1
|
Alanazi M, Weng T, McLeod L, Gearing LJ, Smith JA, Kumar B, Saad MI, Jenkins BJ. Cytosolic DNA sensor AIM2 promotes KRAS-driven lung cancer independent of inflammasomes. Cancer Sci 2024. [PMID: 38594840 DOI: 10.1111/cas.16171] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/10/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024] Open
Abstract
Constitutively active KRAS mutations are among the major drivers of lung cancer, yet the identity of molecular co-operators of oncogenic KRAS in the lung remains ill-defined. The innate immune cytosolic DNA sensor and pattern recognition receptor (PRR) Absent-in-melanoma 2 (AIM2) is best known for its assembly of multiprotein inflammasome complexes and promoting an inflammatory response. Here, we define a role for AIM2, independent of inflammasomes, in KRAS-addicted lung adenocarcinoma (LAC). In genetically defined and experimentally induced (nicotine-derived nitrosamine ketone; NNK) LAC mouse models harboring the KrasG12D driver mutation, AIM2 was highly upregulated compared with other cytosolic DNA sensors and inflammasome-associated PRRs. Genetic ablation of AIM2 in KrasG12D and NNK-induced LAC mouse models significantly reduced tumor growth, coincident with reduced cellular proliferation in the lung. Bone marrow chimeras suggest a requirement for AIM2 in KrasG12D-driven LAC in both hematopoietic (immune) and non-hematopoietic (epithelial) cellular compartments, which is supported by upregulated AIM2 expression in immune and epithelial cells of mutant KRAS lung tissues. Notably, protection against LAC in AIM2-deficient mice is associated with unaltered protein levels of mature Caspase-1 and IL-1β inflammasome effectors. Moreover, genetic ablation of the key inflammasome adapter, ASC, did not suppress KrasG12D-driven LAC. In support of these in vivo findings, AIM2, but not mature Caspase-1, was upregulated in human LAC patient tumor biopsies. Collectively, our findings reveal that endogenous AIM2 plays a tumor-promoting role, independent of inflammasomes, in mutant KRAS-addicted LAC, and suggest innate immune DNA sensing may provide an avenue to explore new therapeutic strategies in lung cancer.
Collapse
Affiliation(s)
- Mohammad Alanazi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Teresa Weng
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Louise McLeod
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Julian A Smith
- Department of Surgery, School of Clinical Sciences/Monash Health, Monash University, Clayton, Victoria, Australia
| | - Beena Kumar
- Department of Anatomical Pathology, Monash Health, Clayton, Victoria, Australia
| | - Mohamed I Saad
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), The University of Adelaide, Adelaide, South Australia, Australia
| |
Collapse
|
2
|
Bichet MC, Adderley J, Avellaneda-Franco L, Magnin-Bougma I, Torriero-Smith N, Gearing LJ, Deffrasnes C, David C, Pepin G, Gantier MP, Lin RCY, Patwa R, Moseley GW, Doerig C, Barr JJ. Mammalian cells internalize bacteriophages and use them as a resource to enhance cellular growth and survival. PLoS Biol 2023; 21:e3002341. [PMID: 37883333 PMCID: PMC10602308 DOI: 10.1371/journal.pbio.3002341] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/19/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate diverse and unexplored symbioses. Yet the impact these bacteriophages may have on mammalian cellular and immunological processes is poorly understood. Here, we applied highly purified phage T4, free from bacterial by-products and endotoxins to mammalian cells and analyzed the cellular responses using luciferase reporter and antibody microarray assays. Phage preparations were applied in vitro to either A549 lung epithelial cells, MDCK-I kidney cells, or primary mouse bone marrow derived macrophages with the phage-free supernatant serving as a comparative control. Highly purified T4 phages were rapidly internalized by mammalian cells and accumulated within macropinosomes but did not activate the inflammatory DNA response TLR9 or cGAS-STING pathways. Following 8 hours of incubation with T4 phage, whole cell lysates were analyzed via antibody microarray that detected expression and phosphorylation levels of human signaling proteins. T4 phage application led to the activation of AKT-dependent pathways, resulting in an increase in cell metabolism, survival, and actin reorganization, the last being critical for macropinocytosis and potentially regulating a positive feedback loop to drive further phage internalization. T4 phages additionally down-regulated CDK1 and its downstream effectors, leading to an inhibition of cell cycle progression and an increase in cellular growth through a prolonged G1 phase. These interactions demonstrate that highly purified T4 phages do not activate DNA-mediated inflammatory pathways but do trigger protein phosphorylation cascades that promote cellular growth and survival. We conclude that mammalian cells are internalizing bacteriophages as a resource to promote cellular growth and metabolism.
Collapse
Affiliation(s)
- Marion C. Bichet
- School of Biological Sciences, Monash University, Clayton, Australia
- ACTALIA, Food Safety Department, Saint-Lô, France
- University of Lorraine, CNRS, LCPME, Vandœuvre-lès-Nancy, France
| | - Jack Adderley
- School of Health and Biomedical Science, RMIT University, Bundoora, Australia
| | | | | | | | - Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Celine Deffrasnes
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Cassandra David
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Genevieve Pepin
- Medical Biology Department, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Ruby CY Lin
- Centre for Infectious Diseases and Microbiology; The Westmead Institute for Medical Research, Westmead, Australia
| | - Ruzeen Patwa
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Gregory W. Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Christian Doerig
- School of Health and Biomedical Science, RMIT University, Bundoora, Australia
| | - Jeremy J. Barr
- School of Biological Sciences, Monash University, Clayton, Australia
| |
Collapse
|
3
|
Ullah TR, Johansen MD, Balka KR, Ambrose RL, Gearing LJ, Roest J, Vivian JP, Sapkota S, Jayasekara WSN, Wenholz DS, Aldilla VR, Zeng J, Miemczyk S, Nguyen DH, Hansbro NG, Venkatraman R, Kang JH, Pang ES, Thomas BJ, Alharbi AS, Rezwan R, O'Keeffe M, Donald WA, Ellyard JI, Wong W, Kumar N, Kile BT, Vinuesa CG, Kelly GE, Laczka OF, Hansbro PM, De Nardo D, Gantier MP. Pharmacological inhibition of TBK1/IKKε blunts immunopathology in a murine model of SARS-CoV-2 infection. Nat Commun 2023; 14:5666. [PMID: 37723181 PMCID: PMC10507085 DOI: 10.1038/s41467-023-41381-9] [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: 01/02/2023] [Accepted: 09/03/2023] [Indexed: 09/20/2023] Open
Abstract
TANK-binding kinase 1 (TBK1) is a key signalling component in the production of type-I interferons, which have essential antiviral activities, including against SARS-CoV-2. TBK1, and its homologue IκB kinase-ε (IKKε), can also induce pro-inflammatory responses that contribute to pathogen clearance. While initially protective, sustained engagement of type-I interferons is associated with damaging hyper-inflammation found in severe COVID-19 patients. The contribution of TBK1/IKKε signalling to these responses is unknown. Here we find that the small molecule idronoxil inhibits TBK1/IKKε signalling through destabilisation of TBK1/IKKε protein complexes. Treatment with idronoxil, or the small molecule inhibitor MRT67307, suppresses TBK1/IKKε signalling and attenuates cellular and molecular lung inflammation in SARS-CoV-2-challenged mice. Our findings additionally demonstrate that engagement of STING is not the major driver of these inflammatory responses and establish a critical role for TBK1/IKKε signalling in SARS-CoV-2 hyper-inflammation.
Collapse
Affiliation(s)
- Tomalika R Ullah
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Matt D Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Katherine R Balka
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Rebecca L Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - James Roest
- St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Julian P Vivian
- St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
- Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Sunil Sapkota
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - W Samantha N Jayasekara
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Daniel S Wenholz
- Noxopharm Limited, Chatswood, NSW, Australia
- School of Chemistry, UNSW Sydney, Kensington, NSW, Australia
| | - Vina R Aldilla
- School of Chemistry, UNSW Sydney, Kensington, NSW, Australia
| | - Jun Zeng
- MedChemSoft Solutions, Ferntree Gully, VIC, Australia
| | - Stefan Miemczyk
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Duc H Nguyen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Nicole G Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Rajan Venkatraman
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jung Hee Kang
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ee Shan Pang
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Belinda J Thomas
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Monash Lung and Sleep, Monash Medical Centre, Clayton, VIC, Australia
| | - Arwaf S Alharbi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Turabah, Saudi Arabia
| | - Refaya Rezwan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Meredith O'Keeffe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | | | - Julia I Ellyard
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Wilson Wong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Kensington, NSW, Australia
| | - Benjamin T Kile
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Carola G Vinuesa
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Francis Crick Institute, London, UK
| | | | | | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Dominic De Nardo
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
4
|
Marks ZRC, Campbell NK, Mangan NE, Vandenberg CJ, Gearing LJ, Matthews AY, Gould JA, Tate MD, Wray-McCann G, Ying L, Rosli S, Brockwell N, Parker BS, Lim SS, Bilandzic M, Christie EL, Stephens AN, de Geus E, Wakefield MJ, Ho GY, McNally O, McNeish IA, Bowtell DDL, de Weerd NA, Scott CL, Bourke NM, Hertzog PJ. Interferon-ε is a tumour suppressor and restricts ovarian cancer. Nature 2023; 620:1063-1070. [PMID: 37587335 DOI: 10.1038/s41586-023-06421-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
High-grade serous ovarian cancers have low survival rates because of their late presentation with extensive peritoneal metastases and frequent chemoresistance1, and require new treatments guided by novel insights into pathogenesis. Here we describe the intrinsic tumour-suppressive activities of interferon-ε (IFNε). IFNε is constitutively expressed in epithelial cells of the fallopian tube, the cell of origin of high-grade serous ovarian cancers, and is then lost during development of these tumours. We characterize its anti-tumour activity in several preclinical models: ovarian cancer patient-derived xenografts, orthotopic and disseminated syngeneic models, and tumour cell lines with or without mutations in Trp53 and Brca genes. We use manipulation of the IFNε receptor IFNAR1 in different cell compartments, differential exposure status to IFNε and global measures of IFN signalling to show that the mechanism of the anti-tumour activity of IFNε involves direct action on tumour cells and, crucially, activation of anti-tumour immunity. IFNε activated anti-tumour T and natural killer cells and prevented the accumulation and activation of myeloid-derived suppressor cells and regulatory T cells. Thus, we demonstrate that IFNε is an intrinsic tumour suppressor in the female reproductive tract whose activities in models of established and advanced ovarian cancer, distinct from other type I IFNs, are compelling indications of potential new therapeutic approaches for ovarian cancer.
Collapse
Affiliation(s)
- Zoe R C Marks
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Nicole K Campbell
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Niamh E Mangan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Cassandra J Vandenberg
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Antony Y Matthews
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Jodee A Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Michelle D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Georgie Wray-McCann
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Le Ying
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Sarah Rosli
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Natasha Brockwell
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Belinda S Parker
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - San S Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Maree Bilandzic
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | | | - Andrew N Stephens
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Eveline de Geus
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Orla McNally
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
- Royal Women's Hospital, Parkville, Victoria, Australia
| | - Iain A McNeish
- Ovarian Cancer Action Research Centre, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - David D L Bowtell
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Nicole A de Weerd
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Royal Women's Hospital, Parkville, Victoria, Australia
| | - Nollaig M Bourke
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
- Department of Medical Gerontology, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
5
|
D'Adamo GL, Chonwerawong M, Gearing LJ, Marcelino VR, Gould JA, Rutten EL, Solari SM, Khoo PWR, Wilson TJ, Thomason T, Gulliver EL, Hertzog PJ, Giles EM, Forster SC. Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease. Cell Rep Med 2023; 4:101124. [PMID: 37467722 PMCID: PMC10394256 DOI: 10.1016/j.xcrm.2023.101124] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/19/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade-specific metagenomic analysis identifies key, functionally distinct Enterococcus clades associated with either IBD or health. Strain-specific in vitro validation demonstrates differences in cell cytotoxicity and inflammatory signaling in intestinal epithelial cells, consistent with the colonic mucosa-specific response measured in patients with IBD. This demonstrates the importance of strain-specific phenotypes and consideration of anatomical sites in exploring the dysregulated host-bacterial interactions in IBD.
Collapse
Affiliation(s)
- Gemma L D'Adamo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Jodee A Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Rutten
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Sean M Solari
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Patricia W R Khoo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia
| | - Trevor J Wilson
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; MHTP Medical Genomics Facility, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Tamblyn Thomason
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Gulliver
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Edward M Giles
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia.
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia.
| |
Collapse
|
6
|
Gressier E, Schulte-Schrepping J, Petrov L, Brumhard S, Stubbemann P, Hiller A, Obermayer B, Spitzer J, Kostevc T, Whitney PG, Bachem A, Odainic A, van de Sandt C, Nguyen THO, Ashhurst T, Wilson K, Oates CVL, Gearing LJ, Meischel T, Hochheiser K, Greyer M, Clarke M, Kreutzenbeck M, Gabriel SS, Kastenmüller W, Kurts C, Londrigan SL, Kallies A, Kedzierska K, Hertzog PJ, Latz E, Chen YCE, Radford KJ, Chopin M, Schroeder J, Kurth F, Gebhardt T, Sander LE, Sawitzki B, Schultze JL, Schmidt SV, Bedoui S. CD4 + T cell calibration of antigen-presenting cells optimizes antiviral CD8 + T cell immunity. Nat Immunol 2023; 24:979-990. [PMID: 37188942 DOI: 10.1038/s41590-023-01517-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/13/2023] [Indexed: 05/17/2023]
Abstract
Antiviral CD8+ T cell immunity depends on the integration of various contextual cues, but how antigen-presenting cells (APCs) consolidate these signals for decoding by T cells remains unclear. Here, we describe gradual interferon-α/interferon-β (IFNα/β)-induced transcriptional adaptations that endow APCs with the capacity to rapidly activate the transcriptional regulators p65, IRF1 and FOS after CD4+ T cell-mediated CD40 stimulation. While these responses operate through broadly used signaling components, they induce a unique set of co-stimulatory molecules and soluble mediators that cannot be elicited by IFNα/β or CD40 alone. These responses are critical for the acquisition of antiviral CD8+ T cell effector function, and their activity in APCs from individuals infected with severe acute respiratory syndrome coronavirus 2 correlates with milder disease. These observations uncover a sequential integration process whereby APCs rely on CD4+ T cells to select the innate circuits that guide antiviral CD8+ T cell responses.
Collapse
Affiliation(s)
- Elise Gressier
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Jonas Schulte-Schrepping
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Lev Petrov
- Translational Immunology, Berlin Institute of Health (BIH) & Charité University Medicine, Berlin, Germany
| | - Sophia Brumhard
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Paula Stubbemann
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Hiller
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany
| | - Jasper Spitzer
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Tomislav Kostevc
- Translational Immunology, Berlin Institute of Health (BIH) & Charité University Medicine, Berlin, Germany
| | - Paul G Whitney
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Annabell Bachem
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alexandru Odainic
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Carolien van de Sandt
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Ashhurst
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, Centenary Institute and University of Sydney, Sydney, New South Wales, Australia
| | - Kayla Wilson
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Clare V L Oates
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Tina Meischel
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Katharina Hochheiser
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marie Greyer
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michele Clarke
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Sarah S Gabriel
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wolfgang Kastenmüller
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Christian Kurts
- Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Sarah L Londrigan
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Yu-Chen E Chen
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Kristen J Radford
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael Chopin
- Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jan Schroeder
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Florian Kurth
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas Gebhardt
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leif E Sander
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Birgit Sawitzki
- Translational Immunology, Berlin Institute of Health (BIH) & Charité University Medicine, Berlin, Germany
| | - Joachim L Schultze
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, Bonn, Germany
| | | | - Sammy Bedoui
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
- Institute of Experimental Immunology, University of Bonn, Bonn, Germany.
| |
Collapse
|
7
|
Coldbeck-Shackley RC, Romeo O, Rosli S, Gearing LJ, Gould JA, Lim SS, Van der Hoek KH, Eyre NS, Shue B, Robertson SA, Best SM, Tate MD, Hertzog PJ, Beard MR. Constitutive expression and distinct properties of IFN-epsilon protect the female reproductive tract from Zika virus infection. PLoS Pathog 2023; 19:e1010843. [PMID: 36897927 PMCID: PMC10032502 DOI: 10.1371/journal.ppat.1010843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/22/2023] [Accepted: 02/03/2023] [Indexed: 03/11/2023] Open
Abstract
The immunological surveillance factors controlling vulnerability of the female reproductive tract (FRT) to sexually transmitted viral infections are not well understood. Interferon-epsilon (IFNɛ) is a distinct, immunoregulatory type-I IFN that is constitutively expressed by FRT epithelium and is not induced by pathogens like other antiviral IFNs α, β and λ. We show the necessity of IFNɛ for Zika Virus (ZIKV) protection by: increased susceptibility of IFNɛ-/- mice; their "rescue" by intravaginal recombinant IFNɛ treatment and blockade of protective endogenous IFNɛ by neutralising antibody. Complementary studies in human FRT cell lines showed IFNɛ had potent anti-ZIKV activity, associated with transcriptome responses similar to IFNλ but lacking the proinflammatory gene signature of IFNα. IFNɛ activated STAT1/2 pathways similar to IFNα and λ that were inhibited by ZIKV-encoded non-structural (NS) proteins, but not if IFNε exposure preceded infection. This scenario is provided by the constitutive expression of endogenous IFNε. However, the IFNɛ expression was not inhibited by ZIKV NS proteins despite their ability to antagonise the expression of IFNβ or λ. Thus, the constitutive expression of IFNɛ provides cellular resistance to viral strategies of antagonism and maximises the antiviral activity of the FRT. These results show that the unique spatiotemporal properties of IFNε provides an innate immune surveillance network in the FRT that is a significant barrier to viral infection with important implications for prevention and therapy.
Collapse
Affiliation(s)
- Rosa C Coldbeck-Shackley
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Ornella Romeo
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Sarah Rosli
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia
| | - Jodee A Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia
| | - San S Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia
| | - Kylie H Van der Hoek
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Nicholas S Eyre
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Byron Shue
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Sarah A Robertson
- Robinson Research Institute, The University of Adelaide, South Australia, Australia
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton Montana, United States of America
| | - Michelle D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia
| | - Michael R Beard
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| |
Collapse
|
8
|
Leibel SL, McVicar RN, Murad R, Kwong EM, Clark AE, Alvarado A, Grimmig BA, Nuryyev R, Young RE, Lee JC, Peng W, Zhu YP, Griffis E, Nowell CJ, Liu K, James B, Alarcon S, Malhotra A, Gearing LJ, Hertzog PJ, Galapate CM, Galenkamp KM, Commisso C, Smith DM, Sun X, Carlin AF, Croker BA, Snyder EY. The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense. bioRxiv 2023:2023.01.26.525578. [PMID: 36747824 PMCID: PMC9900938 DOI: 10.1101/2023.01.26.525578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes an acute respiratory distress syndrome (ARDS) that resembles surfactant deficient RDS. Using a novel multi-cell type, human induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system, validated against primary lung cells, we found that inflammatory cytokine/chemokine production and interferon (IFN) responses are dynamically regulated autonomously within the lung following SARS-CoV-2 infection, an intrinsic defense mechanism mediated by surfactant proteins (SP). Single cell RNA sequencing revealed broad infectability of most lung cell types through canonical (ACE2) and non-canonical (endocytotic) viral entry routes. SARS-CoV-2 triggers rapid apoptosis, impairing viral dissemination. In the absence of surfactant protein B (SP-B), resistance to infection was impaired and cytokine/chemokine production and IFN responses were modulated. Exogenous surfactant, recombinant SP-B, or genomic correction of the SP-B deletion restored resistance to SARS-CoV-2 and improved viability.
Collapse
|
9
|
Dankers W, Northcott M, Bennett T, D’Cruz A, Sherlock R, Gearing LJ, Hertzog P, Russ B, Miceli I, Scheer S, Fujishiro M, Hayakawa K, Ikeda K, Morand EF, Jones SA. Type 1 interferon suppresses expression and glucocorticoid induction of glucocorticoid-induced leucine zipper (GILZ). Front Immunol 2022; 13:1034880. [PMID: 36505447 PMCID: PMC9727222 DOI: 10.3389/fimmu.2022.1034880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/02/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
SLE is a systemic multi-organ autoimmune condition associated with reduced life expectancy and quality of life. Glucocorticoids (GC) are heavily relied on for SLE treatment but are associated with detrimental metabolic effects. Type 1 interferons (IFN) are central to SLE pathogenesis and may confer GC insensitivity. Glucocorticoid-induced leucine zipper (GILZ) mediates many effects of GC relevant to SLE pathogenesis, but the effect of IFN on GC regulation of GILZ is unknown. We performed in vitro experiments using human PBMC to examine the effect of IFN on GILZ expression. JAK inhibitors tofacitinib and tosylate salt were used in vivo and in vitro respectively to investigate JAK-STAT pathway dependence of our observations. ChiP was performed to examine glucocorticoid receptor (GR) binding at the GILZ locus. Several public data sets were mined for correlating clinical data. High IFN was associated with suppressed GILZ and reduced GILZ relevant to GC exposure in a large SLE population. IFN directly reduced GILZ expression and suppressed the induction of GILZ by GC in vitro in human leukocytes. IFN actions on GILZ expression were dependent on the JAK1/Tyk2 pathway, as evidenced by loss of the inhibitory effect of IFN on GILZ in the presence of JAK inhibitors. Activation of this pathway led to reduced GR binding in key regulatory regions of the GILZ locus. IFN directly suppresses GILZ expression and GILZ upregulation by GC, indicating a potential mechanism for IFN-induced GC resistance. This work has important implications for the ongoing development of targeted GC-sparing therapeutics in SLE.
Collapse
Affiliation(s)
- Wendy Dankers
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Melissa Northcott
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Taylah Bennett
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Akshay D’Cruz
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Rochelle Sherlock
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
| | - Paul Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
| | - Brendan Russ
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Iolanda Miceli
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Sebastian Scheer
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Maki Fujishiro
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Kunihiro Hayakawa
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Keigo Ikeda
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan,Department of Internal Medicine and Rheumatology, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Eric F. Morand
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia
| | - Sarah A. Jones
- Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia,*Correspondence: Sarah A. Jones,
| |
Collapse
|
10
|
Johansen MD, Mahbub RM, Idrees S, Nguyen DH, Miemczyk S, Pathinayake P, Nichol K, Hansbro NG, Gearing LJ, Hertzog PJ, Gallego-Ortega D, Britton WJ, Saunders BM, Wark PA, Faiz A, Hansbro PM. Increased SARS-CoV-2 Infection, Protease, and Inflammatory Responses in Chronic Obstructive Pulmonary Disease Primary Bronchial Epithelial Cells Defined with Single-Cell RNA Sequencing. Am J Respir Crit Care Med 2022; 206:712-729. [PMID: 35549656 PMCID: PMC9799113 DOI: 10.1164/rccm.202108-1901oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rationale: Patients with chronic obstructive pulmonary disease (COPD) develop more severe coronavirus disease (COVID-19); however, it is unclear whether they are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and what mechanisms are responsible for severe disease. Objectives: To determine whether SARS-CoV-2 inoculated primary bronchial epithelial cells (pBECs) from patients with COPD support greater infection and elucidate the effects and mechanisms involved. Methods: We performed single-cell RNA sequencing analysis on differentiated pBECs from healthy subjects and patients with COPD 7 days after SARS-CoV-2 inoculation. We correlated changes with viral titers, proinflammatory responses, and IFN production. Measurements and Main Results: Single-cell RNA sequencing revealed that COPD pBECs had 24-fold greater infection than healthy cells, which was supported by plaque assays. Club/goblet and basal cells were the predominant populations infected and expressed mRNAs involved in viral replication. Proteases involved in SARS-CoV-2 entry/infection (TMPRSS2 and CTSB) were increased, and protease inhibitors (serpins) were downregulated more so in COPD. Inflammatory cytokines linked to COPD exacerbations and severe COVID-19 were increased, whereas IFN responses were blunted. Coexpression analysis revealed a prominent population of club/goblet cells with high type 1/2 IFN responses that were important drivers of immune responses to infection in both healthy and COPD pBECs. Therapeutic inhibition of proteases and inflammatory imbalances reduced viral titers and cytokine responses, particularly in COPD pBECs. Conclusions: COPD pBECs are more susceptible to SARS-CoV-2 infection because of increases in coreceptor expression and protease imbalances and have greater inflammatory responses. A prominent cluster of IFN-responsive club/goblet cells emerges during infection, which may be important drivers of immunity. Therapeutic interventions suppress SARS-CoV-2 replication and consequent inflammation.
Collapse
Affiliation(s)
- Matt D. Johansen
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Rashad M. Mahbub
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Sobia Idrees
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Duc H. Nguyen
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Stefan Miemczyk
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Prabuddha Pathinayake
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
| | - Kristy Nichol
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
| | - Nicole G. Hansbro
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Linden J. Gearing
- Department of Molecular and Translational Sciences, School of Clinical Sciences at Monash Health, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Paul J. Hertzog
- Department of Molecular and Translational Sciences, School of Clinical Sciences at Monash Health, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - David Gallego-Ortega
- Faculty of Engineering and Information Technology, School of Biomedical Engineering, Centre for Single Cell Technology, University of Technology Sydney, Ultimo, New South Wales, Australia;,Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia;,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia; and
| | - Warwick J. Britton
- Centenary Institute, University of Sydney and Department of Clinical Immunology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Bernadette M. Saunders
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Peter A. Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
| | - Alen Faiz
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Philip M. Hansbro
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia;,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
| |
Collapse
|
11
|
Northcott M, Gearing LJ, Bonin J, Koelmeyer R, Hoi A, Hertzog PJ, Morand EF. Immunosuppressant exposure confounds gene expression analysis in systemic lupus erythematosus. Front Immunol 2022; 13:964263. [PMID: 36059457 PMCID: PMC9430375 DOI: 10.3389/fimmu.2022.964263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesThe analysis of gene module expression in SLE is emerging as a tool to identify active biological pathways, with the aim of developing targeted therapies for subsets of patients. Detailed information on the effect of immunosuppressants on gene module expression is lacking. We aimed to examine the impact of medication exposure on gene module expression.MethodsA set of commercially available disease-relevant gene modules were measured in 730 whole blood samples from a dedicated lupus clinic on whom prospectively collected, contemporaneous clinical data including medication exposure were available.ResultsCompared to heathy controls, SLE patients showed over-expression of IFN and under-expression of B cell, T cell and pDC modules. Neutrophil module over-expression and under-expression of B and T cell modules were observed in patients with active lupus nephritis or highly active disease (SLEDAI-2K > 8), while Lupus Low Disease Activity State (LLDAS) had inverse associations. Disease activity in other organ domains was not associated with specific gene modules. In contrast, medications were associated with multiple effects. Glucocorticoid use was associated with under-expression of T cell, B cell and plasmablast modules, and over-expression of neutrophil modules. Mycophenolate and azathioprine exposure were associated with plasmablast module and B cell module under-expression respectively. Disease activity associations with neutrophil over-expression and lymphocyte module under-expression were attenuated by multivariable adjustment for medication exposure.ConclusionMedications have significant effect on gene module expression in SLE patients. These findings emphasize the need to control for medications in studies of gene expression in SLE.
Collapse
Affiliation(s)
- Melissa Northcott
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
| | - Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Julie Bonin
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
| | - Rachel Koelmeyer
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
| | - Alberta Hoi
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
| | - Paul J. Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Eric F. Morand
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
- *Correspondence: Eric F. Morand,
| |
Collapse
|
12
|
Dawson RE, Deswaerte V, West AC, Tang K, West AJ, Balic JJ, Gearing LJ, Saad MI, Yu L, Wu Y, Bhathal PS, Kumar B, Chakrabarti JT, Zavros Y, Oshima H, Klinman DM, Oshima M, Tan P, Jenkins BJ. STAT3-mediated upregulation of the AIM2 DNA sensor links innate immunity with cell migration to promote epithelial tumourigenesis. Gut 2022; 71:1515-1531. [PMID: 34489308 DOI: 10.1136/gutjnl-2020-323916] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/27/2021] [Indexed: 01/26/2023]
Abstract
OBJECTIVE The absent in melanoma 2 (AIM2) cytosolic pattern recognition receptor and DNA sensor promotes the pathogenesis of autoimmune and chronic inflammatory diseases via caspase-1-containing inflammasome complexes. However, the role of AIM2 in cancer is ill-defined. DESIGN The expression of AIM2 and its clinical significance was assessed in human gastric cancer (GC) patient cohorts. Genetic or therapeutic manipulation of AIM2 expression and activity was performed in the genetically engineered gp130 F/F spontaneous GC mouse model, as well as human GC cell line xenografts. The biological role and mechanism of action of AIM2 in gastric tumourigenesis, including its involvement in inflammasome activity and functional interaction with microtubule-associated end-binding protein 1 (EB1), was determined in vitro and in vivo. RESULTS AIM2 expression is upregulated by interleukin-11 cytokine-mediated activation of the oncogenic latent transcription factor STAT3 in the tumour epithelium of GC mouse models and patients with GC. Genetic and therapeutic targeting of AIM2 in gp130 F/F mice suppressed tumourigenesis. Conversely, AIM2 overexpression augmented the tumour load of human GC cell line xenografts. The protumourigenic function of AIM2 was independent of inflammasome activity and inflammation. Rather, in vivo and in vitro AIM2 physically interacted with EB1 to promote epithelial cell migration and tumourigenesis. Furthermore, upregulated expression of AIM2 and EB1 in the tumour epithelium of patients with GC was independently associated with poor patient survival. CONCLUSION AIM2 can play a driver role in epithelial carcinogenesis by linking cytokine-STAT3 signalling, innate immunity and epithelial cell migration, independent of inflammasome activation.
Collapse
Affiliation(s)
- Ruby E Dawson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Virginie Deswaerte
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Alison C West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Ke Tang
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Alice J West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Jesse J Balic
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Mohamed I Saad
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Liang Yu
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Yonghui Wu
- Cellular and Molecular Research, National Cancer Centre of Singapore, Singapore
| | - Prithi S Bhathal
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Beena Kumar
- Department of Anatomical Pathology, Monash Health, Clayton, Victoria, Australia
| | - Jayati T Chakrabarti
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Yana Zavros
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Hiroko Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Dennis M Klinman
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Patrick Tan
- Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.,Genome Institute of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia .,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
13
|
Bourke NM, Achilles SL, Huang SUS, Cumming HE, Lim SS, Papageorgiou I, Gearing LJ, Chapman R, Thakore S, Mangan NE, Mesiano S, Hertzog PJ. Spatiotemporal regulation of human IFNε and innate immunity in the female reproductive tract. JCI Insight 2022; 7:135407. [PMID: 35862222 DOI: 10.1172/jci.insight.135407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 07/22/2020] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Although published studies have demonstrated that interferon epsilon (IFNε) has a crucial role in regulating protective immunity in the mouse female reproductive tract (mFRT), expression and regulation of IFNε in the human female reproductive tract (hFRT) have not been characterised. To characterise human IFNε, we obtained hFRT samples from a well- characterized cohort of women, enabling us to comprehensively assess ex vivo IFNε expression in the hFRT at various stages of the menstrual cycle. We found that among the various types of IFNs, IFNε is uniquely selectively and constitutively expressed in the hFRT epithelium. It has distinct expression patterns in the surface and glandular epithelia of the upper hFRT compared with basal layers of the stratified squamous epithelia of the lower hFRT. There is cyclical variation of IFNε expression in the endometrial epithelium of the upper hFRT and not in the distal FRT, consistent with selective endometrial expression of the progesterone receptor and regulation of the IFNE promoter by progesterone. Since we show IFNε stimulates important protective IFN-regulated genes (IRGs) in FRT epithelium, this characterisation is a key element in understanding the mechanisms of hormonal control of mucosal immunity.
Collapse
Affiliation(s)
| | | | - Stephanie U-Shane Huang
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Helen E Cumming
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - San S Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Irene Papageorgiou
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Ross Chapman
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Suruchi Thakore
- Department of Obstetrics and Gynecology, Case Western Reserve University, Cleveland, United States of America
| | - Niamh E Mangan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Sam Mesiano
- Department of Reproductive Biology, Case Western Reserve University, Cleveland, United States of America
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| |
Collapse
|
14
|
West AJ, Deswaerte V, West AC, Gearing LJ, Tan P, Jenkins BJ. Inflammasome-Associated Gastric Tumorigenesis Is Independent of the NLRP3 Pattern Recognition Receptor. Front Oncol 2022; 12:830350. [PMID: 35299732 PMCID: PMC8921257 DOI: 10.3389/fonc.2022.830350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/28/2022] [Indexed: 12/24/2022] Open
Abstract
Inflammasomes are important multiprotein regulatory complexes of innate immunity and have recently emerged as playing divergent roles in numerous inflammation-associated cancers. Among these include gastric cancer (GC), the third leading cause of cancer-associated death worldwide, and we have previously discovered a pro-tumorigenic role for the key inflammasome adaptor apoptosis-associated speck-like protein containing a CARD (ASC) in the spontaneous genetic gp130F/F mouse model for GC. However, the identity of the specific pattern recognition receptors (PRRs) that activate tumor-promoting inflammasomes during GC is unknown. Here, we investigated the role of the best-characterized inflammasome-associated PRR, nucleotide-binding domain, and leucine-rich repeat containing receptor, pyrin domain-containing (NLRP) 3, in GC. In gastric tumors of gp130F/F mice, although NLRP3 expression was elevated at the mRNA (qPCR) and protein (immunohistochemistry) levels, genetic ablation of NLRP3 in gp130F/F:Nlrp3-/- mice did not alleviate the development of gastric tumors. Similarly, cellular processes associated with tumorigenesis in the gastric mucosa, namely, proliferation, apoptosis, and inflammation, were comparable between gp130F/F and gp130F/F:Nlrp3-/- mice. Furthermore, inflammasome activation levels, determined by immunoblotting and immunohistochemistry for cleaved Caspase-1, which along with ASC is another integral component of inflammasome complexes, were unchanged in gp130F/F and gp130F/F:Nlrp3-/- gastric tumors. We also observed variable NLRP3 expression levels (mRNA and protein) among independent GC patient cohorts, and NLRP3 was not prognostic for survival outcomes. Taken together, these data suggest that NLRP3 does not play a major role in promoting inflammasome-driven gastric tumorigenesis, and thus pave the way for further investigations to uncover the key inflammasome-associated PRR implicated in GC.
Collapse
Affiliation(s)
- Alice J West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Virginie Deswaerte
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Alison C West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Patrick Tan
- Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.,Genome Institute of Singapore, Singapore, Singapore.,Cancer Sciences Institute of Singapore, National University of Singapore, Institute of Singapore, Singapore, Singapore
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| |
Collapse
|
15
|
Lundy J, Gearing LJ, Gao H, West AC, McLeod L, Deswaerte V, Yu L, Porazinski S, Pajic M, Hertzog PJ, Croagh D, Jenkins BJ. TLR2 activation promotes tumour growth and associates with patient survival and chemotherapy response in pancreatic ductal adenocarcinoma. Oncogene 2021; 40:6007-6022. [PMID: 34400766 DOI: 10.1038/s41388-021-01992-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis, and is plagued by a paucity of targeted treatment options and tumour resistance to chemotherapeutics. The causal link between chronic inflammation and PDAC suggests that molecular regulators of the immune system promote disease pathogenesis and/or therapeutic resistance, yet their identity is unclear. Here, we couple endoscopic ultrasound-guided fine-needle aspiration, which captures tumour biopsies from all stages, with whole transcriptome profiling of PDAC patient primary tumours to reveal enrichment of the innate immune Toll-like receptor 2 (TLR2) molecular pathway. Augmented TLR2 expression associated with a 4-gene "TLR2 activation" signature, and was prognostic for survival and predictive for gemcitabine-based chemoresistance. Furthermore, antibody-mediated anti-TLR2 therapy suppressed the growth of human PDAC tumour xenografts, independent of a functional immune system. Our results support TLR2-based therapeutic targeting for precision medicine in PDAC, with further clinical utility that TLR2 activation is prognostic and predictive for chemoresponsiveness.
Collapse
Affiliation(s)
- Joanne Lundy
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Hugh Gao
- Department of Surgery (School of Clinical Sciences at Monash Health), Monash University, Clayton, VIC, Australia
| | - Alison C West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Louise McLeod
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Virginie Deswaerte
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Liang Yu
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Sean Porazinski
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Daniel Croagh
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Surgery (School of Clinical Sciences at Monash Health), Monash University, Clayton, VIC, Australia
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
16
|
Prompsy PB, Toubia J, Gearing LJ, Knight RL, Forster SC, Bracken CP, Gantier MP. Making use of transcription factor enrichment to identify functional microRNA-regulons. Comput Struct Biotechnol J 2021; 19:4896-4903. [PMID: 34522293 PMCID: PMC8426468 DOI: 10.1016/j.csbj.2021.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/31/2022] Open
Abstract
microRNAs (miRNAs) are important modulators of messenger RNA stability and translation, controlling wide gene networks. Albeit generally modest on individual targets, the regulatory effect of miRNAs translates into meaningful pathway modulation through concurrent targeting of regulons with functional convergence. Identification of miRNA-regulons is therefore essential to understand the function of miRNAs and to help realise their therapeutic potential, but it remains challenging due to the large number of false positive target sites predicted per miRNA. In the current work, we investigated whether genes regulated by a given miRNA were under the transcriptional control of a predominant transcription factor (TF). Strikingly we found that for ~50% of the miRNAs analysed, their targets were significantly enriched in at least one common TF. We leveraged such miRNA-TF co-regulatory networks to identify pathways under miRNA control, and demonstrated that filtering predicted miRNA-target interactions (MTIs) relying on such pathways significantly enriched the proportion of predicted true MTIs. To our knowledge, this is the first description of an in- silico pipeline facilitating the identification of miRNA-regulons, to help understand miRNA function.
Collapse
Affiliation(s)
- Pacôme B Prompsy
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia.,CNRS UMR3244, Institut Curie, PSL Research University, Paris 75005, France.,Translational Research Department, Institut Curie, PSL Research University, Paris 75005, France
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Frome Road, Adelaide, South Australia 5000, Australia.,School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Randle L Knight
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia.,School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.,Department of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| |
Collapse
|
17
|
Budden CF, Gearing LJ, Kaiser R, Standke L, Hertzog PJ, Latz E. Inflammasome-induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses. J Extracell Vesicles 2021; 10:e12127. [PMID: 34377374 PMCID: PMC8329986 DOI: 10.1002/jev2.12127] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/29/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Infectious organisms and damage of cells can activate inflammasomes, which mediate tissue inflammation and adaptive immunity. These mechanisms evolved to curb the spread of microbes and to induce repair of the damaged tissue. Chronic activation of inflammasomes, however, contributes to non-resolving inflammatory responses that lead to immuno-pathologies. Inflammasome-activated cells undergo an inflammatory cell death associated with the release of potent pro-inflammatory cytokines and poorly characterized extracellular vesicles (EVs). Since inflammasome-induced EVs could signal inflammasome pathway activation in patients with chronic inflammation and modulate bystander cell activation, we performed a systems analysis of the ribonucleic acid (RNA) content and function of two EV classes. We show that EVs released from inflammasome-activated macrophages carry a specific RNA signature and contain interferon β (IFNβ). EV-associated IFNβ induces an interferon signature in bystander cells and results in dampening of NLRP3 inflammasome responses. EVs could, therefore, serve as biomarkers for inflammasome activation and act to prevent systemic hyper-inflammatory states by restricting NLRP3 activation in bystander cells.
Collapse
Affiliation(s)
- Christina F. Budden
- Institute of Innate ImmunityUniversity HospitalUniversity of BonnBonnGermany
- Department of Microbiology and ImmunologyThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia
| | - Linden J. Gearing
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia
- Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Romina Kaiser
- Institute of Innate ImmunityUniversity HospitalUniversity of BonnBonnGermany
| | - Lena Standke
- Institute of Innate ImmunityUniversity HospitalUniversity of BonnBonnGermany
- Department of Microbiology and ImmunologyThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Paul J. Hertzog
- Department of Microbiology and ImmunologyThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia
- Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Eicke Latz
- Institute of Innate ImmunityUniversity HospitalUniversity of BonnBonnGermany
- Department of Infectious Diseases and ImmunologyUniversity of Massachusetts Medical SchoolWorcesterMassachusettsUSA
- German Centre for Neurodegenerative Diseases (DZNE)BonnGermany
| |
Collapse
|
18
|
Northcott M, Gearing LJ, Nim HT, Nataraja C, Hertzog P, Jones SA, Morand EF. Glucocorticoid gene signatures in systemic lupus erythematosus and the effects of type I interferon: a cross-sectional and in-vitro study. Lancet Rheumatol 2021; 3:e357-e370. [PMID: 38279391 DOI: 10.1016/s2665-9913(21)00006-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/14/2020] [Accepted: 01/06/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Glucocorticoids, used as a therapy in systemic lupus erythematosus (SLE), interact with the cytoplasmic glucocorticoid receptor to modulate gene transcription. Minimising the use of glucocorticoids is a goal in SLE; however, pharmacological measures to support clinical guidelines are scarce. We evaluated glucocorticoid-regulated genes for their potential use as biomarkers of glucocorticoid exposure in SLE. We examined interactions between changes in gene expression that are induced by glucocorticoids and type I interferon. METHODS Genes regulated by glucocorticoids and type I interferon were analysed in relation to glucocorticoid exposure in adult patients meeting the American College of Rheumatology criteria for SLE from three cross-sectional cohorts: a local cohort from a tertiary hospital in Melbourne, VIC, Australia, and two public datasets (GSE49454, Hospital de la Conception, Marseille, France, and GSE88884, patients enrolled in a large, multicentre clinical trial). RNA sequencing was done using RNA from healthy donor leucocytes treated with the glucocorticoid dexamethasone, or type I interferon, or both. FINDINGS Glucocorticoid-regulated genes were analysed in a local SLE cohort (n=18) and public dataset GSE49454 (n=62). Five genes correlated with glucocorticoid dose in both cohorts and were combined to make a glucocorticoid gene signature. Validity of the glucocorticoid gene signature was tested in the public dataset GSE88884 (n=1756). A dose-dependent association was observed with glucocorticoid dose (p<0·0001), and the glucocorticoid gene signature had moderate ability to identify patients taking high-dose glucocorticoid (area under the curve [AUC]=0·77) although was less discriminatory when including all doses (AUC=0·69). We saw no effect of glucocorticoid dose on type I interferon -regulated gene expression. Patients with a high type I interferon gene signature had reduced glucocorticoid gene signature expression compared with patients with a low type I interferon gene signature matched for glucocorticoid dose, suggesting type I interferon inhibits glucocorticoid-stimulated gene expression. In RNA sequencing experiments, type I interferon impaired the expression of glucocorticoid-induced genes, whereas dexamethasone had minimal effect on the expression of type I interferon-stimulated genes. We identified genes regulated by dexamethasone but not affected by type I interferon; combined signatures using these genes also showed moderate ability to distinguish patients taking glucocorticoids. INTERPRETATION A gene signature for glucocorticoid exposure was identified, but the substantial effect of type I interferon on glucocorticoid-induced genes might limit its application in SLE. These data confirm the insensitivity of type I interferon-regulated genes to glucocorticoids, and together support the concept that type I interferon has a role in glucocorticoid resistance in SLE. FUNDING Lupus Research Alliance and Australian National Health and Medical Research Council.
Collapse
Affiliation(s)
- Melissa Northcott
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
| | - Linden J Gearing
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Hieu T Nim
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia; Systems Biology Laboratory, Monash University, Clayton, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Champa Nataraja
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
| | - Paul Hertzog
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Sarah A Jones
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia
| | - Eric F Morand
- Centre for Inflammatory Diseases, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
19
|
Nataraja C, Dankers W, Flynn J, Lee JPW, Zhu W, Vincent FB, Gearing LJ, Ooi J, Pervin M, Cristofaro MA, Sherlock R, Hasnat MA, Harris J, Morand EF, Jones SA. GILZ Regulates the Expression of Pro-Inflammatory Cytokines and Protects Against End-Organ Damage in a Model of Lupus. Front Immunol 2021; 12:652800. [PMID: 33889157 PMCID: PMC8056982 DOI: 10.3389/fimmu.2021.652800] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Glucocorticoid-induced leucine zipper (GILZ) mimics many of the anti-inflammatory effects of glucocorticoids, suggesting it as a point of therapeutic intervention that could bypass GC adverse effects. We previously reported that GILZ down-regulation is a feature of human SLE, and loss of GILZ permits the development of autoantibodies and lupus-like autoimmunity in mice. To further query the contribution of GILZ to protection against autoimmune inflammation, we studied the development of the lupus phenotype in Lyn-deficient (Lyn-/-) mice in which GILZ expression was genetically ablated. In Lyn-/- mice, splenomegaly, glomerulonephritis, anti-dsDNA antibody titres and cytokine expression were exacerbated by GILZ deficiency, while other autoantibody titres and glomerular immune complex deposition were unaffected. Likewise, in patients with SLE, GILZ was inversely correlated with IL23A, and in SLE patients not taking glucocorticoids, GILZ was also inversely correlated with BAFF and IL18. This suggests that at the onset of autoimmunity, GILZ protects against tissue injury by modulating pro-inflammatory pathways, downstream of antibodies, to regulate the cycle of inflammation in SLE.
Collapse
Affiliation(s)
- Champa Nataraja
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Wendy Dankers
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Jacqueline Flynn
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Jacinta P W Lee
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Wendy Zhu
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Fabien B Vincent
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Department of Molecular and Translational Science, Hudson Institute, Melbourne, VIC, Australia
| | - Joshua Ooi
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Mehnaz Pervin
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Megan A Cristofaro
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Rochelle Sherlock
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Md Abul Hasnat
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - James Harris
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Eric F Morand
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| | - Sarah A Jones
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health, Melbourne, VIC, Australia
| |
Collapse
|
20
|
Li J, Hardy K, Olshansky M, Barugahare A, Gearing LJ, Prier JE, Sng XYX, Nguyen MLT, Piovesan D, Russ BE, La Gruta NL, Hertzog PJ, Rao S, Turner SJ. KDM6B-dependent chromatin remodeling underpins effective virus-specific CD8 + T cell differentiation. Cell Rep 2021; 34:108839. [PMID: 33730567 DOI: 10.1016/j.celrep.2021.108839] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/26/2020] [Revised: 11/24/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Naive CD8+ T cell activation results in an autonomous program of cellular proliferation and differentiation. However, the mechanisms that underpin this process are unclear. Here, we profile genome-wide changes in chromatin accessibility, gene transcription, and the deposition of a key chromatin modification (H3K27me3) early after naive CD8+ T cell activation. Rapid upregulation of the histone demethylase KDM6B prior to the first cell division is required for initiating H3K27me3 removal at genes essential for subsequent T cell differentiation and proliferation. Inhibition of KDM6B-dependent H3K27me3 demethylation limits the magnitude of an effective primary virus-specific CD8+ T cell response and the formation of memory CD8+ T cell populations. Accordingly, we define the early spatiotemporal events underpinning early lineage-specific chromatin reprogramming that are necessary for autonomous CD8+ T cell proliferation and differentiation.
Collapse
Affiliation(s)
- Jasmine Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kristine Hardy
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Bruce, ACT 2617, Australia
| | - Moshe Olshansky
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Adele Barugahare
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Linden J Gearing
- Hudson Institute for Medical Research, Clayton, VIC 3168, Australia
| | - Julia E Prier
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michelle Ly Thai Nguyen
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Dana Piovesan
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Brendan E Russ
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Paul J Hertzog
- Hudson Institute for Medical Research, Clayton, VIC 3168, Australia
| | - Sudha Rao
- QIMR Berghofer Gene Regulation and Translational Medicine Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Hudson Institute for Medical Research, Clayton, VIC 3168, Australia.
| |
Collapse
|
21
|
Dowling JK, Afzal R, Gearing LJ, Cervantes-Silva MP, Annett S, Davis GM, De Santi C, Assmann N, Dettmer K, Gough DJ, Bantug GR, Hamid FI, Nally FK, Duffy CP, Gorman AL, Liddicoat AM, Lavelle EC, Hess C, Oefner PJ, Finlay DK, Davey GP, Robson T, Curtis AM, Hertzog PJ, Williams BRG, McCoy CE. Mitochondrial arginase-2 is essential for IL-10 metabolic reprogramming of inflammatory macrophages. Nat Commun 2021; 12:1460. [PMID: 33674584 PMCID: PMC7936006 DOI: 10.1038/s41467-021-21617-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 01/29/2021] [Indexed: 01/31/2023] Open
Abstract
Mitochondria are important regulators of macrophage polarisation. Here, we show that arginase-2 (Arg2) is a microRNA-155 (miR-155) and interleukin-10 (IL-10) regulated protein localized at the mitochondria in inflammatory macrophages, and is critical for IL-10-induced modulation of mitochondrial dynamics and oxidative respiration. Mechanistically, the catalytic activity and presence of Arg2 at the mitochondria is crucial for oxidative phosphorylation. We further show that Arg2 mediates this process by increasing the activity of complex II (succinate dehydrogenase). Moreover, Arg2 is essential for IL-10-mediated downregulation of the inflammatory mediators succinate, hypoxia inducible factor 1α (HIF-1α) and IL-1β in vitro. Accordingly, HIF-1α and IL-1β are highly expressed in an LPS-induced in vivo model of acute inflammation using Arg2-/- mice. These findings shed light on a new arm of IL-10-mediated metabolic regulation, working to resolve the inflammatory status of the cell.
Collapse
Affiliation(s)
- Jennifer K Dowling
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- FutureNeuro, SFI Research Centre, Dublin 2, Ireland
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Remsha Afzal
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Mariana P Cervantes-Silva
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Stephanie Annett
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Gavin M Davis
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Nadine Assmann
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
- Immunobiology Laboratory, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Daniel J Gough
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Glenn R Bantug
- Immunobiology Laboratory, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Fidinny I Hamid
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Frances K Nally
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Conor P Duffy
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Aoife L Gorman
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Alex M Liddicoat
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Ed C Lavelle
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Christoph Hess
- Immunobiology Laboratory, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - David K Finlay
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Gavin P Davey
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Tracy Robson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Annie M Curtis
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Bryan R G Williams
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Claire E McCoy
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
- FutureNeuro, SFI Research Centre, Dublin 2, Ireland.
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia.
| |
Collapse
|
22
|
Owen KL, Gearing LJ, Zanker DJ, Brockwell NK, Khoo WH, Roden DL, Cmero M, Mangiola S, Hong MK, Spurling AJ, McDonald M, Chan C, Pasam A, Lyons RJ, Duivenvoorden HM, Ryan A, Butler LM, Mariadason JM, Giang Phan T, Hayes VM, Sandhu S, Swarbrick A, Corcoran NM, Hertzog PJ, Croucher PI, Hovens C, Parker BS. Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone. EMBO Rep 2020; 21:e50162. [PMID: 32314873 PMCID: PMC7271653 DOI: 10.15252/embr.202050162] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
The latency associated with bone metastasis emergence in castrate-resistant prostate cancer is attributed to dormancy, a state in which cancer cells persist prior to overt lesion formation. Using single-cell transcriptomics and ex vivo profiling, we have uncovered the critical role of tumor-intrinsic immune signaling in the retention of cancer cell dormancy. We demonstrate that loss of tumor-intrinsic type I IFN occurs in proliferating prostate cancer cells in bone. This loss suppresses tumor immunogenicity and therapeutic response and promotes bone cell activation to drive cancer progression. Restoration of tumor-intrinsic IFN signaling by HDAC inhibition increased tumor cell visibility, promoted long-term antitumor immunity, and blocked cancer growth in bone. Key findings were validated in patients, including loss of tumor-intrinsic IFN signaling and immunogenicity in bone metastases compared to primary tumors. Data herein provide a rationale as to why current immunotherapeutics fail in bone-metastatic prostate cancer, and provide a new therapeutic strategy to overcome the inefficacy of immune-based therapies in solid cancers.
Collapse
|
23
|
Faridi P, Li C, Ramarathinam SH, Illing PT, Mifsud NA, Ayala R, Song J, Gearing LJ, Croft NP, Purcell AW. Response to Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands". Sci Immunol 2020; 4:4/38/eaaw8457. [PMID: 31420321 DOI: 10.1126/sciimmunol.aaw8457] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
This is our response to the Technical Comment by Rolfs et al. where we point out errors in their reanalysis of our data.
Collapse
Affiliation(s)
- Pouya Faridi
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Chen Li
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Biology, Institute of Molecular Systems Biology, ETH-Zürich, Zürich 8093, Switzerland
| | - Sri H Ramarathinam
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rochelle Ayala
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jiangning Song
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, Victoria 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| |
Collapse
|
24
|
MacPherson L, Anokye J, Yeung MM, Lam EYN, Chan YC, Weng CF, Yeh P, Knezevic K, Butler MS, Hoegl A, Chan KL, Burr ML, Gearing LJ, Willson T, Liu J, Choi J, Yang Y, Bilardi RA, Falk H, Nguyen N, Stupple PA, Peat TS, Zhang M, de Silva M, Carrasco-Pozo C, Avery VM, Khoo PS, Dolezal O, Dennis ML, Nuttall S, Surjadi R, Newman J, Ren B, Leaver DJ, Sun Y, Baell JB, Dovey O, Vassiliou GS, Grebien F, Dawson SJ, Street IP, Monahan BJ, Burns CJ, Choudhary C, Blewitt ME, Voss AK, Thomas T, Dawson MA. HBO1 is required for the maintenance of leukaemia stem cells. Nature 2020; 577:266-270. [PMID: 31827282 DOI: 10.1038/s41586-019-1835-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [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: 09/05/2018] [Accepted: 11/12/2019] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukaemia (AML) is a heterogeneous disease characterized by transcriptional dysregulation that results in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, but most show only modest efficacy owing to an inability to effectively eradicate leukaemia stem cells (LSCs)1. Here, to specifically identify novel dependencies in LSCs, we screened a bespoke library of small hairpin RNAs that target chromatin regulators in a unique ex vivo mouse model of LSCs. We identify the MYST acetyltransferase HBO1 (also known as KAT7 or MYST2) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance. Using CRISPR domain screening and quantitative mass spectrometry, we identified the histone acetyltransferase domain of HBO1 as being essential in the acetylation of histone H3 at K14. H3 acetylated at K14 (H3K14ac) facilitates the processivity of RNA polymerase II to maintain the high expression of key genes (including Hoxa9 and Hoxa10) that help to sustain the functional properties of LSCs. To leverage this dependency therapeutically, we developed a highly potent small-molecule inhibitor of HBO1 and demonstrate its mode of activity as a competitive analogue of acetyl-CoA. Inhibition of HBO1 phenocopied our genetic data and showed efficacy in a broad range of human cell lines and primary AML cells from patients. These biological, structural and chemical insights into a therapeutic target in AML will enable the clinical translation of these findings.
Collapse
Affiliation(s)
- Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Juliana Anokye
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Miriam M Yeung
- Peter MacCallum Cancer Centre, Melbourne, 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
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen-Fang Weng
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul Yeh
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Miriam S Butler
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Annabelle Hoegl
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kah-Lok Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marian L Burr
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Linden J Gearing
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tracy Willson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joy Liu
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Jarny Choi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yuqing Yang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca A Bilardi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hendrik Falk
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Nghi Nguyen
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Paul A Stupple
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Thomas S Peat
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Ming Zhang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Melanie de Silva
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Catalina Carrasco-Pozo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Vicky M Avery
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Poh Sim Khoo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Children's Cancer Institute, Kensington, New South Wales, Australia
| | - Olan Dolezal
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Matthew L Dennis
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Stewart Nuttall
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Regina Surjadi
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Janet Newman
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Bin Ren
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - David J Leaver
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jonathan B Baell
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Oliver Dovey
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sarah-Jane Dawson
- 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
| | - Ian P Street
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Brendon J Monahan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The 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.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
| |
Collapse
|
25
|
Marks ZRC, Campbell N, deWeerd NA, Lim SS, Gearing LJ, Bourke NM, Hertzog PJ. PROPERTIES AND FUNCTIONS OF THE NOVEL TYPE I INTERFERON EPSILON. Semin Immunol 2019; 43:101328. [PMID: 31734130 DOI: 10.1016/j.smim.2019.101328] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 11/17/2022]
Abstract
Interferon epsilon (IFNε) is a type I IFN with unusual patterns of expression and therefore, function. It is constitutively expressed by reproductive tract epithelium and regulated by hormones during estrus cycle, reproduction, and menopause and by exogenous hormones. The IFNe protein is encoded by a gene in the type I IFN locus, binds to IFNAR1 and 2 which are required for signaling via the JAK STAT pathway. Its affinity for binding receptors and transducing signals is less potent than IFNα or β subtypes in vitro. Nevertheless, in vivo experiments indicate its efficacy in regulating mucosal immune responses and protecting from bacterial and viral infections. These studies demonstrate a different mechanism of action to type I IFNs. In this organ system with dynamic fluxes in cellularity, requirement to tolerate an implanted fetus, and be protected from disease, there is co-option of a special IFN from a family of effective immunoregulators, with unique controls and modified potency to make it a safe and effective constitutive reproductive tract cytokine.
Collapse
Affiliation(s)
- Zoe R C Marks
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Nicole Campbell
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Nicole A deWeerd
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - San S Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Nollaig M Bourke
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia; Department of Medical Gerontology, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia.
| |
Collapse
|
26
|
Faridi P, Li C, Ramarathinam SH, Vivian JP, Illing PT, Mifsud NA, Ayala R, Song J, Gearing LJ, Hertzog PJ, Ternette N, Rossjohn J, Croft NP, Purcell AW. A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands. Sci Immunol 2019; 3:3/28/eaar3947. [PMID: 30315122 DOI: 10.1126/sciimmunol.aar3947] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 05/29/2018] [Accepted: 08/31/2018] [Indexed: 12/19/2022]
Abstract
The diversity of peptides displayed by class I human leukocyte antigen (HLA) plays an essential role in T cell immunity. The peptide repertoire is extended by various posttranslational modifications, including proteasomal splicing of peptide fragments from distinct regions of an antigen to form nongenomically templated cis-spliced sequences. Previously, it has been suggested that a fraction of the immunopeptidome constitutes such cis-spliced peptides; however, because of computational limitations, it has not been possible to assess whether trans-spliced peptides (i.e., the fusion of peptide segments from distinct antigens) are also bound and presented by HLA molecules, and if so, in what proportion. Here, we have developed and applied a bioinformatic workflow and demonstrated that trans-spliced peptides are presented by HLA-I, and their abundance challenges current models of proteasomal splicing that predict cis-splicing as the most probable outcome. These trans-spliced peptides display canonical HLA-binding sequence features and are as frequently identified as cis-spliced peptides found bound to a number of different HLA-A and HLA-B allotypes. Structural analysis reveals that the junction between spliced peptides is highly solvent exposed and likely to participate in T cell receptor interactions. These results highlight the unanticipated diversity of the immunopeptidome and have important implications for autoimmunity, vaccine design, and immunotherapy.
Collapse
Affiliation(s)
- Pouya Faridi
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Chen Li
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Biology, Institute of Molecular Systems Biology,ETH Zurich, Zurich 8093, Switzerland
| | - Sri H Ramarathinam
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rochelle Ayala
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jiangning Song
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, Victoria 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia
| | | | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine,Heath Park, Cardiff CF14 4XN, UK
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| |
Collapse
|
27
|
Gearing LJ, Cumming HE, Chapman R, Finkel AM, Woodhouse IB, Luu K, Gould JA, Forster SC, Hertzog PJ. CiiiDER: A tool for predicting and analysing transcription factor binding sites. PLoS One 2019; 14:e0215495. [PMID: 31483836 PMCID: PMC6726224 DOI: 10.1371/journal.pone.0215495] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/05/2019] [Indexed: 12/30/2022] Open
Abstract
The availability of large amounts of high-throughput genomic, transcriptomic and epigenomic data has provided opportunity to understand regulation of the cellular transcriptome with an unprecedented level of detail. As a result, research has advanced from identifying gene expression patterns associated with particular conditions to elucidating signalling pathways that regulate expression. There are over 1,000 transcription factors (TFs) in vertebrates that play a role in this regulation. Determining which of these are likely to be controlling a set of genes can be assisted by computational prediction, utilising experimentally verified binding site motifs. Here we present CiiiDER, an integrated computational toolkit for transcription factor binding analysis, written in the Java programming language, to make it independent of computer operating system. It is operated through an intuitive graphical user interface with interactive, high-quality visual outputs, making it accessible to all researchers. CiiiDER predicts transcription factor binding sites (TFBSs) across regulatory regions of interest, such as promoters and enhancers derived from any species. It can perform an enrichment analysis to identify TFs that are significantly over- or under-represented in comparison to a bespoke background set and thereby elucidate pathways regulating sets of genes of pathophysiological importance.
Collapse
Affiliation(s)
- Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Helen E. Cumming
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Ross Chapman
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Alexander M. Finkel
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Isaac B. Woodhouse
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Kevin Luu
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Jodee A. Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Samuel C. Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
| | - Paul J. Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia
- * E-mail:
| |
Collapse
|
28
|
Brockwell NK, Rautela J, Owen KL, Gearing LJ, Deb S, Harvey K, Spurling A, Zanker D, Chan CL, Cumming HE, Deng N, Zakhour JM, Duivenvoorden HM, Robinson T, Harris M, White M, Fox J, Ooi C, Kumar B, Thomson J, Potasz N, Swarbrick A, Hertzog PJ, Molloy TJ, Toole SO, Ganju V, Parker BS. Tumor inherent interferon regulators as biomarkers of long-term chemotherapeutic response in TNBC. NPJ Precis Oncol 2019; 3:21. [PMID: 31482136 PMCID: PMC6715634 DOI: 10.1038/s41698-019-0093-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 08/09/2019] [Indexed: 02/07/2023] Open
Abstract
Patients diagnosed with triple negative breast cancer (TNBC) have an increased risk of rapid metastasis compared to other subtypes. Predicting long-term survival post-chemotherapy in patients with TNBC is difficult, yet enhanced infiltration of tumor infiltrating lymphocytes (TILs) has been associated with therapeutic response and reduced risk of metastatic relapse. Immune biomarkers that predict the immune state of a tumor and risk of metastatic relapse pre- or mid-neoadjuvant chemotherapy are urgently needed to allow earlier implementation of alternate therapies that may reduce TNBC patient mortality. Utilizing a neoadjuvant chemotherapy trial where TNBC patients had sequential biopsies taken, we demonstrate that measurement of T-cell subsets and effector function, specifically CD45RO expression, throughout chemotherapy predicts risk of metastatic relapse. Furthermore, we identified the tumor inherent interferon regulatory factor IRF9 as a marker of active intratumoral type I and II interferon (IFN) signaling and reduced risk of distant relapse. Functional implications of tumor intrinsic IFN signaling were demonstrated using an immunocompetent mouse model of TNBC, where enhanced type I IFN signaling increased anti-tumor immunity and metastasis-free survival post-chemotherapy. Using two independent adjuvant cohorts we were able to validate loss of IRF9 as a poor prognostic biomarker pre-chemotherapy. Thus, IRF9 expression may offer early insight into TNBC patient prognosis and tumor heat, allowing for identification of patients that are unlikely to respond to chemotherapy alone and could benefit from further immune-based therapeutic intervention.
Collapse
Affiliation(s)
- Natasha K. Brockwell
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Cancer Immunology and Therapeutics Programs, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jai Rautela
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Katie L. Owen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Cancer Immunology and Therapeutics Programs, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | | | - Kate Harvey
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Alex Spurling
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Cancer Immunology and Therapeutics Programs, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Damien Zanker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Cancer Immunology and Therapeutics Programs, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Chia-Ling Chan
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Helen E. Cumming
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Niantao Deng
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Jasmine M. Zakhour
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
| | - Hendrika M. Duivenvoorden
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
| | - Tina Robinson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
| | | | | | - Jane Fox
- Monash Health, Clayton, VIC Australia
- Monash Health School of Clinical Sciences, Monash University, Clayton, VIC Australia
| | | | | | | | | | - Alex Swarbrick
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Paul J. Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Tim J. Molloy
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW Australia
- St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW Australia
| | - Sandra O’ Toole
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Sydney, NSW Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW Australia
- Sydney Medical School, University of Sydney, Sydney, NSW Australia
- Australian Clinical Labs, Bella Vista, NSW Australia
| | - Vinod Ganju
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
- Monash Health, Clayton, VIC Australia
| | - Belinda S. Parker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Cancer Immunology and Therapeutics Programs, Peter MacCallum Cancer Centre, Melbourne, Australia
| |
Collapse
|
29
|
Prier JE, Li J, Gearing LJ, Olshansky M, Sng XYX, Hertzog PJ, Turner SJ. Early T-BET Expression Ensures an Appropriate CD8 + Lineage-Specific Transcriptional Landscape after Influenza A Virus Infection. J Immunol 2019; 203:1044-1054. [PMID: 31227580 DOI: 10.4049/jimmunol.1801431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/31/2019] [Indexed: 01/12/2023]
Abstract
Virus infection triggers large-scale changes in the phenotype and function of naive CD8+ T cells, resulting in the generation of effector and memory T cells that are then critical for immune clearance. The T-BOX family of transcription factors (TFs) are known to play a key role in T cell differentiation, with mice deficient for the TF T-BET (encoded by Tbx21) unable to generate optimal virus-specific effector responses. Although the importance of T-BET in directing optimal virus-specific T cell responses is accepted, the precise timing and molecular mechanism of action remains unclear. Using a mouse model of influenza A virus infection, we demonstrate that although T-BET is not required for early CD8+ T cell activation and cellular division, it is essential for early acquisition of virus-specific CD8+ T cell function and sustained differentiation and expansion. Whole transcriptome analysis at this early time point showed that Tbx21 deficiency resulted in global dysregulation in early programming events with inappropriate lineage-specific signatures apparent with alterations in the potential TF binding landscape. Assessment of histone posttranslational modifications within the Ifng locus demonstrated that Tbx21 -/- CD8+ T cells were unable to activate "poised" enhancer elements compared with wild-type CD8+ T cells, correlating with diminished Ifng transcription. In all, these data support a model whereby T-BET serves to promote appropriate chromatin remodeling at specific gene loci that underpins appropriate CD8+ T cell lineage-specific commitment and differentiation.
Collapse
Affiliation(s)
- Julia E Prier
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jasmine Li
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Linden J Gearing
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Moshe Olshansky
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Paul J Hertzog
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Stephen J Turner
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia; .,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
30
|
Low LY, Harrison PF, Gould J, Powell DR, Choo JM, Forster SC, Chapman R, Gearing LJ, Cheung JK, Hertzog P, Rood JI. Concurrent Host-Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection. mBio 2018; 9:e00473-18. [PMID: 29588405 PMCID: PMC5874911 DOI: 10.1128/mbio.00473-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 11/20/2022] Open
Abstract
To obtain an insight into host-pathogen interactions in clostridial myonecrosis, we carried out comparative transcriptome analysis of both the bacterium and the host in a murine Clostridium perfringens infection model, which is the first time that such an investigation has been conducted. Analysis of the host transcriptome from infected muscle tissues indicated that many genes were upregulated compared to the results seen with mock-infected mice. These genes were enriched for host defense pathways, including Toll-like receptor (TLR) and Nod-like receptor (NLR) signaling components. Real-time PCR confirmed that host TLR2 and NLRP3 inflammasome genes were induced in response to C. perfringens infection. Comparison of the transcriptome of C. perfringens cells from the infected tissues with that from broth cultures showed that host selective pressure induced a global change in C. perfringens gene expression. A total of 33% (923) of C. perfringens genes were differentially regulated, including 10 potential virulence genes that were upregulated relative to their expression in vitro These genes encoded putative proteins that may be involved in the synthesis of cell wall-associated macromolecules, in adhesion to host cells, or in protection from host cationic antimicrobial peptides. This report presents the first successful expression profiling of coregulated transcriptomes of bacterial and host genes during a clostridial myonecrosis infection and provides new insights into disease pathogenesis and host-pathogen interactions.IMPORTANCEClostridium perfringens is the causative agent of traumatic clostridial myonecrosis, or gas gangrene. In this study, we carried out transcriptional analysis of both the host and the bacterial pathogen in a mouse myonecrosis infection. The results showed that in comparison to mock-infected control tissues, muscle tissues from C. perfringens-infected mice had a significantly altered gene expression profile. In particular, the expression of many genes involved in the innate immune system was upregulated. Comparison of the expression profiles of C. perfringens cells isolated from the infected tissues with those from equivalent broth cultures identified many potential virulence genes that were significantly upregulated in vivo These studies have provided a new understanding of the range of factors involved in host-pathogen interactions in a myonecrosis infection.
Collapse
Affiliation(s)
- Lee-Yean Low
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Clayton, Australia
| | - Jodee Gould
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Clayton, Australia
| | - Jocelyn M Choo
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Samuel C Forster
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Ross Chapman
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Linden J Gearing
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Jackie K Cheung
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Paul Hertzog
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Julian I Rood
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| |
Collapse
|
31
|
Keniry A, Gearing LJ, Jansz N, Liu J, Holik AZ, Hickey PF, Kinkel SA, Moore DL, Breslin K, Chen K, Liu R, Phillips C, Pakusch M, Biben C, Sheridan JM, Kile BT, Carmichael C, Ritchie ME, Hilton DJ, Blewitt ME. Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing. Epigenetics Chromatin 2016; 9:16. [PMID: 27195021 PMCID: PMC4870784 DOI: 10.1186/s13072-016-0064-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/31/2016] [Indexed: 11/16/2022] Open
Abstract
Background
The presence of histone 3 lysine 9 (H3K9) methylation on the mouse inactive X chromosome has been controversial over the last 15 years, and the functional role of H3K9 methylation in X chromosome inactivation in any species has remained largely unexplored. Results Here we report the first genomic analysis of H3K9 di- and tri-methylation on the inactive X: we find they are enriched at the intergenic, gene poor regions of the inactive X, interspersed between H3K27 tri-methylation domains found in the gene dense regions. Although H3K9 methylation is predominantly non-genic, we find that depletion of H3K9 methylation via depletion of H3K9 methyltransferase Set domain bifurcated 1 (Setdb1) during the establishment of X inactivation, results in failure of silencing for around 150 genes on the inactive X. By contrast, we find a very minor role for Setdb1-mediated H3K9 methylation once X inactivation is fully established. In addition to failed gene silencing, we observed a specific failure to silence X-linked long-terminal repeat class repetitive elements. Conclusions Here we have shown that H3K9 methylation clearly marks the murine inactive X chromosome. The role of this mark is most apparent during the establishment phase of gene silencing, with a more muted effect on maintenance of the silent state. Based on our data, we hypothesise that Setdb1-mediated H3K9 methylation plays a role in epigenetic silencing of the inactive X via silencing of the repeats, which itself facilitates gene silencing through alterations to the conformation of the whole inactive X chromosome. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0064-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Linden J Gearing
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Joy Liu
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Aliaksei Z Holik
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Sarah A Kinkel
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Darcy L Moore
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ruijie Liu
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Catherine Phillips
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Miha Pakusch
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Christine Biben
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Julie M Sheridan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Benjamin T Kile
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Catherine Carmichael
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.,Department of Genetics, University of Melbourne, Melbourne, VIC 3010 Australia
| |
Collapse
|
32
|
Dai Z, Sheridan JM, Gearing LJ, Moore DL, Su S, Wormald S, Wilcox S, O'Connor L, Dickins RA, Blewitt ME, Ritchie ME. edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens. F1000Res 2014; 3:95. [PMID: 24860646 PMCID: PMC4023662 DOI: 10.12688/f1000research.3928.2] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2014] [Indexed: 12/15/2022] Open
Abstract
Pooled library sequencing screens that perturb gene function in a high-throughput manner are becoming increasingly popular in functional genomics research. Irrespective of the mechanism by which loss of function is achieved, via either RNA interference using short hairpin RNAs (shRNAs) or genetic mutation using single guide RNAs (sgRNAs) with the CRISPR-Cas9 system, there is a need to establish optimal analysis tools to handle such data. Our open-source processing pipeline in edgeR provides a complete analysis solution for screen data, that begins with the raw sequence reads and ends with a ranked list of candidate genes for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, genes in the rows) with options for allowing mismatches and small shifts in sequence position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or generalized linear modeling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.
Collapse
Affiliation(s)
- Zhiyin Dai
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Julie M Sheridan
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Linden J Gearing
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Darcy L Moore
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shian Su
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Sam Wormald
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Stephen Wilcox
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Liam O'Connor
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Ross A Dickins
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| |
Collapse
|
33
|
Dai Z, Sheridan JM, Gearing LJ, Moore DL, Su S, Wormald S, Wilcox S, O'Connor L, Dickins RA, Blewitt ME, Ritchie ME. edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens. F1000Res 2014. [PMID: 24860646 DOI: 10.12688/f1000research.3928.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pooled library sequencing screens that perturb gene function in a high-throughput manner are becoming increasingly popular in functional genomics research. Irrespective of the mechanism by which loss of function is achieved, via either RNA interference using short hairpin RNAs (shRNAs) or genetic mutation using single guide RNAs (sgRNAs) with the CRISPR-Cas9 system, there is a need to establish optimal analysis tools to handle such data. Our open-source processing pipeline in edgeR provides a complete analysis solution for screen data, that begins with the raw sequence reads and ends with a ranked list of candidate genes for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, genes in the rows) with options for allowing mismatches and small shifts in sequence position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or generalized linear modeling that can handle complex experimental designs. A detailed users' guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.
Collapse
Affiliation(s)
- Zhiyin Dai
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Julie M Sheridan
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Linden J Gearing
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Darcy L Moore
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shian Su
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Sam Wormald
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Stephen Wilcox
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Liam O'Connor
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Ross A Dickins
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| |
Collapse
|
34
|
McColl B, Kao BR, Lourthai P, Chan K, Wardan H, Roosjen M, Delagneau O, Gearing LJ, Blewitt ME, Svasti S, Fucharoen S, Vadolas J. An in vivo model for analysis of developmental erythropoiesis and globin gene regulation. FASEB J 2014; 28:2306-17. [PMID: 24443374 DOI: 10.1096/fj.13-246637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Expression of fetal γ-globin in adulthood ameliorates symptoms of β-hemoglobinopathies by compensating for the mutant β-globin. Reactivation of the silenced γ-globin gene is therefore of substantial clinical interest. To study the regulation of γ-globin expression, we created the GG mice, which carry an intact 183-kb human β-globin locus modified to express enhanced green fluorescent protein (eGFP) from the Gγ-globin promoter. GG embryos express eGFP first in the yolk sac blood islands and then in the aorta-gonad mesonephros and the fetal liver, the sites of normal embryonic hematopoiesis. eGFP expression in erythroid cells peaks at E9.5 and then is rapidly silenced (>95%) and maintained at low levels into adulthood, demonstrating appropriate developmental regulation of the human β-globin locus. In vitro knockdown of the epigenetic regulator DNA methyltransferase-1 in GG primary erythroid cells increases the proportion of eGFP(+) cells in culture from 41.9 to 74.1%. Furthermore, eGFP fluorescence is induced >3-fold after treatment of erythroid precursors with epigenetic drugs known to induce γ-globin expression, demonstrating the suitability of the Gγ-globin eGFP reporter for evaluation of γ-globin inducers. The GG mouse model is therefore a valuable model system for genetic and pharmacologic studies of the regulation of the β-globin locus and for discovery of novel therapies for the β-hemoglobinopathies.
Collapse
Affiliation(s)
- Bradley McColl
- 2Cell and Gene Therapy Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Roosjen M, McColl B, Kao B, Gearing LJ, Blewitt ME, Vadolas J. Transcriptional regulators Myb and BCL11A interplay with DNA methyltransferase 1 in developmental silencing of embryonic and fetal β-like globin genes. FASEB J 2013; 28:1610-20. [PMID: 24371119 DOI: 10.1096/fj.13-242669] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The clinical symptoms of hemoglobin disorders such as β-thalassemia and sickle cell anemia are significantly ameliorated by the persistent expression of γ-globin after birth. This knowledge has driven the discovery of important regulators that silence γ-globin postnatally. Improved understanding of the γ- to β-globin switching mechanism holds the key to devising targeted therapies for β-hemoglobinopathies. To further investigate this mechanism, we used the murine erythroleukemic (MEL) cell line containing an intact 183-kb human β-globin locus, in which the (G)γ- and β-globin genes are replaced by DsRed and eGFP fluorescent reporters, respectively. Following RNA interference (RNAi)-mediated knockdown of two key transcriptional regulators, Myb and BCL11A, we observed a derepression of γ-globin, measured by DsRed fluorescence and qRT-PCR (P<0.001). Interestingly, double knockdown of Myb and DNA methyltransferase 1 (DNMT1) resulted in a robust induction of ε-globin, (up to 20% of total β-like globin species) compared to single knockdowns (P<0.001). Conversely, double knockdowns of BCL11A and DNMT1 enhanced γ-globin expression (up to 90% of total β-like globin species) compared to single knockdowns (P<0.001). Moreover, following RNAi treatment, expression of human β-like globin genes mirrored the expression levels of their endogenous murine counterparts. These results demonstrate that Myb and BCL11A cooperate with DNMT1 to achieve developmental repression of embryonic and fetal β-like globin genes in the adult erythroid environment.
Collapse
Affiliation(s)
- Mark Roosjen
- 1Cell and Gene Therapy Group, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd., Parkville, VIC 3052, Australia.
| | | | | | | | | | | |
Collapse
|
36
|
McCoy CE, Carpenter S, Pålsson-McDermott EM, Gearing LJ, O'Neill LAJ. Glucocorticoids inhibit IRF3 phosphorylation in response to Toll-like receptor-3 and -4 by targeting TBK1 activation. J Biol Chem 2008; 283:14277-85. [PMID: 18356163 DOI: 10.1074/jbc.m709731200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Phosphorylation of the transcription factor interferon regulatory factor 3 (IRF3) is essential for the induction of promoters which contain the interferon-stimulated response element (ISRE). IRF3 can be activated by Toll-like receptor 3 (TLR3) in response to the double-stranded RNA mimic poly(I-C) and by TLR4 in response to lipopolysaccharide (LPS). Here we have analyzed the effect of the glucocorticoid dexamethasone on this response. Dexamethasone inhibited the induction of the ISRE-dependent gene RANTES (regulated on activation normal T cell expressed and secreted) in both U373-CD14 cells and human peripheral blood mononuclear cells and also an ISRE luciferase construct, activated by either TLR3 or TLR4. It also inhibited increased phosphorylation of IRF3 in its N terminus in response to LPS and in its C terminus on Ser-396 in response to either poly(I-C) or LPS. Several dexamethasone-induced phosphatases were tested for possible involvement in these effects; MKP1 did not appear to be involved, although MKP2 and MKP5 both partially inhibited induction of the ISRE, pointing to their possible involvement in the effect of dexamethasone. Importantly, we found that dexamethasone could inhibit TBK1 kinase activity and TBK1 phosphorylation on Ser-172, both of which are required for IRF3 phosphorylation downstream of TLR3 and TLR4 stimulation. Our study, therefore, demonstrates that TBK1 is a target for dexamethasone, common to both TLR3 and TLR4 signaling.
Collapse
Affiliation(s)
- Claire E McCoy
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | | | | | | | | |
Collapse
|