australia
| | - Matthew Firth
- Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Melbourne, 3004 VIC, Australia
| | - Lynn M Corcoran
- Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Mark A Dawson
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3010 VIC, Australia
| | - Gabrielle T Belz
- Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Ricky W Johnstone
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, 3002 VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3010 VIC, Australia.
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17
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Gilan O, Lam EYN, Becher I, Lugo D, Cannizzaro E, Joberty G, Ward A, Wiese M, Fong CY, Ftouni S, Tyler D, Stanley K, MacPherson L, Weng CF, Chan YC, Ghisi M, Smil D, Carpenter C, Brown P, Garton N, Blewitt ME, Bannister AJ, Kouzarides T, Huntly BJP, Johnstone RW, Drewes G, Dawson SJ, Arrowsmith CH, Grandi P, Prinjha RK, Dawson MA. Functional interdependence of BRD4 and DOT1L in MLL leukemia. Nat Struct Mol Biol 2016; 23:673-81. [PMID: 27294782 DOI: 10.1038/nsmb.3249] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [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: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 02/06/2023]
Abstract
Targeted therapies against disruptor of telomeric silencing 1-like (DOT1L) and bromodomain-containing protein 4 (BRD4) are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukemogenic transcription programs remain unclear. Using quantitative proteomics, chemoproteomics and biochemical fractionation, we found that native BRD4 and DOT1L exist in separate protein complexes. Genetic disruption or small-molecule inhibition of BRD4 and DOT1L showed marked synergistic activity against MLL leukemia cell lines, primary human leukemia cells and mouse leukemia models. Mechanistically, we found a previously unrecognized functional collaboration between DOT1L and BRD4 that is especially important at highly transcribed genes in proximity to superenhancers. DOT1L, via dimethylated histone H3 K79, facilitates histone H4 acetylation, which in turn regulates the binding of BRD4 to chromatin. These data provide new insights into the regulation of transcription and specify a molecular framework for therapeutic intervention in this disease with poor prognosis.
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MESH Headings
- Acetylation
- Animals
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Clinical Trials as Topic
- Disease Models, Animal
- Female
- Gene Expression Regulation, Leukemic
- Histone-Lysine N-Methyltransferase
- Histones/genetics
- Histones/metabolism
- Humans
- Leukemia, Biphenotypic, Acute/genetics
- Leukemia, Biphenotypic, Acute/metabolism
- Leukemia, Biphenotypic, Acute/pathology
- Male
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mice
- Mice, Inbred C57BL
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Primary Cell Culture
- Protein Binding
- Proteomics/methods
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Signal Transduction
- T-Lymphocytes/metabolism
- T-Lymphocytes/pathology
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Isabelle Becher
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Dave Lugo
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | | | - Gerard Joberty
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Aoife Ward
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Meike Wiese
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Chun Yew Fong
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sarah Ftouni
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dean Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kym Stanley
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Chen-Fang Weng
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Margherita Ghisi
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Peter Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Neil Garton
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge, UK
- Cambridge Stem Cell Institute, Cambridge, UK
| | - Ricky W Johnstone
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Paola Grandi
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
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18
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Fong CY, Gilan O, Lam EYN, Rubin AF, Ftouni S, Tyler D, Stanley K, Sinha D, Yeh P, Morison J, Giotopoulos G, Lugo D, Jeffrey P, Lee SCW, Carpenter C, Gregory R, Ramsay RG, Lane SW, Abdel-Wahab O, Kouzarides T, Johnstone RW, Dawson SJ, Huntly BJP, Prinjha RK, Papenfuss AT, Dawson MA. BET inhibitor resistance emerges from leukaemia stem cells. Nature 2015; 525:538-42. [PMID: 26367796 PMCID: PMC6069604 DOI: 10.1038/nature14888] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [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: 11/04/2014] [Accepted: 07/03/2015] [Indexed: 12/19/2022]
Abstract
Bromodomain and extra terminal protein (BET) inhibitors are first-in-class targeted therapies that deliver a new therapeutic opportunity by directly targeting bromodomain proteins that bind acetylated chromatin marks. Early clinical trials have shown promise, especially in acute myeloid leukaemia, and therefore the evaluation of resistance mechanisms is crucial to optimize the clinical efficacy of these drugs. Here we use primary mouse haematopoietic stem and progenitor cells immortalized with the fusion protein MLL-AF9 to generate several single-cell clones that demonstrate resistance, in vitro and in vivo, to the prototypical BET inhibitor, I-BET. Resistance to I-BET confers cross-resistance to chemically distinct BET inhibitors such as JQ1, as well as resistance to genetic knockdown of BET proteins. Resistance is not mediated through increased drug efflux or metabolism, but is shown to emerge from leukaemia stem cells both ex vivo and in vivo. Chromatin-bound BRD4 is globally reduced in resistant cells, whereas the expression of key target genes such as Myc remains unaltered, highlighting the existence of alternative mechanisms to regulate transcription. We demonstrate that resistance to BET inhibitors, in human and mouse leukaemia cells, is in part a consequence of increased Wnt/β-catenin signalling, and negative regulation of this pathway results in restoration of sensitivity to I-BET in vitro and in vivo. Together, these findings provide new insights into the biology of acute myeloid leukaemia, highlight potential therapeutic limitations of BET inhibitors, and identify strategies that may enhance the clinical utility of these unique targeted therapies.
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MESH Headings
- Animals
- Azepines/pharmacology
- Benzodiazepines/pharmacology
- Cell Cycle Proteins
- Cell Line, Tumor
- Cells, Cultured
- Chromatin/metabolism
- Clone Cells/drug effects
- Clone Cells/metabolism
- Clone Cells/pathology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic/drug effects
- Genes, myc/genetics
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/drug effects
- Hematopoietic Stem Cells/metabolism
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Molecular Targeted Therapy
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/metabolism
- Transcription, Genetic/drug effects
- Triazoles/pharmacology
- Wnt Signaling Pathway/drug effects
- beta Catenin/metabolism
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Affiliation(s)
- Chun Yew Fong
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Alan F Rubin
- Bioinformatics Division, The Walter &Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sarah Ftouni
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Dean Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
| | - Kym Stanley
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Devbarna Sinha
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Paul Yeh
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Jessica Morison
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust-MRC Stem Cell Institute, Cambridge CB2 0XY, UK
| | - George Giotopoulos
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust-MRC Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Dave Lugo
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Philip Jeffrey
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christopher Carpenter
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA
| | - Richard Gregory
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Robert G Ramsay
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
| | - Steven W Lane
- QIMR Berghofer Medical Research Institute, University of Queensland, Brisbane, Queensland 4029, Australia
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Ricky W Johnstone
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust-MRC Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Anthony T Papenfuss
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
- Bioinformatics Division, The Walter &Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, Victoria 3002, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
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19
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Gilan O, Diesch J, Amalia M, Jastrzebski K, Chueh AC, Verrills NM, Pearson RB, Mariadason JM, Tulchinsky E, Hannan RD, Dhillon AS. PR55α-containing protein phosphatase 2A complexes promote cancer cell migration and invasion through regulation of AP-1 transcriptional activity. Oncogene 2015; 34:1340. [PMID: 25740609 DOI: 10.1038/onc.2014.460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Diesch J, Sanij E, Gilan O, Love C, Tran H, Fleming NI, Ellul J, Amalia M, Haviv I, Pearson RB, Tulchinsky E, Mariadason JM, Sieber OM, Hannan RD, Dhillon AS. Widespread FRA1-dependent control of mesenchymal transdifferentiation programs in colorectal cancer cells. PLoS One 2014; 9:e88950. [PMID: 24658684 PMCID: PMC3962334 DOI: 10.1371/journal.pone.0088950] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 01/16/2014] [Indexed: 12/31/2022] Open
Abstract
Tumor invasion and metastasis involves complex remodeling of gene expression programs governing epithelial homeostasis. Mutational activation of the RAS-ERK is a frequent occurrence in many cancers and has been shown to drive overexpression of the AP-1 family transcription factor FRA1, a potent regulator of migration and invasion in a variety of tumor cell types. However, the nature of FRA1 transcriptional targets and the molecular pathways through which they promote tumor progression remain poorly understood. We found that FRA1 was strongly expressed in tumor cells at the invasive front of human colorectal cancers (CRCs), and that its depletion suppressed mesenchymal-like features in CRC cells in vitro. Genome-wide analysis of FRA1 chromatin occupancy and transcriptional regulation identified epithelial-mesenchymal transition (EMT)-related genes as a major class of direct FRA1 targets in CRC cells. Expression of the pro-mesenchymal subset of these genes predicted adverse outcomes in CRC patients, and involved FRA-1-dependent regulation and cooperation with TGFβ signaling pathway. Our findings reveal an unexpectedly widespread and direct role for FRA1 in control of epithelial-mesenchymal plasticity in CRC cells, and suggest that FRA1 plays an important role in mediating cross talk between oncogenic RAS-ERK and TGFβ signaling networks during tumor progression.
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Affiliation(s)
- Jeannine Diesch
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Elaine Sanij
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
| | - Omer Gilan
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Christopher Love
- Walter and Eliza Institute of Medical Research, Victoria, Australia
| | - Hoanh Tran
- Ludwig Institute for Cancer Research, Victoria, Australia
| | | | - Jason Ellul
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Marcia Amalia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Izhak Haviv
- Faculty of Medicine, Bar-Ilan University, Tel-Aviv, Israel
| | - Richard B. Pearson
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Eugene Tulchinsky
- School of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | | | - Oliver M. Sieber
- Walter and Eliza Institute of Medical Research, Victoria, Australia
| | - Ross D. Hannan
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
- School of Biomedical Sciences, University of Queensland, Queensland, Australia
| | - Amardeep S. Dhillon
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
- * E-mail:
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21
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Gilan O, Diesch J, Amalia M, Jastrzebski K, Chueh AC, Verrills NM, Pearson RB, Mariadason JM, Tulchinsky E, Hannan RD, Dhillon AS. PR55α-containing protein phosphatase 2A complexes promote cancer cell migration and invasion through regulation of AP-1 transcriptional activity. Oncogene 2014; 34:1333-9. [DOI: 10.1038/onc.2014.26] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 12/17/2013] [Accepted: 12/18/2013] [Indexed: 01/11/2023]
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22
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Pakay JL, Diesch J, Gilan O, Yip YY, Sayan E, Kolch W, Mariadason JM, Hannan RD, Tulchinsky E, Dhillon AS. A 19S proteasomal subunit cooperates with an ERK MAPK-regulated degron to regulate accumulation of Fra-1 in tumour cells. Oncogene 2011; 31:1817-24. [DOI: 10.1038/onc.2011.375] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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