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McLeish E, Sooda A, Slater N, Beer K, Cooper I, Mastaglia FL, Needham M, Coudert JD. Identification of distinct immune signatures in inclusion body myositis by peripheral blood immunophenotyping using machine learning models. Clin Transl Immunology 2024; 13:e1504. [PMID: 38585335 PMCID: PMC10990804 DOI: 10.1002/cti2.1504] [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] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/13/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Objective Inclusion body myositis (IBM) is a progressive late-onset muscle disease characterised by preferential weakness of quadriceps femoris and finger flexors, with elusive causes involving immune, degenerative, genetic and age-related factors. Overlapping with normal muscle ageing makes diagnosis and prognosis problematic. Methods We characterised peripheral blood leucocytes in 81 IBM patients and 45 healthy controls using flow cytometry. Using a random forest classifier, we identified immune changes in IBM compared to HC. K-means clustering and the random forest one-versus-rest model classified patients into three immunophenotypic clusters. Functional outcome measures including mTUG, 2MWT, IBM-FRS, EAT-10, knee extension and grip strength were assessed across clusters. Results The random forest model achieved a 94% AUC ROC with 82.76% specificity and 100% sensitivity. Significant differences were found in IBM patients, including increased CD8+ T-bet+ cells, CD4+ T cells skewed towards a Th1 phenotype and altered γδ T cell repertoire with a reduced proportion of Vγ9+Vδ2+ cells. IBM patients formed three clusters: (i) activated and inflammatory CD8+ and CD4+ T-cell profile and the highest proportion of anti-cN1A-positive patients in cluster 1; (ii) limited inflammation in cluster 2; (iii) highly differentiated, pro-inflammatory T-cell profile in cluster 3. Additionally, no significant differences in patients' age and gender were detected between immunophenotype clusters; however, worsening trends were detected with several functional outcomes. Conclusion These findings unveil distinct immune profiles in IBM, shedding light on underlying pathological mechanisms for potential immunoregulatory therapeutic development.
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Affiliation(s)
- Emily McLeish
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWAAustralia
| | - Anuradha Sooda
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWAAustralia
| | - Nataliya Slater
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWAAustralia
| | - Kelly Beer
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWAAustralia
- Perron Institute for Neurological and Translational ScienceNedlandsWAAustralia
| | - Ian Cooper
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWAAustralia
- Perron Institute for Neurological and Translational ScienceNedlandsWAAustralia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational ScienceNedlandsWAAustralia
| | - Merrilee Needham
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWAAustralia
- Perron Institute for Neurological and Translational ScienceNedlandsWAAustralia
- School of MedicineUniversity of Notre Dame AustraliaFremantleWAAustralia
- Department of NeurologyFiona Stanley HospitalMurdochWAAustralia
| | - Jerome D Coudert
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWAAustralia
- Perron Institute for Neurological and Translational ScienceNedlandsWAAustralia
- School of MedicineUniversity of Notre Dame AustraliaFremantleWAAustralia
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Slater N, Sooda A, McLeish E, Beer K, Brusch A, Shakya R, Bundell C, James I, Chopra A, Mastaglia FL, Needham M, Coudert JD. High-resolution HLA genotyping in inclusion body myositis refines 8.1 ancestral haplotype association to DRB1*03:01:01 and highlights pathogenic role of arginine-74 of DRβ1 chain. J Autoimmun 2024; 142:103150. [PMID: 38043487 DOI: 10.1016/j.jaut.2023.103150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023]
Abstract
OBJECTIVES Inclusion body myositis (IBM) is a progressive inflammatory-degenerative muscle disease of older individuals, with some patients producing anti-cytosolic 5'-nucleotidase 1A (NT5C1A, aka cN1A) antibodies. Human Leukocyte Antigens (HLA) is the highest genetic risk factor for developing IBM. In this study, we aimed to further define the contribution of HLA alleles to IBM and the production of anti-cN1A antibodies. METHODS We HLA haplotyped a Western Australian cohort of 113 Caucasian IBM patients and 112 ethnically matched controls using Illumina next-generation sequencing. Allele frequency analysis and amino acid alignments were performed using the Genentech/MiDAS bioinformatics package. Allele frequencies were compared using Fisher's exact test. Age at onset analysis was performed using the ggstatsplot package. All analysis was carried out in RStudio version 1.4.1717. RESULTS Our findings validated the independent association of HLA-DRB1*03:01:01 with IBM and attributed the risk to an arginine residue in position 74 within the DRβ1 protein. Conversely, DRB4*01:01:01 and DQA1*01:02:01 were found to have protective effects; the carriers of DRB1*03:01:01 that did not possess these alleles had a fourteenfold increased risk of developing IBM over the general Caucasian population. Furthermore, patients with the abovementioned genotype developed symptoms on average five years earlier than patients without. We did not find any HLA associations with anti-cN1A antibody production. CONCLUSIONS High-resolution HLA sequencing more precisely characterised the alleles associated with IBM and defined a haplotype linked to earlier disease onset. Identification of the critical amino acid residue by advanced biostatistical analysis of immunogenetics data offers mechanistic insights and future directions into uncovering IBM aetiopathogenesis.
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Affiliation(s)
- Nataliya Slater
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia
| | - Anuradha Sooda
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia
| | - Emily McLeish
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia
| | - Kelly Beer
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Anna Brusch
- PathWest Laboratory Medicine, Dept of Clinical Immunology, QEII Medical Centre, Nedlands, WA, Australia
| | - Rakesh Shakya
- PathWest Laboratory Medicine, Dept of Clinical Immunology, QEII Medical Centre, Nedlands, WA, Australia
| | - Christine Bundell
- PathWest Laboratory Medicine, Dept of Clinical Immunology, QEII Medical Centre, Nedlands, WA, Australia
| | - Ian James
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; Murdoch University, Institute for Immunology and Infection Diseases, Murdoch, WA, Australia
| | - Abha Chopra
- Murdoch University, Institute for Immunology and Infection Diseases, Murdoch, WA, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; University of Western Australia, Centre for Neuromuscular & Neurological Disorders, Crawley, WA, Australia
| | - Merrilee Needham
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; University of Notre Dame Australia, School of Medicine, Fremantle, WA, Australia; Fiona Stanley Hospital, Department of Neurology, Murdoch, WA, Australia
| | - Jerome D Coudert
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; University of Notre Dame Australia, School of Medicine, Fremantle, WA, Australia.
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McLeish E, Slater N, Mastaglia FL, Needham M, Coudert JD. From data to diagnosis: how machine learning is revolutionizing biomarker discovery in idiopathic inflammatory myopathies. Brief Bioinform 2023; 25:bbad514. [PMID: 38243695 PMCID: PMC10796252 DOI: 10.1093/bib/bbad514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 01/21/2024] Open
Abstract
Idiopathic inflammatory myopathies (IIMs) are a heterogeneous group of muscle disorders including adult and juvenile dermatomyositis, polymyositis, immune-mediated necrotising myopathy and sporadic inclusion body myositis, all of which present with variable symptoms and disease progression. The identification of effective biomarkers for IIMs has been challenging due to the heterogeneity between IIMs and within IIM subgroups, but recent advances in machine learning (ML) techniques have shown promises in identifying novel biomarkers. This paper reviews recent studies on potential biomarkers for IIM and evaluates their clinical utility. We also explore how data analytic tools and ML algorithms have been used to identify biomarkers, highlighting their potential to advance our understanding and diagnosis of IIM and improve patient outcomes. Overall, ML techniques have great potential to revolutionize biomarker discovery in IIMs and lead to more effective diagnosis and treatment.
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Affiliation(s)
- Emily McLeish
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, Western Australia (WA), Australia
| | - Nataliya Slater
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, Western Australia (WA), Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Merrilee Needham
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, Western Australia (WA), Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- University of Notre Dame Australia, School of Medicine, Fremantle, WA, Australia
- Fiona Stanley Hospital, Department of Neurology, Murdoch, WA, Australia
| | - Jerome D Coudert
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, Western Australia, WA, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- University of Notre Dame Australia, School of Medicine, Fremantle, WA, Australia
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Connor SG, Fairchild TJ, Learmonth YC, Beer K, Cooper I, Boardman G, Teo SYM, Shatahmasseb B, Zhang R, Hiscock K, Coudert JD, Yeap BB, Needham M. Testosterone treatment combined with exercise to improve muscle strength, physical function and quality of life in men affected by inclusion body myositis: A randomised, double-blind, placebo-controlled, crossover trial. PLoS One 2023; 18:e0283394. [PMID: 37040372 PMCID: PMC10089314 DOI: 10.1371/journal.pone.0283394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
INTRODUCTION Inclusion body myositis (IBM) is the most commonly acquired skeletal muscle disease of older adults involving both autoimmune attack and muscle degeneration. As exercise training can improve outcomes in IBM, this study assessed whether a combination of testosterone supplementation and exercise training would improve muscle strength, physical function and quality of life in men affected by IBM, more than exercise alone. METHODS This pilot study was a single site randomised, double-blind, placebo-controlled, crossover study. Testosterone (exercise and testosterone cream) and placebo (exercise and placebo cream) were each delivered for 12 weeks, with a two-week wash-out between the two periods. The primary outcome measure was improvement in quadriceps isokinetic muscle strength. Secondary outcomes included assessment of isokinetic peak flexion force, walk capacity and patient reported outcomes, and other tests, comparing results between the placebo and testosterone arms. A 12-month Open Label Extension (OLE) was offered using the same outcome measures collected at 6 and 12-months. RESULTS 14 men completed the trial. There were no significant improvements in quadriceps extension strength or lean body mass, nor any of the secondary outcomes. Improvement in the RAND Short Form 36 patient reported outcome questionnaire 'emotional wellbeing' sub-category was reported during the testosterone arm compared to the placebo arm (mean difference [95% CI]: 6.0 points, [95% CI 1.7,10.3]). The OLE demonstrated relative disease stability over the 12-month period but with a higher number of testosterone-related adverse events. CONCLUSIONS Adding testosterone supplementation to exercise training did not significantly improve muscle strength or physical function over a 12-week intervention period, compared to exercise alone. However, the combination improved emotional well-being over this period, and relative stabilisation of disease was found during the 12-month OLE. A longer duration trial involving a larger group of participants is warranted.
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Affiliation(s)
| | - Timothy J Fairchild
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Discipline of Exercise Science, Murdoch University, Murdoch, Western Australia, Australia
| | - Yvonne C Learmonth
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Discipline of Exercise Science, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute of Neurological and Translational Sciences, Nedlands, Western Australia, Australia
| | - Kelly Beer
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute of Neurological and Translational Sciences, Nedlands, Western Australia, Australia
| | - Ian Cooper
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute of Neurological and Translational Sciences, Nedlands, Western Australia, Australia
| | - Glenn Boardman
- Research Development Unit, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Shaun Y M Teo
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Discipline of Exercise Science, Murdoch University, Murdoch, Western Australia, Australia
| | - Behnaz Shatahmasseb
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Discipline of Exercise Science, Murdoch University, Murdoch, Western Australia, Australia
| | - Rui Zhang
- Department of Clinical Biochemistry, Pharmacology and Toxicology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
| | - Krystyne Hiscock
- Affinity Clinical Research, Nedlands, Western Australia, Australia
| | - Jerome D Coudert
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute of Neurological and Translational Sciences, Nedlands, Western Australia, Australia
- Division of Medicine, The University of Notre Dame Australia, Fremantle, Western Australia, Australia
| | - Bu B Yeap
- Department of Endocrinology and Diabetes, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
- Medical School, University of Western Australia, Crawley, Western Australia, Australia
| | - Merrilee Needham
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute of Neurological and Translational Sciences, Nedlands, Western Australia, Australia
- Division of Medicine, The University of Notre Dame Australia, Fremantle, Western Australia, Australia
- Department of Neurology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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Coudert JD, Slater N, Sooda A, Beer K, Lim EM, Boyder C, Zhang R, Mastaglia FL, Learmonth YC, Fairchild TJ, Yeap BB, Needham M. Immunoregulatory effects of testosterone supplementation combined with exercise training in men with Inclusion Body Myositis: a double-blind, placebo-controlled, cross-over trial. Clin Transl Immunology 2022; 11:e1416. [PMID: 36188123 PMCID: PMC9495304 DOI: 10.1002/cti2.1416] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/08/2022] [Accepted: 09/07/2022] [Indexed: 11/09/2022] Open
Abstract
Objectives Sporadic Inclusion Body Myositis (IBM) is an inflammatory muscle disease affecting individuals over the age of 45, leading to progressive muscle wasting, disability and loss of independence. Histologically, IBM is characterised by immune changes including myofibres expressing major histocompatibility complex molecules and invaded by CD8+ T cells and macrophages, and by degenerative changes including protein aggregates organised in inclusion bodies, rimmed vacuoles and mitochondrial abnormalities. There is currently no cure, and regular exercise is currently the only recognised treatment effective at limiting muscle weakening, atrophy and loss of function. Testosterone exerts anti-inflammatory effects, inhibiting effector T-cell differentiation and pro-inflammatory cytokine production. Methods We conducted a double-blind, placebo-controlled, cross-over trial in men with IBM, to assess whether a personalised progressive exercise training combined with application of testosterone, reduced the inflammatory immune response associated with this disease over and above exercise alone. To assess intervention efficacy, we immunophenotyped blood immune cells by flow cytometry, and measured serum cytokines and chemokines by Luminex immunoassay. Results Testosterone supplementation resulted in modest yet significant count reduction in the classical monocyte subset as well as eosinophils. Testosterone-independent immunoregulatory effects attributed to exercise included altered proportions of some monocyte, T- and B-cell subsets, and reduced IL-12, IL-17, TNF-α, MIP-1β and sICAM-1 in spite of interindividual variability. Conclusion Overall, our findings indicate anti-inflammatory effects of exercise training in IBM patients, whilst concomitant testosterone supplementation provides some additional changes. Further studies combining testosterone and exercise would be worthwhile in larger cohorts and longer testosterone administration periods.
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Affiliation(s)
- Jerome D Coudert
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch WA Australia.,Perron Institute for Neurological and Translational Science Nedlands WA Australia.,School of Medicine University of Notre Dame Fremantle WA Australia
| | - Nataliya Slater
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch WA Australia
| | - Anuradha Sooda
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch WA Australia
| | - Kelly Beer
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch WA Australia.,Perron Institute for Neurological and Translational Science Nedlands WA Australia
| | - Ee Mun Lim
- Department of Clinical Biochemistry, Pharmacology and Toxicology, PathWest Laboratory Medicine QEII Medical Centre Nedlands WA Australia
| | - Conchita Boyder
- Department of Clinical Biochemistry, Pharmacology and Toxicology, PathWest Laboratory Medicine QEII Medical Centre Nedlands WA Australia
| | - Rui Zhang
- Department of Clinical Biochemistry, Pharmacology and Toxicology, PathWest Laboratory Medicine QEII Medical Centre Nedlands WA Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science Nedlands WA Australia
| | - Yvonne C Learmonth
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch WA Australia.,Perron Institute for Neurological and Translational Science Nedlands WA Australia.,Discipline of Exercise Science Murdoch University Murdoch WA Australia
| | - Timothy J Fairchild
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch WA Australia.,Discipline of Exercise Science Murdoch University Murdoch WA Australia
| | - Bu B Yeap
- Medical School University of Western Australia Perth WA Australia.,Department of Endocrinology and Diabetes Fiona Stanley Hospital Perth WA Australia
| | - Merrilee Needham
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch WA Australia.,Perron Institute for Neurological and Translational Science Nedlands WA Australia.,School of Medicine University of Notre Dame Fremantle WA Australia.,Department of Neurology Fiona Stanley Hospital Perth WA Australia
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McLeish E, Slater N, Sooda A, Wilson A, Coudert JD, Lloyd TE, Needham M. Inclusion body myositis: The interplay between ageing, muscle degeneration and autoimmunity. Best Pract Res Clin Rheumatol 2022; 36:101761. [PMID: 35760741 DOI: 10.1016/j.berh.2022.101761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Inclusion body myositis (IBM) is a slowly progressive muscle disease affecting ageing individuals. IBM presents with a distinctive pattern of weakness involving the quadriceps and finger flexor muscles, although other muscles including pharyngeal muscles become affected over time. Pathological hallmarks of IBM include autoimmune features, including endomysial infiltration by highly differentiated T cells, as well as degenerative features marked by intramyofibre protein aggregates organised into inclusion bodies. Despite some progress in understanding the cellular pathways involved in IBM, it remains untreatable, and the progression of the disease leads to progressive weakness, disability, wheelchair dependency and loss of independence. Therefore, there is an urgent need to improve our understanding of the underlying mechanisms and pathways involved in this disease to identify new treatment targets. Here, we discuss the current understanding of aetiopathogenesis, the interrelationship between autoimmunity and degeneration, and how ageing is a major influencer of both these features.
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Affiliation(s)
- E McLeish
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
| | - N Slater
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - A Sooda
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - A Wilson
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J D Coudert
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia; Perron Institute for Neurological and Translational Science, Perth, WA, Australia; School of Medicine, University of Notre Dame, Fremantle, WA, Australia
| | - T E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - M Needham
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia; Perron Institute for Neurological and Translational Science, Perth, WA, Australia; School of Medicine, University of Notre Dame, Fremantle, WA, Australia; Fiona Stanley Hospital, Department of Neurology, Perth, WA, Australia
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Coudert JD, McLeish E, Sooda A, Slater N, Beer K, Paramalingam S, Lamont PJ, Needham M. Isolation of Live Leukocytes from Human Inflammatory Muscles. Methods Protoc 2021; 4:mps4040075. [PMID: 34698225 PMCID: PMC8544523 DOI: 10.3390/mps4040075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/09/2021] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023] Open
Abstract
In inflammatory myopathies, the self-reactive immune cells involved in muscle aggression have been studied mostly using histological assessment of muscle biopsy sections; this methodology provides the advantage of visualizing and identifying cells within the tissue, but it does not allow further investigation. To gain access to live and isolated cells, many studies utilized blood samples; however, in the absence of biological tools to discriminate the leukocytes associated with the autoimmune process from those that emerged from responses against pathogens, the information observed on circulating immune cells often lacks in specificity, and thus result interpretation may prove difficult. In order to selectively retrieve self-reactive immune cells, we developed a protocol to isolate live leukocytes from human muscle biopsies, which allows for further analysis using a large range of methodologies. The protocol uses enzymatic digestion to release live leukocytes from freshly collected skeletal muscle samples, followed by filtration and separation of the leukocytes from the myocytes by density gradient centrifugation. The isolated cells can be submitted immediately to various analysis strategies to characterize ex vivo the specific cellular and molecular mechanisms responsible for self-directed immune muscle aggression or may be placed in culture for expansion.
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Affiliation(s)
- Jerome D. Coudert
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (E.M.); (A.S.); (N.S.); (K.B.); (M.N.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
- School of Medicine, University of Notre Dame, Fremantle, WA 6160, Australia
- Correspondence:
| | - Emily McLeish
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (E.M.); (A.S.); (N.S.); (K.B.); (M.N.)
| | - Anuradha Sooda
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (E.M.); (A.S.); (N.S.); (K.B.); (M.N.)
| | - Nataliya Slater
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (E.M.); (A.S.); (N.S.); (K.B.); (M.N.)
| | - Kelly Beer
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (E.M.); (A.S.); (N.S.); (K.B.); (M.N.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Shereen Paramalingam
- Department of Rheumatology, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
| | | | - Merrilee Needham
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (E.M.); (A.S.); (N.S.); (K.B.); (M.N.)
- School of Medicine, University of Notre Dame, Fremantle, WA 6160, Australia
- Department of Neurology, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
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Alves E, McLeish E, Blancafort P, Coudert JD, Gaudieri S. Manipulating the NKG2D Receptor-Ligand Axis Using CRISPR: Novel Technologies for Improved Host Immunity. Front Immunol 2021; 12:712722. [PMID: 34456921 PMCID: PMC8397441 DOI: 10.3389/fimmu.2021.712722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/21/2021] [Accepted: 07/28/2021] [Indexed: 12/26/2022] Open
Abstract
The activating immune receptor natural killer group member D (NKG2D) and its cognate ligands represent a fundamental surveillance system of cellular distress, damage or transformation. Signaling through the NKG2D receptor-ligand axis is critical for early detection of viral infection or oncogenic transformation and the presence of functional NKG2D ligands (NKG2D-L) is associated with tumor rejection and viral clearance. Many viruses and tumors have developed mechanisms to evade NKG2D recognition via transcriptional, post-transcriptional or post-translational interference with NKG2D-L, supporting the concept that circumventing immune evasion of the NKG2D receptor-ligand axis may be an attractive therapeutic avenue for antiviral therapy or cancer immunotherapy. To date, the complexity of the NKG2D receptor-ligand axis and the lack of specificity of current NKG2D-targeting therapies has not allowed for the precise manipulation required to optimally harness NKG2D-mediated immunity. However, with the discovery of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins, novel opportunities have arisen in the realm of locus-specific gene editing and regulation. Here, we give a brief overview of the NKG2D receptor-ligand axis in humans and discuss the levels at which NKG2D-L are regulated and dysregulated during viral infection and oncogenesis. Moreover, we explore the potential for CRISPR-based technologies to provide novel therapeutic avenues to improve and maximize NKG2D-mediated immunity.
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Affiliation(s)
- Eric Alves
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Emily McLeish
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Pilar Blancafort
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Perth, WA, Australia
- The Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Jerome D. Coudert
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- School of Medicine, University of Notre Dame, Fremantle, WA, Australia
| | - Silvana Gaudieri
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
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Lawler NG, Gray N, Kimhofer T, Boughton B, Gay M, Yang R, Morillon AC, Chin ST, Ryan M, Begum S, Bong SH, Coudert JD, Edgar D, Raby E, Pettersson S, Richards T, Holmes E, Whiley L, Nicholson JK. Systemic Perturbations in Amine and Kynurenine Metabolism Associated with Acute SARS-CoV-2 Infection and Inflammatory Cytokine Responses. J Proteome Res 2021; 20:2796-2811. [PMID: 33724837 PMCID: PMC7986977 DOI: 10.1021/acs.jproteome.1c00052] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [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: 01/20/2021] [Indexed: 01/06/2023]
Abstract
We performed quantitative metabolic phenotyping of blood plasma in parallel with cytokine/chemokine analysis from participants who were either SARS-CoV-2 (+) (n = 10) or SARS-CoV-2 (-) (n = 49). SARS-CoV-2 positivity was associated with a unique metabolic phenotype and demonstrated a complex systemic response to infection, including severe perturbations in amino acid and kynurenine metabolic pathways. Nine metabolites were elevated in plasma and strongly associated with infection (quinolinic acid, glutamic acid, nicotinic acid, aspartic acid, neopterin, kynurenine, phenylalanine, 3-hydroxykynurenine, and taurine; p < 0.05), while four metabolites were lower in infection (tryptophan, histidine, indole-3-acetic acid, and citrulline; p < 0.05). This signature supports a systemic metabolic phenoconversion following infection, indicating possible neurotoxicity and neurological disruption (elevations of 3-hydroxykynurenine and quinolinic acid) and liver dysfunction (reduction in Fischer's ratio and elevation of taurine). Finally, we report correlations between the key metabolite changes observed in the disease with concentrations of proinflammatory cytokines and chemokines showing strong immunometabolic disorder in response to SARS-CoV-2 infection.
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Affiliation(s)
- Nathan G. Lawler
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Nicola Gray
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Torben Kimhofer
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Berin Boughton
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Melvin Gay
- Bruker Pty Ltd., Preston,
VIC 3072, Australia
| | - Rongchang Yang
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Aude-Claire Morillon
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Sung-Tong Chin
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Monique Ryan
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Sofina Begum
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
- Department of Metabolism Digestion and Reproduction,
Faculty of Medicine, Imperial College London, Sir Alexander
Fleming Building, South Kensington, London SW7 2AZ, U.K.
| | - Sze How Bong
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
| | - Jerome D. Coudert
- Centre for Molecular Medicine & Innovative
Therapeutics, Murdoch University, Perth, WA 6150,
Australia
| | - Dale Edgar
- State Adult Burn Unit, Fiona Stanley
Hospital, Murdoch, WA 6150, Australia
- Burn Injury Research Node, The University of
Notre Dame, Fremantle, WA 6160, Australia
- Fiona Wood Foundation,
Murdoch, WA 6150, Australia
| | - Edward Raby
- Department of Microbiology, PathWest
Laboratory Medicine, Perth, WA 6009, Australia
- Department of Infectious Diseases, Fiona
Stanley Hospital, Perth, WA 6150, Australia
| | - Sven Pettersson
- Singapore National Neuro Science
Centre, Singapore Mandalay Road, Singapore 308232,
Singapore
- Lee Kong Chian School of Medicine,
Nanyang Technological University, Mandalay Road, Singapore
308232, Singapore
- Department of Life Science Centre,
Sunway University, 55100 Kuala Lumpur,
Malaysia
| | - Toby Richards
- Medical School, Faculty of Health and Medical
Sciences, University of Western Australia, Nedlands, WA 6009,
Australia
| | - Elaine Holmes
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
- Department of Metabolism Digestion and Reproduction,
Faculty of Medicine, Imperial College London, Sir Alexander
Fleming Building, South Kensington, London SW7 2AZ, U.K.
| | - Luke Whiley
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
- Perron Institute for Neurological and
Translational Science, Nedlands, WA 6009,
Australia
| | - Jeremy K. Nicholson
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, WA 6150, Australia
- Medical School, Faculty of Health and Medical
Sciences, University of Western Australia, Nedlands, WA 6009,
Australia
- Institute of Global Health Innovation,
Imperial College London, Level 1, Faculty Building South
Kensington Campus, London SW7 2AZ, U.K.
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10
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Lodge S, Nitschke P, Kimhofer T, Coudert JD, Begum S, Bong SH, Richards T, Edgar D, Raby E, Spraul M, Schaefer H, Lindon JC, Loo RL, Holmes E, Nicholson JK. NMR Spectroscopic Windows on the Systemic Effects of SARS-CoV-2 Infection on Plasma Lipoproteins and Metabolites in Relation to Circulating Cytokines. J Proteome Res 2021; 20:1382-1396. [PMID: 33426894 PMCID: PMC7805607 DOI: 10.1021/acs.jproteome.0c00876] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [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: 11/02/2020] [Indexed: 02/08/2023]
Abstract
To investigate the systemic metabolic effects of SARS-CoV-2 infection, we analyzed 1H NMR spectroscopic data on human blood plasma and co-modeled with multiple plasma cytokines and chemokines (measured in parallel). Thus, 600 MHz 1H solvent-suppressed single-pulse, spin-echo, and 2D J-resolved spectra were collected on plasma recorded from SARS-CoV-2 rRT-PCR-positive patients (n = 15, with multiple sampling timepoints) and age-matched healthy controls (n = 34, confirmed rRT-PCR negative), together with patients with COVID-19/influenza-like clinical symptoms who tested SARS-CoV-2 negative (n = 35). We compared the single-pulse NMR spectral data with in vitro diagnostic research (IVDr) information on quantitative lipoprotein profiles (112 parameters) extracted from the raw 1D NMR data. All NMR methods gave highly significant discrimination of SARS-CoV-2 positive patients from controls and SARS-CoV-2 negative patients with individual NMR methods, giving different diagnostic information windows on disease-induced phenoconversion. Longitudinal trajectory analysis in selected patients indicated that metabolic recovery was incomplete in individuals without detectable virus in the recovery phase. We observed four plasma cytokine clusters that expressed complex differential statistical relationships with multiple lipoproteins and metabolites. These included the following: cluster 1, comprising MIP-1β, SDF-1α, IL-22, and IL-1α, which correlated with multiple increased LDL and VLDL subfractions; cluster 2, including IL-10 and IL-17A, which was only weakly linked to the lipoprotein profile; cluster 3, which included IL-8 and MCP-1 and were inversely correlated with multiple lipoproteins. IL-18, IL-6, and IFN-γ together with IP-10 and RANTES exhibited strong positive correlations with LDL1-4 subfractions and negative correlations with multiple HDL subfractions. Collectively, these data show a distinct pattern indicative of a multilevel cellular immune response to SARS CoV-2 infection interacting with the plasma lipoproteome giving a strong and characteristic immunometabolic phenotype of the disease. We observed that some patients in the respiratory recovery phase and testing virus-free were still metabolically highly abnormal, which indicates a new role for these technologies in assessing full systemic recovery.
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Affiliation(s)
- Samantha Lodge
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
- Centre for Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Murdoch, Western
Australia 6150, Australia
| | - Philipp Nitschke
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
| | - Torben Kimhofer
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
- Centre for Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Murdoch, Western
Australia 6150, Australia
| | - Jerome D. Coudert
- Centre for Molecular Medicine and Innovative
Therapeutics, Murdoch University, Harry Perkins Building,
Perth, Western Australia 6150, Australia
- Perron Institute for Neurological and
Translational Science, Nedlands, Western Australia 6009,
Australia
- School of Medicine, University of Notre
Dame, Fremantle, Western Australia 6160,
Australia
| | - Sofina Begum
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
- Section of Nutrition Research , Department of Metabolism,
Nutrition and Reproduction, Faculty of Medicine, Sir Alexander Fleming Building,
Imperial College London, London SW7 2AZ,
U.K.
| | - Sze-How Bong
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
| | - Toby Richards
- Division of Surgery, Medical School, Faculty of Health
and Medical Sciences, University of Western Australia, Harry
Perkins Building, Robert Warren Drive, Murdoch, Perth, Western Australia 6150,
Australia
| | - Dale Edgar
- Faculty of Health and Medical Sciences,
University of Western Australia, Harry Perkins Building,
Robert Warren Drive, Murdoch, Perth, Western Australia 6150,
Australia
| | - Edward Raby
- Department of Clinical Microbiology,
PathWest Laboratory Medicine WA, Murdoch, Perth, Western
Australia 6150, Australia
| | | | | | - John C. Lindon
- Division of Systems Medicine, Department of
Metabolism, Nutrition and Reproduction, Faculty of Medicine, Sir Alexander Fleming
Building, Imperial College London, London SW7 2AZ,
U.K.
| | - Ruey Leng Loo
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
- Centre for Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Murdoch, Western
Australia 6150, Australia
| | - Elaine Holmes
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
- Centre for Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Murdoch, Western
Australia 6150, Australia
- Section of Nutrition Research , Department of Metabolism,
Nutrition and Reproduction, Faculty of Medicine, Sir Alexander Fleming Building,
Imperial College London, London SW7 2AZ,
U.K.
| | - Jeremy K. Nicholson
- Australian National Phenome Centre, Health Futures
Institute, Murdoch University, Harry Perkins Building, Perth,
Western Australia 6150, Australia
- Centre for Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Murdoch, Western
Australia 6150, Australia
- Division of Surgery, Medical School, Faculty of Health
and Medical Sciences, University of Western Australia, Harry
Perkins Building, Robert Warren Drive, Murdoch, Perth, Western Australia 6150,
Australia
- Institute of Global Health Innovation,
Imperial College London, Level 1, Faculty Building South
Kensington Campus, London SW7 2NA, U.K.
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11
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Young A, Ngiow SF, Gao Y, Patch AM, Barkauskas DS, Messaoudene M, Lin G, Coudert JD, Stannard KA, Zitvogel L, Degli-Esposti MA, Vivier E, Waddell N, Linden J, Huntington ND, Souza-Fonseca-Guimaraes F, Smyth MJ. A2AR Adenosine Signaling Suppresses Natural Killer Cell Maturation in the Tumor Microenvironment. Cancer Res 2017; 78:1003-1016. [PMID: 29229601 DOI: 10.1158/0008-5472.can-17-2826] [Citation(s) in RCA: 242] [Impact Index Per Article: 34.6] [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: 09/14/2017] [Revised: 10/31/2017] [Accepted: 12/06/2017] [Indexed: 12/25/2022]
Abstract
Extracellular adenosine is a key immunosuppressive metabolite that restricts activation of cytotoxic lymphocytes and impairs antitumor immune responses. Here, we show that engagement of A2A adenosine receptor (A2AR) acts as a checkpoint that limits the maturation of natural killer (NK) cells. Both global and NK-cell-specific conditional deletion of A2AR enhanced proportions of terminally mature NK cells at homeostasis, following reconstitution, and in the tumor microenvironment. Notably, A2AR-deficient, terminally mature NK cells retained proliferative capacity and exhibited heightened reconstitution in competitive transfer assays. Moreover, targeting A2AR specifically on NK cells also improved tumor control and delayed tumor initiation. Taken together, our results establish A2AR-mediated adenosine signaling as an intrinsic negative regulator of NK-cell maturation and antitumor immune responses. On the basis of these findings, we propose that administering A2AR antagonists concurrently with NK cell-based therapies may heighten therapeutic benefits by augmenting NK cell-mediated antitumor immunity.Significance: Ablating adenosine signaling is found to promote natural killer cell maturation and antitumor immunity and reduce tumor growth. Cancer Res; 78(4); 1003-16. ©2017 AACR.
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MESH Headings
- Animals
- Cell Line, Tumor
- Heterografts
- Humans
- Killer Cells, Natural/immunology
- Killer Cells, Natural/pathology
- Male
- Melanoma, Experimental/immunology
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Receptor, Adenosine A2A/deficiency
- Receptor, Adenosine A2A/immunology
- Receptor, Adenosine A2A/metabolism
- Signal Transduction/immunology
- Tumor Microenvironment/immunology
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Affiliation(s)
- Arabella Young
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Shin Foong Ngiow
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
- Department of Microbiology and Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Yulong Gao
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Ann-Marie Patch
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Deborah S Barkauskas
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | - Gene Lin
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, and Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Jerome D Coudert
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kimberley A Stannard
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
- University Paris-Saclay, Kremlin Bicêtre, France
- CIC1428, Gustave Roussy Cancer Campus, Villejuif, France
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, France
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Joel Linden
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, and Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Nicholas D Huntington
- Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
- School of Medicine, University of Queensland, Herston, Queensland, Australia
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12
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Schuster IS, Coudert JD, Andoniou CE, Degli-Esposti MA. "Natural Regulators": NK Cells as Modulators of T Cell Immunity. Front Immunol 2016; 7:235. [PMID: 27379097 PMCID: PMC4905977 DOI: 10.3389/fimmu.2016.00235] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [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: 03/08/2016] [Accepted: 05/31/2016] [Indexed: 12/28/2022] Open
Abstract
Natural killer (NK) cells are known as frontline responders capable of rapidly mediating a response upon encountering transformed or infected cells. Recent findings indicate that NK cells, in addition to acting as innate effectors, can also regulate adaptive immune responses. Here, we review recent studies on the immunoregulatory function of NK cells with a specific focus on their ability to affect the generation of early, as well as long-term antiviral T cell responses, and their role in modulating immune pathology and disease. In addition, we summarize the current knowledge of the factors governing regulatory NK cell responses and discuss origin, tissue specificity, and open questions about the classification of regulatory NK cells as classical NK cells versus group 1 innate lymphoid cells.
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Affiliation(s)
- Iona S Schuster
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Jerome D Coudert
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Christopher E Andoniou
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
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13
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Forbes CA, Scalzo AA, Degli-Esposti MA, Coudert JD. Ly49C Impairs NK Cell Memory in Mouse Cytomegalovirus Infection. J Immunol 2016; 197:128-40. [PMID: 27233959 DOI: 10.4049/jimmunol.1600199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/03/2016] [Indexed: 01/06/2023]
Abstract
NK cells possess inhibitory receptors that are responsible for self-MHC class I recognition; beyond their inhibitory function, accumulating evidence indicates that such receptors confer NK cell functional competence through an unclear process termed "licensing." Ly49C is the main self-specific inhibitory Ly49 receptor in H-2(b) C57BL/6 (B6) mice. We used B6 Ly49C-transgenic and B6 β2 microglobulin (β2m)-knockout Ly49C-transgenic mice to investigate the impact of licensing through this inhibitory receptor in precursor and mature NK cells. We found that self-specific inhibitory receptors affected NK cell precursor survival and proliferation at particular developmental stages in an MHC class I-dependent manner. The presence of Ly49C impacted the NK cell repertoire in a β2m-dependent manner, with reduced Ly49A(+), Ly49G2(+), and Ly49D(+) subsets, an increased DNAM-1(+) subset, and higher NKG2D expression. Licensed NK cells displayed a skewed distribution of the maturation stages, which was characterized by differential CD27 and CD11b expression, toward the mature phenotypes. We found that Ly49C-mediated licensing induced a split effect on NK cell functions, with increased cytokine-production capabilities following engagement of various activating receptors while cytotoxicity remained unchanged. Analysis of licensed NK cell functions in vivo, in a system of mouse CMV infection, indicated that licensing did not play a major role in the NK cell antiviral response during acute infection, but it strongly impaired the generation and/or persistence of memory NK cells. This study unravels multifaceted effects of licensing on NK cell populations and their functions.
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Affiliation(s)
- Catherine A Forbes
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia 6009, Australia; and
| | - Anthony A Scalzo
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia 6009, Australia; and
| | - Mariapia A Degli-Esposti
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia 6009, Australia; and Centre for Ophthalmology and Vision Science, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jerome D Coudert
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia 6009, Australia; and Centre for Ophthalmology and Vision Science, University of Western Australia, Crawley, Western Australia 6009, Australia
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14
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Forbes CA, Coudert JD. Mechanisms regulating NK cell activation during viral infection. Future Virol 2015. [DOI: 10.2217/fvl.14.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT NK cells constitute a population of lymphocytes involved in innate immune functions. They play a critical role in antiviral immune surveillance. Viruses have evolved with their host species for millions of years, each exerting a selective pressure upon the other. As a corollary, the pathways used by the immune system that are critical to control viral infection can be revealed by defining the role of viral gene products that are nonessential for virus replication. We relate here the battery of resources available to NK cells to recognize and eliminate viruses and reciprocally the immune evasion mechanisms developed by viruses to prevent NK cell activation.
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Affiliation(s)
- Catherine A Forbes
- Centre for Experimental Immunology, Lions Eye Institute, 2 Verdun St, Nedlands, WA 6009, Australia
| | - Jerome D Coudert
- Centre for Experimental Immunology, Lions Eye Institute, 2 Verdun St, Nedlands, WA 6009, Australia
- Centre for Ophthalmology & Vision Science, M517, University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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15
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Schuster IS, Wikstrom ME, Brizard G, Coudert JD, Estcourt MJ, Manzur M, O'Reilly LA, Smyth MJ, Trapani JA, Hill GR, Andoniou CE, Degli-Esposti MA. TRAIL+ NK cells control CD4+ T cell responses during chronic viral infection to limit autoimmunity. Immunity 2015; 41:646-56. [PMID: 25367576 DOI: 10.1016/j.immuni.2014.09.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [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: 03/13/2014] [Accepted: 09/03/2014] [Indexed: 01/02/2023]
Abstract
Natural killer (NK) cells have been reported to control adaptive immune responses that occur in lymphoid organs at the early stages of immune challenge. The physiological purpose of such regulatory activity remains unclear, because it generally does not confer a survival advantage. We found that NK cells specifically eliminated activated CD4(+) T cells in the salivary gland during chronic murine cytomegalovirus (MCMV) infection. This was dependent on TNF-related apoptosis inducing ligand (TRAIL) expression by NK cells. Although NK cell-mediated deletion of CD4(+) T cells prolonged the chronicity of infection, it also constrained viral-induced autoimmunity. In the absence of this activity, chronic infection was associated with a Sjogren's-like syndrome characterized by focal lymphocytic infiltration into the glands, production of autoantibodies, and reduced saliva and tear secretion. Thus, NK cells are an important homeostatic control that balances the efficacy of adaptive immune responses with the risk of developing autoimmunity.
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Affiliation(s)
- Iona S Schuster
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Matthew E Wikstrom
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Geraldine Brizard
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Jerome D Coudert
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Marie J Estcourt
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Mitali Manzur
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Lorraine A O'Reilly
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Joseph A Trapani
- Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Geoffrey R Hill
- Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Christopher E Andoniou
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, WA 6009, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia.
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16
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Forbes CA, Scalzo AA, Degli-Esposti MA, Coudert JD. Ly49C-dependent control of MCMV Infection by NK cells is cis-regulated by MHC Class I molecules. PLoS Pathog 2014; 10:e1004161. [PMID: 24873973 PMCID: PMC4038614 DOI: 10.1371/journal.ppat.1004161] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/20/2014] [Indexed: 11/18/2022] Open
Abstract
Natural Killer (NK) cells are crucial in early resistance to murine cytomegalovirus (MCMV) infection. In B6 mice, the activating Ly49H receptor recognizes the viral m157 glycoprotein on infected cells. We previously identified a mutant strain (MCMVG1F) whose variant m157 also binds the inhibitory Ly49C receptor. Here we show that simultaneous binding of m157 to the two receptors hampers Ly49H-dependent NK cell activation as Ly49C-mediated inhibition destabilizes NK cell conjugation with their targets and prevents the cytoskeleton reorganization that precedes killing. In B6 mice, as most Ly49H+ NK cells do not co-express Ly49C, the overall NK cell response remains able to control MCMVm157G1F infection. However, in B6 Ly49C transgenic mice where all NK cells express the inhibitory receptor, MCMV infection results in altered NK cell activation associated with increased viral replication. Ly49C-mediated inhibition also regulates Ly49H-independent NK cell activation. Most interestingly, MHC class I regulates Ly49C function through cis-interactions that mask the receptor and restricts m157 binding. B6 Ly49C Tg, β2m ko mice, whose Ly49C receptors are unmasked due to MHC class I deficient expression, are highly susceptible to MCMVm157G1F and are unable to control a low-dose infection. Our study provides novel insights into the mechanisms that regulate NK cell activation during viral infection.
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Affiliation(s)
- Catherine A. Forbes
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Anthony A. Scalzo
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Mariapia A. Degli-Esposti
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
- Centre for Ophthalmology and Vision Science, M517, University of Western Australia, Crawley, Western Australia, Australia
| | - Jerome D. Coudert
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
- Centre for Ophthalmology and Vision Science, M517, University of Western Australia, Crawley, Western Australia, Australia
- * E-mail:
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Corbett AJ, Coudert JD, Forbes CA, Scalzo AA. Functional consequences of natural sequence variation of murine cytomegalovirus m157 for Ly49 receptor specificity and NK cell activation. J Immunol 2010; 186:1713-22. [PMID: 21187440 DOI: 10.4049/jimmunol.1003308] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Ly49H activating receptor on C57BL/6 (B6) NK cells plays a key role in early resistance to murine cytomegalovirus (MCMV) infection through specific recognition of the MCMV-encoded MHC class I-like molecule m157 expressed on infected cells. The m157 molecule is also recognized by the Ly49I inhibitory receptor from the 129/J mouse strain. The m157 gene is highly sequence variable among MCMV isolates, with many m157 variants unable to bind Ly49H(B6). In this study, we have sought to define if m157 variability leads to a wider spectrum of interactions with other Ly49 molecules and if this modifies host susceptibility to MCMV. We have identified novel m157-Ly49 receptor interactions, involving Ly49C inhibitory receptors from B6, BALB/c, and NZB mice, as well as the Ly49H(NZB) activation receptor. Using an MCMV recombinant virus in which m157(K181) was replaced with m157(G1F), which interacts with both Ly49H(B6) and Ly49C(B6), we show that the m157(G1F)-Ly49C interactions cause no apparent attenuating effect on viral clearance in B6 mice. Hence, when m157 can bind both inhibitory and activation NK cell receptors, the outcome is still activation. Thus, these data indicate that whereas m157 variants predominately interact with inhibitory Ly49 receptors, these interactions do not profoundly interfere with early NK cell responses.
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Affiliation(s)
- Alexandra J Corbett
- Centre for Ophthalmology and Vision Science, University of Western Australia, Crawley, Western Australia 6009, Australia
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Foucras G, Coudert JD, Coureau C, Guéry JC. Dendritic cells prime in vivo alloreactive CD4 T lymphocytes toward type 2 cytokine- and TGF-beta-producing cells in the absence of CD8 T cell activation. J Immunol 2000; 165:4994-5003. [PMID: 11046027 DOI: 10.4049/jimmunol.165.9.4994] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mechanisms that influence the polarization of CD4 T cells specific for allogeneic MHC class II molecules in vivo are still poorly understood. We have examined the pathway of alloreactive CD4 T cell differentiation in a situation in which only CD4 T cells could be activated in vivo. In this report we show that priming of adult mice with allogeneic APC, in the absence of MHC class I-T cell interactions, induces a strong expansion of type 2 cytokine-producing allohelper T cells. These alloantigen-specific CD4 T cells directly recognize native allogeneic MHC class II molecules on APC and secrete, in addition to the prototypic Th2 cytokines IL-4, IL-5, and IL-10, large amounts of TGF-beta. The default Th2-phenotype acquisition is not genetically controlled and occurred both in BALB/c and C57BL/6 mice. CD8 T cells are the principal cell type that controls CD4 T cell differentiation in vivo. Furthermore, we demonstrate that strong Th2 priming can be induced not only with allogeneic splenocytes but also with a low number of bone marrow-derived dendritic cells. Finally, using a passive transfer system, we provide direct evidence that CD8 T cell expansion in situ promotes alloreactive Th1 cell development principally by preventing their default development to the Th2 pathway in a mechanism that is largely IFN-gamma independent. Therefore, this work demonstrates that type 2 cytokine production represents a dominant pathway of alloreactive CD4 T cell differentiation in adult mice, a phenomenon that was initially thought to occur only during the neonatal period.
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Affiliation(s)
- G Foucras
- Institut National de la Santé et de la Recherche Médicale Unité 28, Institut Fédératif de Recherche 30, Hôpital Purpan, Toulouse, France
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Coudert JD, Foucras G, Demur C, Coureau C, Mazerolles C, Delsol G, Druet P, Guéry JC. Lethal host-versus-graft disease and hypereosinophilia in the absence of MHC I-T-cell interactions. J Clin Invest 2000; 105:1125-32. [PMID: 10772657 PMCID: PMC300836 DOI: 10.1172/jci9243] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [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: 12/22/1999] [Accepted: 03/07/2000] [Indexed: 11/17/2022] Open
Abstract
Neonatal injection of semiallogeneic spleen cells in BALB/c mice induces a self-limited state of chimerism that promotes the differentiation of donor-specific CD4 T cells toward the Th2 phenotype. Here we show that injection of spleen cells from beta2-microglobulin-deficient (BALB/c x C57BL/6) F1 mice into BALB/c newborns with a disrupted beta2-microglobulin (beta2m) gene results in a lethal lymphoproliferative disorder associated with uncontrolled Th2 response, long-term persistence of donor B cells, and sustained blood eosinophilia. Autoimmune manifestations are also enhanced and characterized by a severe autoantibody-mediated glomerulonephritis. Histological examination of the spleen shows a hyperplasia of periarteriolar lymphoid sheaths, with accumulation of eosinophils and basophils, and variable degree of fibrosis. Perivascular lymphoid infiltrates with eosinophils are also found in the lung and are correlated with disease severity. Such abnormalities are almost absent using beta2m-sufficient mice. These data demonstrate that induction of lymphoid chimerism in the absence of MHC class I-T-cell interactions results in a lethal form of host-versus-graft disease that represents a unique model of Th2-dependent chronic inflammatory disease associated with an hypereosinophilic syndrome in mice.
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Affiliation(s)
- J D Coudert
- Institut National de la Santé et de la Recherche Médicale (INSERM) U28, Institut Fédératif de Recherche 30, and Université Paul Sabatier, Toulouse, France
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