1
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Chan WF, Coughlan HD, Ruhle M, Iannarella N, Alvarado C, Groom JR, Keenan CR, Kueh AJ, Wheatley AK, Smyth GK, Allan RS, Johanson TM. Survey of activation-induced genome architecture reveals a novel enhancer of Myc. Immunol Cell Biol 2023; 101:345-357. [PMID: 36710659 PMCID: PMC10952581 DOI: 10.1111/imcb.12626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023]
Abstract
The transcription factor Myc is critically important in driving cell proliferation, a function that is frequently dysregulated in cancer. To avoid this dysregulation Myc is tightly controlled by numerous layers of regulation. One such layer is the use of distal regulatory enhancers to drive Myc expression. Here, using chromosome conformation capture to examine B cells of the immune system in the first hours after their activation, we reveal a previously unidentified enhancer of Myc. The interactivity of this enhancer coincides with a dramatic, but discrete, spike in Myc expression 3 h post-activation. However, genetic deletion of this region, has little impact on Myc expression, Myc protein level or in vitro and in vivo cell proliferation. Examination of the enhancer deleted regulatory landscape suggests that enhancer redundancy likely sustains Myc expression. This work highlights not only the importance of temporally examining enhancers, but also the complexity and dynamics of the regulation of critical genes such as Myc.
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Affiliation(s)
- Wing Fuk Chan
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Michelle Ruhle
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Carolina Alvarado
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Joanna R Groom
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Christine R Keenan
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Adam K Wheatley
- Department of Microbiology and ImmunologyUniversity of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- School of Mathematics and StatisticsThe University of MelbourneParkvilleVICAustralia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVICAustralia
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2
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Zhang S, Rautela J, Bediaga NG, Kolesnik TB, You Y, Nie J, Dagley LF, Bedo J, Wang H, Sun L, Sutherland R, Surgenor E, Iannarella N, Allan R, Souza-Fonseca-Guimaraes F, Xie Y, Wang Q, Zhang Y, Xu Y, Nutt SL, Lew AM, Huntington ND, Nicholson SE, Chopin M, Zhan Y. CIS controls the functional polarization of GM-CSF-derived macrophages. Cell Mol Immunol 2023; 20:65-79. [PMID: 36471114 PMCID: PMC9794780 DOI: 10.1038/s41423-022-00957-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
The cytokine granulocyte-macrophage-colony stimulating factor (GM-CSF) possesses the capacity to differentiate monocytes into macrophages (MØs) with opposing functions, namely, proinflammatory M1-like MØs and immunosuppressive M2-like MØs. Despite the importance of these opposing biological outcomes, the intrinsic mechanism that regulates the functional polarization of MØs under GM-CSF signaling remains elusive. Here, we showed that GM-CSF-induced MØ polarization resulted in the expression of cytokine-inducible SH2-containing protein (CIS) and that CIS deficiency skewed the differentiation of monocytes toward immunosuppressive M2-like MØs. CIS deficiency resulted in hyperactivation of the JAK-STAT5 signaling pathway, consequently promoting downregulation of the transcription factor Interferon Regulatory Factor 8 (IRF8). Loss- and gain-of-function approaches highlighted IRF8 as a critical regulator of the M1-like polarization program. In vivo, CIS deficiency induced the differentiation of M2-like macrophages, which promoted strong Th2 immune responses characterized by the development of severe experimental asthma. Collectively, our results reveal a CIS-modulated mechanism that clarifies the opposing actions of GM-CSF in MØ differentiation and uncovers the role of GM-CSF in controlling allergic inflammation.
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Affiliation(s)
- Shengbo Zhang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jai Rautela
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- oNKo-Innate Pty Ltd, Moonee Ponds, VIC, Australia
| | - Naiara G Bediaga
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tatiana B Kolesnik
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Yue You
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Junli Nie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Laura F Dagley
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Bedo
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Computing and Information Systems, University of Melbourne, Parkville, VIC, Australia
| | - Hanqing Wang
- Department of Respiratory Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Centre, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Sun
- College of Biological Science, Anhui Normal University, Hefei, China
| | - Robyn Sutherland
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Elliot Surgenor
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Nadia Iannarella
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Rhys Allan
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Yi Xie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Duke, Singapore
| | - Qike Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yuxia Zhang
- Department of Respiratory Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Centre, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yuekang Xu
- College of Biological Science, Anhui Normal University, Hefei, China
| | - Stephen L Nutt
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew M Lew
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Nicholas D Huntington
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- oNKo-Innate Pty Ltd, Moonee Ponds, VIC, Australia
| | - Sandra E Nicholson
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Michaël Chopin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Yifan Zhan
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
- Drug Discovery, Shanghai Huaota Biopharm, Shanghai, China.
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3
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Chan WF, Coughlan HD, Iannarella N, Smyth GK, Johanson TM, Keenan CR, Allan RS. Identification and characterization of the long noncoding RNA Dreg1 as a novel regulator of Gata3. Immunol Cell Biol 2020; 99:323-332. [PMID: 32970351 DOI: 10.1111/imcb.12408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/03/2020] [Accepted: 09/22/2020] [Indexed: 01/05/2023]
Abstract
The eukaryotic genome is three-dimensionally segregated into discrete globules of topologically associating domains (TADs), within which numerous cis-regulatory elements such as enhancers and promoters interact to regulate gene expression. In this study, we identify a T-cell-specific sub-TAD containing the Gata3 locus, and reveal a previously uncharacterized long noncoding RNA (Dreg1) within a distant enhancer lying approximately 280 kb downstream of Gata3. Dreg1 expression is highly correlated with that of Gata3 during early immune system development and T helper type 2 cell differentiation. Inhibition and overexpression of Dreg1 suggest that it may be involved in the establishment, but not in the maintenance of Gata3 expression. Overall, we propose that Dreg1 is a novel regulator of Gata3 and may inform therapeutic strategies in diseases such allergy and lymphoma, where Gata3 has a pathological role.
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Affiliation(s)
- Wing Fuk Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Christine R Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
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4
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Keenan CR, Iannarella N, Garnham AL, Brown AC, Kim RY, Horvat JC, Hansbro PM, Nutt SL, Allan RS. Polycomb repressive complex 2 is a critical mediator of allergic inflammation. JCI Insight 2019; 4:127745. [PMID: 31092733 DOI: 10.1172/jci.insight.127745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Strategies that intervene with the development of immune-mediated diseases are urgently needed, as current treatments mostly focus on alleviating symptoms rather than reversing the disease. Targeting enzymes involved in epigenetic modifications to chromatin represents an alternative strategy that has the potential to perturb the function of the lymphocytes that drive the immune response. Here, we report that 2 major epigenetic silencing pathways are increased after T cell activation. By specific inactivation of these molecules in the T cell compartment in vivo, we demonstrate that the polycomb repressive complex 2 (PRC2) is essential for the generation of allergic responses. Furthermore, we show that small-molecule inhibition of the PRC2 methyltransferase, enhancer of zeste homolog 2 (Ezh2), reduces allergic inflammation in mice. Therefore, by systematically surveying the pathways involved in epigenetic gene silencing we have identified Ezh2 as a target for the suppression of allergic disease.
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Affiliation(s)
- Christine R Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandra C Brown
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia
| | - Richard Y Kim
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia
| | - Jay C Horvat
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
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5
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Vasanthakumar A, Xu D, Lun AT, Kueh AJ, van Gisbergen KP, Iannarella N, Li X, Yu L, Wang D, Williams BR, Lee SC, Majewski IJ, Godfrey DI, Smyth GK, Alexander WS, Herold MJ, Kallies A, Nutt SL, Allan RS. A non-canonical function of Ezh2 preserves immune homeostasis. EMBO Rep 2017; 18:619-631. [PMID: 28223321 DOI: 10.15252/embr.201643237] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [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: 08/18/2016] [Revised: 01/18/2017] [Accepted: 01/22/2017] [Indexed: 12/22/2022] Open
Abstract
Enhancer of zeste 2 (Ezh2) mainly methylates lysine 27 of histone-H3 (H3K27me3) as part of the polycomb repressive complex 2 (PRC2) together with Suz12 and Eed. However, Ezh2 can also modify non-histone substrates, although it is unclear whether this mechanism has a role during development. Here, we present evidence for a chromatin-independent role of Ezh2 during T-cell development and immune homeostasis. T-cell-specific depletion of Ezh2 induces a pronounced expansion of natural killer T (NKT) cells, although Ezh2-deficient T cells maintain normal levels of H3K27me3. In contrast, removal of Suz12 or Eed destabilizes canonical PRC2 function and ablates NKT cell development completely. We further show that Ezh2 directly methylates the NKT cell lineage defining transcription factor PLZF, leading to its ubiquitination and subsequent degradation. Sustained PLZF expression in Ezh2-deficient mice is associated with the expansion of a subset of NKT cells that cause immune perturbation. Taken together, we have identified a chromatin-independent function of Ezh2 that impacts on the development of the immune system.
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Affiliation(s)
- Ajithkumar Vasanthakumar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Dakang Xu
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou, China.,Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Aaron Tl Lun
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Klaas Pjm van Gisbergen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Xiaofang Li
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou, China.,Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Liang Yu
- Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Die Wang
- Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Bryan Rg Williams
- Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Stanley Cw Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Ian J Majewski
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Vic., Australia.,ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, Vic., Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Mathematics and Statistics, The University of Melbourne, Parkville, Vic., Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Axel Kallies
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia .,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia .,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
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