1
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Ratnatunga CN, Tungatt K, Proietti C, Halstrom S, Holt MR, Lutzky VP, Price P, Doolan DL, Bell SC, Field MA, Kupz A, Thomson RM, Miles JJ. Characterizing and correcting immune dysfunction in non-tuberculous mycobacterial disease. Front Immunol 2022; 13:1047781. [PMID: 36439147 PMCID: PMC9686449 DOI: 10.3389/fimmu.2022.1047781] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/25/2022] [Indexed: 10/29/2023] Open
Abstract
Non-tuberculous mycobacterial pulmonary disease (NTM-PD) is a chronic, progressive, and growing worldwide health burden associated with mounting morbidity, mortality, and economic costs. Improvements in NTM-PD management are urgently needed, which requires a better understanding of fundamental immunopathology. Here, we examine temporal dynamics of the immune compartment during NTM-PD caused by Mycobacterium avium complex (MAC) and Mycobactereoides abscessus complex (MABS). We show that active MAC infection is characterized by elevated T cell immunoglobulin and mucin-domain containing-3 expression across multiple T cell subsets. In contrast, active MABS infection was characterized by increased expression of cytotoxic T-lymphocyte-associated protein 4. Patients who failed therapy closely mirrored the healthy individual immune phenotype, with circulating immune network appearing to 'ignore' infection in the lung. Interestingly, immune biosignatures were identified that could inform disease stage and infecting species with high accuracy. Additionally, programmed cell death protein 1 blockade rescued antigen-specific IFN-γ secretion in all disease stages except persistent infection, suggesting the potential to redeploy checkpoint blockade inhibitors for NTM-PD. Collectively, our results provide new insight into species-specific 'immune chatter' occurring during NTM-PD and provide new targets, processes and pathways for diagnostics, prognostics, and treatments needed for this emerging and difficult to treat disease.
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Affiliation(s)
- Champa N. Ratnatunga
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
- Queensland Institute of Medical Research (QIMR) Berghofer, Brisbane, QLD, Australia
- Faculty of Medicine, University of Peradeniya, Kandy, Sri Lanka
| | - Katie Tungatt
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Carla Proietti
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Sam Halstrom
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Michael R. Holt
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
- Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
- Gallipoli Medical Research Institute, Greenslopes Private Hospital Foundation, Brisbane, QLD, Australia
| | - Viviana P. Lutzky
- Queensland Institute of Medical Research (QIMR) Berghofer, Brisbane, QLD, Australia
| | - Patricia Price
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Denise L. Doolan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Scott C. Bell
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
- Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Matt A. Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
| | - Andreas Kupz
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Rachel M. Thomson
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
- Division of Infection and Immunity, University Hospital Wales, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom
| | - John J. Miles
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Queensland Institute of Medical Research (QIMR) Berghofer, Brisbane, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
- Division of Infection and Immunity, University Hospital Wales, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, Wales, United Kingdom
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2
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Karunathilake RP, Hewage S, Vidanapathirana G, Kumara A, Ranasinghe P, Noordeen F, Gawarammana I, Ratnatunga CN. Pre-vaccination RT-PCR negative contacts in workplace settings show high, SARS COV-2 neutralizing antibody levels. BMC Public Health 2022; 22:1961. [PMID: 36284261 PMCID: PMC9593990 DOI: 10.1186/s12889-022-14381-5] [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: 06/29/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Asymptomatic SARS-CoV-2 infection occurring in RT-PCR negative individuals represent a poorly characterized cohort with important infection control connotations. While household and community-based studies have evaluated seroprevalence of antibody and transmission dynamics in this group, workplace-based data is currently unavailable. Methods A cohort study was carried out in July 2021, during and immediately following the peak of the 3rd wave of COVID-19 in Sri Lanka, prior to mass vaccination. A total of 92 unvaccinated individuals between the ages of 17–65 years were purposively sampled from an office and two factory settings. The selected cohort that had been exposed to RT-PCR positive cases in the workplace was tested RT-PCR negative. Serological samples collected six weeks post exposure were tested for anti-SARS-CoV-2 neutralizing antibody. Results The seroprevalence for SARS-CoV-2 specific neutralizing antibodies in the overall cohort was 63.04% (58/92). Seroprevalences in the office setting, factory setting 1 and factory setting 2 were 69.2% (9/13), 55.7% (34/61) and 83.33% (15/18), respectively. Primary risk factor associated with seropositivity was face to face contact with no mask for > 15 min (p < 0.024, Odds Ratio (OR); 5.58, 95%CI;1.292– 25.65). Individuals with workspace exposure had significantly higher levels of neutralizing antibodies than those who did not (percentage neutralization in assay 63.3% (SD:21)vs 45.7% (SD:20), p = 0.0042), as did individuals who engaged socially without protective measures (62.4 (SD:21.6)% vs 49.7 (SD:21)%, p = 0.026). Conclusion There was a high seroprevalence for SARS-CoV-2 specific neutralizing antibodies among RT-PCR negative contacts in workplace settings in Sri Lanka. Higher levels of transmission of SARS-CoV-2 infection than estimated based on RT-PCR positive contact data indicate need for targeted infection control measures in these settings during future outbreaks. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-14381-5.
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Affiliation(s)
- Ridma P Karunathilake
- grid.11139.3b0000 0000 9816 8637Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, 20400 Sri Lanka
| | - Sameera Hewage
- Office of the Regional Director of Health Services, Kandy, Sri Lanka
| | - Gihani Vidanapathirana
- grid.11139.3b0000 0000 9816 8637Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, 20400 Sri Lanka ,grid.11139.3b0000 0000 9816 8637Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Peradeniya, Kandy, Sri Lanka
| | - Athula Kumara
- grid.11139.3b0000 0000 9816 8637Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, 20400 Sri Lanka
| | | | - Faseeha Noordeen
- grid.11139.3b0000 0000 9816 8637Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, 20400 Sri Lanka
| | - Indika Gawarammana
- grid.11139.3b0000 0000 9816 8637Department of Medicine, Faculty of Medicine, University of Peradeniya, Peradeniya, 20400 Sri Lanka
| | - Champa N Ratnatunga
- grid.11139.3b0000 0000 9816 8637Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, 20400 Sri Lanka
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3
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Cobos C, Bansal PS, Wilson DT, Jones L, Zhao G, Field MA, Eichenberger RM, Pickering DA, Ryan RYM, Ratnatunga CN, Miles JJ, Ruscher R, Giacomin PR, Navarro S, Loukas A, Daly NL. Peptides derived from hookworm anti-inflammatory proteins suppress inducible colitis in mice and inflammatory cytokine production by human cells. Front Med (Lausanne) 2022; 9:934852. [PMID: 36186812 PMCID: PMC9524151 DOI: 10.3389/fmed.2022.934852] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open
Abstract
A decline in the prevalence of parasites such as hookworms appears to be correlated with the rise in non-communicable inflammatory conditions in people from high- and middle-income countries. This correlation has led to studies that have identified proteins produced by hookworms that can suppress inflammatory bowel disease (IBD) and asthma in animal models. Hookworms secrete a family of abundant netrin-domain containing proteins referred to as AIPs (Anti-Inflammatory Proteins), but there is no information on the structure-function relationships. Here we have applied a downsizing approach to the hookworm AIPs to derive peptides of 20 residues or less, some of which display anti-inflammatory effects when co-cultured with human peripheral blood mononuclear cells and oral therapeutic activity in a chemically induced mouse model of acute colitis. Our results indicate that a conserved helical region is responsible, at least in part, for the anti-inflammatory effects. This helical region has potential in the design of improved leads for treating IBD and possibly other inflammatory conditions.
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Affiliation(s)
- Claudia Cobos
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paramjit S. Bansal
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - David T. Wilson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Linda Jones
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Guangzu Zhao
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Matthew A. Field
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ramon M. Eichenberger
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren A. Pickering
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Rachael Y. M. Ryan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Champa N. Ratnatunga
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - John J. Miles
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paul R. Giacomin
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Severine Navarro
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Health, Woolworths Centre for Childhood Nutrition Research, Queensland University of Technology, South Brisbane, QLD, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- *Correspondence: Alex Loukas,
| | - Norelle L. Daly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Norelle L. Daly,
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4
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Ratnatunga CN, Lutzky VP, Kupz A, Doolan DL, Reid DW, Field M, Bell SC, Thomson RM, Miles JJ. The Rise of Non-Tuberculosis Mycobacterial Lung Disease. Front Immunol 2020; 11:303. [PMID: 32194556 PMCID: PMC7062685 DOI: 10.3389/fimmu.2020.00303] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [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: 10/25/2019] [Accepted: 02/06/2020] [Indexed: 12/21/2022] Open
Abstract
The incidence and number of deaths from non-tuberculous mycobacterial (NTM) disease have been steadily increasing globally. These lesser known “cousins” of Mycobacterium tuberculosis (TB) were once thought to be harmless environmental saprophytics and only dangerous to individuals with defective lung structure or the immunosuppressed. However, NTM are now commonly infecting seemingly immune competent children and adults at increasing rates through pulmonary infection. This is of concern as the pathology of NTM is difficult to treat. Indeed, NTM have become extremely antibiotic resistant, and now have been found to be internationally dispersed through person-to-person contact. The reasons behind this NTM increase are only beginning to be elucidated. Solutions to the problem are needed given NTM disease is more common in the tropics. Importantly, 40% of the world's population live in the tropics and due to climate change, the Tropics are expanding which will increase NTM infection regions. This review catalogs the global and economic disease burden, at risk populations, treatment options, host-bacterial interaction, immune dynamics, recent developments and research priorities for NTM disease.
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Affiliation(s)
- Champa N. Ratnatunga
- The Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- *Correspondence: Champa N. Ratnatunga
| | - Viviana P. Lutzky
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Andreas Kupz
- The Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Denise L. Doolan
- The Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - David W. Reid
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Matthew Field
- The Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
| | - Scott C. Bell
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Rachel M. Thomson
- Immunology Department, Gallipoli Medical Research Institute, Brisbane, QLD, Australia
| | - John J. Miles
- The Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
- John J. Miles
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5
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Lepletier A, Lutzky VP, Mittal D, Stannard K, Watkins TS, Ratnatunga CN, Smith C, McGuire HM, Kemp RA, Mukhopadhyay P, Waddell N, Smyth MJ, Dougall WC, Miles JJ. The immune checkpoint CD96 defines a distinct lymphocyte phenotype and is highly expressed on tumor-infiltrating T cells. Immunol Cell Biol 2018; 97:152-164. [PMID: 30222899 DOI: 10.1111/imcb.12205] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/13/2018] [Accepted: 09/13/2018] [Indexed: 12/01/2022]
Abstract
CD96 has recently been shown to be a potent immune checkpoint molecule in mice, but a similar role in humans is not known. In this study, we provide a detailed map of CD96 expression across human lymphocyte lineages, the kinetics of CD96 regulation on T-cell activation and co-expression with other conventional and emerging immune checkpoint molecules. We show that CD96 is predominantly expressed by T cells and has a unique lymphocyte expression profile. CD96high T cells exhibited distinct effector functions on activation. Of note, CD96 expression was highly correlated with T-cell markers in primary and metastatic human tumors and was elevated on antigen-experienced T cells and tumor-infiltrating lymphocytes. Collectively, these data demonstrate that CD96 may be a promising immune checkpoint to enhance T-cell function against human cancer and infectious disease.
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Affiliation(s)
- Ailin Lepletier
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Viviana P Lutzky
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Deepak Mittal
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kimberley Stannard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Champa N Ratnatunga
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia.,Centre for Biodiscovery and Molecular Development of Therapeutics, AITHM, James Cook University, Cairns, QLD 4870, Australia
| | - Corey Smith
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Helen M McGuire
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.,Ramaciotti Facility for Human Systems Biology, University of Sydney, Sydney, NSW 2006, Australia
| | - Roslyn A Kemp
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand
| | | | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Mark J Smyth
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - William C Dougall
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia.,Centre for Biodiscovery and Molecular Development of Therapeutics, AITHM, James Cook University, Cairns, QLD 4870, Australia.,Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK.,Medicine, Dentistry and Health, Griffith University, Brisbane, QLD 4111, Australia
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6
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Lutzky VP, Ratnatunga CN, Smith DJ, Kupz A, Doolan DL, Reid DW, Thomson RM, Bell SC, Miles JJ. Anomalies in T Cell Function Are Associated With Individuals at Risk of Mycobacterium abscessus Complex Infection. Front Immunol 2018; 9:1319. [PMID: 29942313 PMCID: PMC6004551 DOI: 10.3389/fimmu.2018.01319] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 05/28/2018] [Indexed: 12/13/2022] Open
Abstract
The increasing global incidence and prevalence of non-tuberculous mycobacteria (NTM) infection is of growing concern. New evidence of person-to-person transmission of multidrug-resistant NTM adds to the global concern. The reason why certain individuals are at risk of NTM infections is unknown. Using high definition flow cytometry, we studied the immune profiles of two groups that are at risk of Mycobacterium abscessus complex infection and matched controls. The first group was cystic fibrosis (CF) patients and the second group was elderly individuals. CF individuals with active M. abscessus complex infection or a history of M. abscessus complex infection exhibited a unique surface T cell phenotype with a marked global deficiency in TNFα production during mitogen stimulation. Importantly, immune-based signatures were identified that appeared to predict at baseline the subset of CF individuals who were at risk of M. abscessus complex infection. In contrast, elderly individuals with M. abscessus complex infection exhibited a separate T cell phenotype underlined by the presence of exhaustion markers and dysregulation in type 1 cytokine release during mitogen stimulation. Collectively, these data suggest an association between T cell signatures and individuals at risk of M. abscessus complex infection, however, validation of these immune anomalies as robust biomarkers will require analysis on larger patient cohorts.
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Affiliation(s)
- Viviana P Lutzky
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Champa N Ratnatunga
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Centre for Biodiscovery and Molecular Development of Therapeutics, Centre for Biosecurity and Tropical Infectious Diseases, AITHM, James Cook University, Cairns, QLD, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Daniel J Smith
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Andreas Kupz
- Centre for Biodiscovery and Molecular Development of Therapeutics, Centre for Biosecurity and Tropical Infectious Diseases, AITHM, James Cook University, Cairns, QLD, Australia
| | - Denise L Doolan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Centre for Biodiscovery and Molecular Development of Therapeutics, Centre for Biosecurity and Tropical Infectious Diseases, AITHM, James Cook University, Cairns, QLD, Australia
| | - David W Reid
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Rachel M Thomson
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Gallipoli Medical Research Institute, Brisbane, QLD, Australia
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Centre for Biodiscovery and Molecular Development of Therapeutics, Centre for Biosecurity and Tropical Infectious Diseases, AITHM, James Cook University, Cairns, QLD, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
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7
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Proietti C, Zakrzewski M, Watkins TS, Berger B, Hasan S, Ratnatunga CN, Brion MJ, Crompton PD, Miles JJ, Doolan DL, Krause L. Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server. Sci Rep 2016; 6:38178. [PMID: 27922118 PMCID: PMC5138638 DOI: 10.1038/srep38178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 12/21/2022] Open
Abstract
Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data.
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Affiliation(s)
- Carla Proietti
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Bernard Berger
- Nestlé Research Centre, Vers-chez-les-Blanc, Lausanne, Switzerland
| | - Shihab Hasan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | | | - Marie-Jo Brion
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health &Medicine, James Cook University, Cairns, QLD, Australia
| | - Denise L Doolan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health &Medicine, James Cook University, Cairns, QLD, Australia
| | - Lutz Krause
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
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8
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Ratnatunga CN, Thevanesam V, Nandadeva D, Madegedara D, Athula Kumara K. Cross-sectional screening of healthcare workers at a regional chest clinic with an interferon gamma release assay: first report from Sri Lanka. ACTA ACUST UNITED AC 2015. [DOI: 10.1071/hi15002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Ratnatunga CN, Thevanesam V, Madegedara D, Dissanayake NLA, Kumara KA. T-SPOT. TB assay and tuberculin skin test for diagnosis and screening of tuberculosis: First report in a Sri lankan population. Asian J Med Sci 2015. [DOI: 10.3126/ajms.v7i1.12595] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Objective: Guidelines encourage evaluation of an Interferon Gamma Release Assay (IGRA) in the local setting, particularly in low/ middle income, Bacillus Calmette Guerin (BCG) vaccinated populations where the assays have shown variable utility. The TSPOT.TB assay and the Tuberculin Skin Test (TST) were compared in diagnosis of active tuberculosis (TB) and in contact screening in an adult Sri Lankan population.Methods: A prospective study including confirmed TB cases (n=75), controls (n-74) and close contacts of smear positive cases (n=27) was carried out at the regional Chest clinic in Kandy district. Clinical history and investigation findings, including TST results were recorded and the TSPOT.TB (Oxford Immunotec) performed.Results: The presence of diabetes and cavitation were significant predictors of TSPOT.TB positivity, while TST had no significant clinical predictors. In the diagnosis of active TB, TSPOT.TB sensitivity was 73.3% (95% CI, 58.6-84.6%) and a specificity was 72% (95% CI, 62.0-85.5%) while the TST sensitivity was 70.7% (95% CI, 54.2-83.3%) and specificity was 64.1% (95% CI, 49.7-76.5%). In contact investigation neither test showed an association with exposure level. Cost estimate was LKR 9400.00 per TSPOT.TB test compared to LKR 200.00 per TST. A high (21%) indeterminate result rate was seen with the TSPOT.TB assayConclusions: This study did not show any advantage in using TSPOT.TB over TST in this setting.Asian Journal of Medical Sciences Vol.7(1) 2015 14-19
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Dassanayake DLB, Wimalaratna H, Nandadewa D, Nugaliyadda A, Ratnatunga CN, Agampodi SB. Predictors of the development of myocarditis or acute renal failure in patients with leptospirosis: an observational study. BMC Infect Dis 2012; 12:4. [PMID: 22243770 PMCID: PMC3292442 DOI: 10.1186/1471-2334-12-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 01/13/2012] [Indexed: 11/19/2022] Open
Abstract
Background Leptospirosis has a varied clinical presentation with complications like myocarditis and acute renal failure. There are many predictors of severity and mortality including clinical and laboratory parameters. Early detection and treatment can reduce complications. Therefore recognizing the early predictors of the complications of leptospirosis is important in patient management. This study was aimed at determining the clinical and laboratory predictors of myocarditis or acute renal failure. Methods This was a prospective descriptive study carried out in the Teaching Hospital, Kandy, from 1st July 2007 to 31st July 2008. Patients with clinical features compatible with leptospirosis case definition were confirmed using the Microscopic Agglutination Test (MAT). Clinical features and laboratory measures done on admission were recorded. Patients were observed for the development of acute renal failure or myocarditis. Chi-square statistics, Fisher's exact test and Mann-Whitney U test were used to compare patients with and without complications. A logistic regression model was used to select final predictor variables. Results Sixty two confirmed leptospirosis patients were included in the study. Seven patients (11.3%) developed acute renal failure and five (8.1%) developed myocarditis while three (4.8%) had both acute renal failure and myocarditis. Conjunctival suffusion - 40 (64.5%), muscle tenderness - 28 (45.1%), oliguria - 20 (32.2%), jaundice - 12 (19.3%), hepatomegaly - 10 (16.1%), arrhythmias (irregular radial pulse) - 8 (12.9%), chest pain - 6 (9.7%), bleeding - 5 (8.1%), and shortness of breath (SOB) 4 (6.4%) were the common clinical features present among the patients. Out of these, only oliguria {odds ratio (OR) = 4.14 and 95% confidence interval (CI) 1.003-17.261}, jaundice (OR = 5.13 and 95% CI 1.149-28.003), and arrhythmias (OR = 5.774 and 95% CI 1.001-34.692), were predictors of myocarditis or acute renal failure and none of the laboratory measures could predict the two complications. Conclusions This study shows that out of clinical and laboratory variables, only oliguria, jaundice and arrhythmia are strong predictors of development of acute renal failure or myocarditis in patients with leptospirosis presented to Teaching Hospital of Kandy, Sri Lanka.
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Dassanayake D, Agampodi SB, Nugaliyadda A, Wimalaratna H, Nandadewa D, Ratnatunga CN. Predictors of the development of myocarditis and acute renal failure in patients with leptospirosis. ACTA ACUST UNITED AC 2012. [DOI: 10.4103/1755-6783.98627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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