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Odia T, Malherbe ST, Meier S, Maasdorp E, Kleynhans L, du Plessis N, Loxton AG, Zak DE, Thompson E, Duffy FJ, Kuivaniemi H, Ronacher K, Winter J, Walzl G, Tromp G. The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment. Front Immunol 2021; 11:596173. [PMID: 33643286 PMCID: PMC7902901 DOI: 10.3389/fimmu.2020.596173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
Pulmonary tuberculosis (PTB) is characterized by lung granulomas, inflammation and tissue destruction. Here we used within-subject peripheral blood gene expression over time to correlate with the within-subject lung metabolic activity, as measured by positron emission tomography (PET) to identify biological processes and pathways underlying overall resolution of lung inflammation. We used next-generation RNA sequencing and [18F]FDG PET-CT data, collected at diagnosis, week 4, and week 24, from 75 successfully cured PTB patients, with the [18F]FDG activity as a surrogate for lung inflammation. Our linear mixed-effects models required that for each individual the slope of the line of [18F]FDG data in the outcome and the slope of the peripheral blood transcript expression data correlate, i.e., the slopes of the outcome and explanatory variables had to be similar. Of 10,295 genes that changed as a function of time, we identified 639 genes whose expression profiles correlated with decreasing [18F]FDG uptake levels in the lungs. Gene enrichment over-representation analysis revealed that numerous biological processes were significantly enriched in the 639 genes, including several well known in TB transcriptomics such as platelet degranulation and response to interferon gamma, thus validating our novel approach. Others not previously associated with TB pathobiology included smooth muscle contraction, a set of pathways related to mitochondrial function and cell death, as well as a set of pathways connecting transcription, translation and vesicle formation. We observed up-regulation in genes associated with B cells, and down-regulation in genes associated with platelet activation. We found 254 transcription factor binding sites to be enriched among the 639 gene promoters. In conclusion, we demonstrated that of the 10,295 gene expression changes in peripheral blood, only a subset of 639 genes correlated with inflammation in the lungs, and the enriched pathways provide a description of the biology of resolution of lung inflammation as detectable in peripheral blood. Surprisingly, resolution of PTB inflammation is positively correlated with smooth muscle contraction and, extending our previous observation on mitochondrial genes, shows the presence of mitochondrial stress. We focused on pathway analysis which can enable therapeutic target discovery and potential modulation of the host response to TB.
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Affiliation(s)
- Trust Odia
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Stephanus T Malherbe
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Stuart Meier
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Elizna Maasdorp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Léanie Kleynhans
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Nelita du Plessis
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Andre G Loxton
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Daniel E Zak
- Center for Infectious Disease Research, Seattle, WA, United States
| | - Ethan Thompson
- Center for Infectious Disease Research, Seattle, WA, United States
| | - Fergal J Duffy
- Center for Infectious Disease Research, Seattle, WA, United States.,Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Helena Kuivaniemi
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Katharina Ronacher
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Translational Research Institute, Mater Research Institute - The University of Queensland, Brisbane, QLD, Australia
| | - Jill Winter
- Catalysis Foundation for Health, San Ramon, CA, United States
| | - Gerhard Walzl
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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Cahalane AM, Purcell YM, Lavelle LP, McEvoy SH, Ryan ER, O'Toole E, Malone DE. Which is the best current guideline for the diagnosis and management of cystic pancreatic neoplasms? An appraisal using evidence-based practice methods. Eur Radiol 2016; 26:3121-8. [PMID: 26762943 DOI: 10.1007/s00330-015-4160-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIM Cystic pancreatic neoplasms (CPNs) are an increasingly diagnosed entity. Their heterogeneity poses complex diagnostic and management challenges. Despite frequently encountering these entities, particularly in the context of the increased imaging of patients in modern medicine, doctors have to rely on incomplete and ambiguous published literature. The aim of this project was to review the guidelines relating to CPNs using evidence-based practice (EBP) methods. METHODS A search of both the primary and secondary literature was performed. Five sets of guidelines were identified which were then methodologically appraised by the AGREE II instrument, a validated and widely utilised tool for guideline development assessment. RESULTS The 2014 'Italian consensus guidelines for the diagnostic work-up and follow-up of cystic pancreatic neoplasms' were found to be the most methodologically sound guidelines, on the basis of both the overall score and average weighted domain score. CONCLUSIONS The current best guidelines were identified. The Appraisal of Guidelines for Research and Evaluation (AGREE II) instrument can be used for retrospective review of published guidelines or as a roadmap for guideline-writing groups. All guidelines found were methodologically limited. Further longitudinal/prospective studies are required to improve the level of evidence. KEY POINTS • Cystic pancreatic neoplasms (CPNs) are an increasingly encountered entity in modern medicine. • Clinical uncertainty remains with regard to optimal diagnostic and management strategies. • The Italian consensus guidelines for cystic pancreatic neoplasms are currently the best guidelines.
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Affiliation(s)
| | - Y M Purcell
- St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - L P Lavelle
- St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - S H McEvoy
- St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - E R Ryan
- St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - E O'Toole
- National Cancer Control Programme, King's Inns House, 200 Parnell Street, Dublin 1, Ireland
| | - D E Malone
- St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
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