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Djukanović R, Brinkman P, Kolmert J, Gomez C, Schofield J, Brandsma J, Shapanis A, Skipp PJS, Postle A, Wheelock C, Dahlén SE, Sterk PJ, Brown T, Jackson DJ, Mansur A, Pavord I, Patel M, Brightling C, Siddiqui S, Bradding P, Sabroe I, Saralaya D, Chishimba L, Porter J, Robinson D, Fowler SJ, Howarth PH, Little L, Oliver T, Hill K, Stanton L, Allen A, Ellis D, Griffiths G, Harrison T, Akenroye A, Lasky-Su J, Heaney L, Chaudhuri R, Kurukulaaratchy R. Biomarker Predictors of Clinical Efficacy of the Anti-IgE Biologic, Omalizumab, in Severe Asthma in Adults: Results of the SoMOSA Study. Am J Respir Crit Care Med 2024. [PMID: 38635834 DOI: 10.1164/rccm.202310-1730oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/18/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND The anti-IgE monoclonal, omalizumab, is widely used for severe asthma. This study aimed to identify biomarkers that predict clinical improvement during one year of omalizumab treatment. METHODS 1-year, open-label, Study of Mechanisms of action of Omalizumab in Severe Asthma (SoMOSA) involving 216 severe (GINA step 4/5) uncontrolled atopic asthmatics (≥2 severe exacerbations in previous year) on high-dose inhaled corticosteroids, long-acting β-agonists, ± mOCS. It had two phases: 0-16 weeks, to assess early clinical improvement by Global Evaluation of Therapeutic Effectiveness (GETE), and 16-52 weeks, to assess late responses by ≥50% reduction in exacerbations or dose of maintenance oral corticosteroids (mOCS). All participants provided samples (exhaled breath, blood, sputum, urine) before and after 16 weeks of omalizumab treatment. RESULTS 191 patients completed phase 1; 63% had early improvement. Of 173 who completed phase 2, 69% had reduced exacerbations by ≥50%, while 57% (37/65) on mOCS reduced their dose by ≥50%. The primary outcome 2, 3-dinor-11-β-PGF2α, GETE and standard clinical biomarkers (blood and sputum eosinophils, exhaled nitric oxide, serum IgE) did not predict either clinical response. Five breathomics (GC-MS) and 5 plasma lipid biomarkers strongly predicted the ≥50% reduction in exacerbations (receiver operating characteristic area under the curve (AUC): 0.780 and 0.922, respectively) and early responses (AUC:0.835 and 0.949, respectively). In independent cohorts, the GC-MS biomarkers differentiated between severe and mild asthma. Conclusions This is the first discovery of omics biomarkers that predict improvement to a biologic for asthma. Their prospective validation and development for clinical use is justified. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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Affiliation(s)
- Ratko Djukanović
- Southampton University, Clinical and Experimental Sciences and Southampton NIHR Respiratory Biomedical Research Unit, Southampton, United Kingdom of Great Britain and Northern Ireland;
| | - Paul Brinkman
- Amsterdam UMC - Locatie AMC, 26066, Pulmonary Medicine, Amsterdam, North Holland, Netherlands
| | - Johan Kolmert
- Karolinska Institutet, Institute of Environmental Medicine, Stockholm, Sweden
| | - Cristina Gomez
- Karolinska Institutet Institute of Environmental Medicine, 193414, Stockholm, Sweden
- Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - James Schofield
- University of Southampton Centre for Biological Sciences, 98463, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Joost Brandsma
- University of Southampton Faculty of Medicine, NIHR Southampton Biomedical Research Centre, CES, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Andy Shapanis
- Southampton University, Biological Sciences, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Paul J S Skipp
- University of Southampton Centre for Biological Sciences, 98463, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Anthony Postle
- University of Southampton, Clinical & Experimental Sciences, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Craig Wheelock
- Karolinska Institutet, 27106, Medical Biochemistry and Biophysics, Stockholm, Stockholm County, Sweden
| | - Sven-Erik Dahlén
- Karolinska Intitutet, Centre for Allergy Research, Stockholm, Sweden
| | - Peter J Sterk
- University of Amsterdam, Academic Medical Center, Pulmonology, F5-259, Amsterdam, Netherlands
| | - Thomas Brown
- Portsmouth Hospitals NHS Trust, Respiratory Medicine, Portsmouth, Hampshire, United Kingdom of Great Britain and Northern Ireland
| | - David J Jackson
- Guy's and St. Thomas' Hospitals, Guy's Severe Asthma Centre, London, United Kingdom of Great Britain and Northern Ireland
| | - Adel Mansur
- Birmingham Heartlands Hospital, Respiratory Medicine, Birmingham, West Midlands, United Kingdom of Great Britain and Northern Ireland
| | - Ian Pavord
- Oxford University, Nuffield department of Medicine, Respiratory Medicine, Oxford, Oxfordshire, United Kingdom of Great Britain and Northern Ireland
| | - Mitesh Patel
- University Hospitals Plymouth NHS Trust, 6634, Respiratory Medicine and R&D, Plymouth, United Kingdom of Great Britain and Northern Ireland
| | - Christopher Brightling
- University of Leicester, Department of Infection, Immunity and Inflammation, Leicester, United Kingdom of Great Britain and Northern Ireland
| | - Salman Siddiqui
- Imperial College London, 4615, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Peter Bradding
- Leicester Institute for Lung Health, Department of Infection, Immunity and Inflammation, Leicester, United Kingdom of Great Britain and Northern Ireland
| | - Ian Sabroe
- University of Sheffield, Division of Genomic Medicine, Sheffield, United Kingdom of Great Britain and Northern Ireland
| | - Dinesh Saralaya
- Bradford Teaching Hospitals NHS Foundation Trust, 1906, Bradford, United Kingdom of Great Britain and Northern Ireland
| | - Livingstone Chishimba
- Liverpool School of Tropical Medicine, 9655, Clinical Sciences, Liverpool, United Kingdom of Great Britain and Northern Ireland
| | - Joanna Porter
- University College London, Centre for Inflammation and Tissue Repair, London, United Kingdom of Great Britain and Northern Ireland
| | - Douglas Robinson
- University College London, 4919, UCL Respiratory and NIHR University College London Hospitals Biomedical Research Centre, London, United Kingdom of Great Britain and Northern Ireland
| | - Stephen J Fowler
- University of Manchester, Respiratory Research Group, Manchester, United Kingdom of Great Britain and Northern Ireland
| | - Peter H Howarth
- University of Southampton, 7423, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Louisa Little
- Southampton University Hospitals NHS Trust, 7425, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Thomas Oliver
- University of Southampton Faculty of Medicine, 12211, Southampton Clinical Trials Unit, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Kayleigh Hill
- University of Southampton Faculty of Medicine, 12211, Southampton Clinical trials Unit, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Louise Stanton
- University of Southampton Faculty of Medicine, 12211, Southampton Clinical Trials Unit, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Alexander Allen
- University of Southampton Faculty of Medicine, 12211, Southampton Clinical Trials Unit, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Deborah Ellis
- University of Southampton Faculty of Medicine, 12211, Southampton Clinical Trials Unit, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Gareth Griffiths
- University of Southampton Faculty of Medicine, 12211, Southampton Clinical Trials Unit, Southampton, United Kingdom of Great Britain and Northern Ireland
| | - Tim Harrison
- University of Nottingham, 6123, Division of Respiratory Medicine and Respiratory Research Unit, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Ayobami Akenroye
- Brigham and Women's Hospital, 1861, Medicine (Allergy & Clinical Immunology), Boston, Massachusetts, United States
| | - Jessica Lasky-Su
- Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Liam Heaney
- Belfast City Hospital, Regional Respiratory Centre, Belfast, United Kingdom of Great Britain and Northern Ireland
| | - Rekha Chaudhuri
- Gartnavel General Hospital, 59731, Glasgow, United Kingdom of Great Britain and Northern Ireland
- Glasgow Caledonian University School of Health and Life Sciences, 150824, Glasgow, United Kingdom of Great Britain and Northern Ireland
| | - Ramesh Kurukulaaratchy
- St. Mary's Hospital Nhs Trust, David Hide Asthma & Allergy Research Centre, Newport, United Kingdom of Great Britain and Northern Ireland
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Brandsma J, Schofield JPR, Yang X, Strazzeri F, Barber C, Goss VM, Koster G, Bakke PS, Caruso M, Chanez P, Dahlén SE, Fowler SJ, Horváth I, Krug N, Montuschi P, Sanak M, Sandström T, Shaw DE, Chung KF, Singer F, Fleming LJ, Adcock IM, Pandis I, Bansal AT, Corfield J, Sousa AR, Sterk PJ, Sánchez-García RJ, Skipp PJ, Postle AD, Djukanović R. Stratification of asthma by lipidomic profiling of induced sputum supernatant. J Allergy Clin Immunol 2023; 152:117-125. [PMID: 36918039 DOI: 10.1016/j.jaci.2023.02.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/09/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND Asthma is a chronic respiratory disease with significant heterogeneity in its clinical presentation and pathobiology. There is need for improved understanding of respiratory lipid metabolism in asthma patients and its relation to observable clinical features. OBJECTIVE We performed a comprehensive, prospective, cross-sectional analysis of the lipid composition of induced sputum supernatant obtained from asthma patients with a range of disease severities, as well as from healthy controls. METHODS Induced sputum supernatant was collected from 211 adults with asthma and 41 healthy individuals enrolled onto the U-BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes) study. Sputum lipidomes were characterized by semiquantitative shotgun mass spectrometry and clustered using topologic data analysis to identify lipid phenotypes. RESULTS Shotgun lipidomics of induced sputum supernatant revealed a spectrum of 9 molecular phenotypes, highlighting not just significant differences between the sputum lipidomes of asthma patients and healthy controls, but also within the asthma patient population. Matching clinical, pathobiologic, proteomic, and transcriptomic data helped inform the underlying disease processes. Sputum lipid phenotypes with higher levels of nonendogenous, cell-derived lipids were associated with significantly worse asthma severity, worse lung function, and elevated granulocyte counts. CONCLUSION We propose a novel mechanism of increased lipid loading in the epithelial lining fluid of asthma patients resulting from the secretion of extracellular vesicles by granulocytic inflammatory cells, which could reduce the ability of pulmonary surfactant to lower surface tension in asthmatic small airways, as well as compromise its role as an immune regulator.
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Affiliation(s)
- Joost Brandsma
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; National Institute for Health Research Southampton Biomedical Research Centre, Southampton, United Kingdom.
| | - James P R Schofield
- National Institute for Health Research Southampton Biomedical Research Centre, Southampton, United Kingdom; Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Xian Yang
- Data Science Institute, Imperial College, London, United Kingdom
| | - Fabio Strazzeri
- Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Clair Barber
- National Institute for Health Research Southampton Biomedical Research Centre, Southampton, United Kingdom
| | - Victoria M Goss
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; National Institute for Health Research Southampton Biomedical Research Centre, Southampton, United Kingdom
| | - Grielof Koster
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; National Institute for Health Research Southampton Biomedical Research Centre, Southampton, United Kingdom
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Massimo Caruso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Pascal Chanez
- Department of Respiratory Diseases, Aix-Marseille University, Marseille, France
| | - Sven-Erik Dahlén
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Stephen J Fowler
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Academic Health Centre and NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Ildikó Horváth
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Paolo Montuschi
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Rome, Italy; National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Marek Sanak
- Department of Medicine, Jagiellonian University, Krakow, Poland
| | - Thomas Sandström
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Dominick E Shaw
- National Institute for Health Research Biomedical Research Unit, University of Nottingham, Nottingham, United Kingdom
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Florian Singer
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, Graz, Austria
| | - Louise J Fleming
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Ioannis Pandis
- Data Science Institute, Imperial College, London, United Kingdom
| | - Aruna T Bansal
- Acclarogen Ltd, St John's Innovation Centre, Cambridge, United Kingdom
| | | | - Ana R Sousa
- Respiratory Therapy Unit, GlaxoSmithKline, London, United Kingdom
| | - Peter J Sterk
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Paul J Skipp
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Anthony D Postle
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ratko Djukanović
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; National Institute for Health Research Southampton Biomedical Research Centre, Southampton, United Kingdom
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Fazli M, Oppong C, Som T, Ko ER, Tsalik EL, Chenoweth J, Brandsma J, Woods C, Letizia A, Fox A, Faix D, Vantha T, Oduro G, Schully KL, Bertram R, Clark DV, Striegel DA. Multi-layer gene bundling: A new approach to gene clustering. J Crit Care 2023. [DOI: 10.1016/j.jcrc.2022.154201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Blair PW, Mehta R, Oppong CK, Tin S, Ko E, Tsalik EL, Chenoweth J, Rozo M, Adams N, Beckett C, Woods CW, Striegel DA, Salvador MG, Brandsma J, McKean L, Mahle RE, Hulsey WR, Krishnan S, Prouty M, Letizia A, Fox A, Faix D, Lawler JV, Duplessis C, Gregory MG, Vantha T, Owusu-Ofori AK, Ansong D, Oduro G, Schully KL, Clark DV. Screening tools for predicting mortality of adults with suspected sepsis: an international sepsis cohort validation study. BMJ Open 2023; 13:e067840. [PMID: 36806137 PMCID: PMC9944645 DOI: 10.1136/bmjopen-2022-067840] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
OBJECTIVES We evaluated the performance of commonly used sepsis screening tools across prospective sepsis cohorts in the USA, Cambodia and Ghana. DESIGN Prospective cohort studies. SETTING AND PARTICIPANTS From 2014 to 2021, participants with two or more SIRS (Systemic Inflammatory Response Syndrome) criteria and suspected infection were enrolled in emergency departments and medical wards at hospitals in Cambodia and Ghana and hospitalised participants with suspected infection were enrolled in the USA. Cox proportional hazards regression was performed, and Harrell's C-statistic calculated to determine 28-day mortality prediction performance of the quick Sequential Organ Failure Assessment (qSOFA) score ≥2, SIRS score ≥3, National Early Warning Score (NEWS) ≥5, Modified Early Warning Score (MEWS) ≥5 or Universal Vital Assessment (UVA) score ≥2. Screening tools were compared with baseline risk (age and sex) with the Wald test. RESULTS The cohorts included 567 participants (42.9% women) including 187 participants from Kumasi, Ghana, 200 participants from Takeo, Cambodia and 180 participants from Durham, North Carolina in the USA. The pooled mortality was 16.4% at 28 days. The mortality prediction accuracy increased from baseline risk with the MEWS (C-statistic: 0.63, 95% CI 0.58 to 0.68; p=0.002), NEWS (C-statistic: 0.68; 95% CI 0.64 to 0.73; p<0.001), qSOFA (C-statistic: 0.70, 95% CI 0.64 to 0.75; p<0.001), UVA score (C-statistic: 0.73, 95% CI 0.69 to 0.78; p<0.001), but not with SIRS (0.60; 95% CI 0.54 to 0.65; p=0.13). Within individual cohorts, only the UVA score in Ghana performed better than baseline risk (C-statistic: 0.77; 95% CI 0.71 to 0.83; p<0.001). CONCLUSIONS Among the cohorts, MEWS, NEWS, qSOFA and UVA scores performed better than baseline risk, largely driven by accuracy improvements in Ghana, while SIRS scores did not improve prognostication accuracy. Prognostication scores should be validated within the target population prior to clinical use.
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Affiliation(s)
- Paul W Blair
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Rittal Mehta
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | | | - Som Tin
- Takeo Provincial Referral Hospital, Takeo, Cambodia
| | - Emily Ko
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Duke University School of Medicine, Durham, North Carolina, USA
- Danaher Diagnostics, Washington, D.C, USA
| | - Josh Chenoweth
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Michelle Rozo
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Nehkonti Adams
- Naval Medical Research Center Infectious Diseases Directorate, Bethesda, Maryland, USA
| | - Charmagne Beckett
- Naval Medical Research Center Infectious Diseases Directorate, Bethesda, Maryland, USA
| | - Christopher W Woods
- Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | - Deborah A Striegel
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Mark G Salvador
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Joost Brandsma
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Lauren McKean
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Rachael E Mahle
- Duke University School of Medicine, Durham, North Carolina, USA
| | - William R Hulsey
- Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Subramaniam Krishnan
- Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Michael Prouty
- US Naval Medical Research Unit No 2, Phnom Penh, Cambodia
| | - Andrew Letizia
- Naval Medical Research Unit-3 Ghana Detachment, Accra, Ghana
| | - Anne Fox
- Naval Medical Research Unit-3 Ghana Detachment, Accra, Ghana
| | - Dennis Faix
- US Naval Medical Research Unit No 2, Phnom Penh, Cambodia
| | - James V Lawler
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Chris Duplessis
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Frederick, Maryland, USA
| | - Michael G Gregory
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Frederick, Maryland, USA
| | - Te Vantha
- Takeo Provincial Referral Hospital, Takeo, Cambodia
| | | | - Daniel Ansong
- Emergency Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | | | - Kevin L Schully
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
| | - Danielle V Clark
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, USA
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Brandsma J, Chenoweth JG, Gregory MK, Krishnan S, Blair PW, Striegel DA, Mehta R, Schully KL, Dumler JS, Sikorski CDRCS, O’Connor K, Reichert-Scrivner SA, Paguirigan CM, Uyehara CFT, Ngauy COLV, Myers CA, Clark DV. Assessing the use of a micro-sampling device for measuring blood protein levels in healthy subjects and COVID-19 patients. PLoS One 2022; 17:e0272572. [PMID: 35947596 PMCID: PMC9365123 DOI: 10.1371/journal.pone.0272572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/21/2022] [Indexed: 11/29/2022] Open
Abstract
Background Venous phlebotomy performed by trained personnel is critical for patient diagnosis and monitoring of chronic disease, but has limitations in resource-constrained settings, and represents an infection control challenge during outbreaks. Self-collection devices have the potential to shift phlebotomy closer to the point of care, supporting telemedicine strategies and virtual clinical trials. Here we assess a capillary blood micro-sampling device, the Tasso Serum Separator Tube (SST), for measuring blood protein levels in healthy subjects and non-hospitalized COVID-19 patients. Methods 57 healthy controls and 56 participants with mild/moderate COVID-19 were recruited at two U.S. military healthcare facilities. Healthy controls donated Tasso SST capillary serum, venous plasma and venous serum samples at multiple time points, while COVID-19 patients donated a single Tasso SST serum sample at enrolment. Concentrations of 17 protein inflammatory biomarkers were measured in all biospecimens by Ella multi-analyte immune-assay. Results Tasso SST serum protein measurements in healthy control subjects were highly reproducible, but their agreements with matched venous samples varied. Most of the selected proteins, including CRP, Ferritin, IL-6 and PCT, were well-correlated between Tasso SST and venous serum with little sample type bias, but concentrations of D-dimer, IL-1B and IL-1Ra were not. Self-collection at home with delayed sample processing was associated with significant concentrations differences for several analytes compared to supervised, in-clinic collection with rapid processing. Finally, Tasso SST serum protein concentrations were significantly elevated in in non-hospitalized COVID-19 patients compared with healthy controls. Conclusions Self-collection of capillary blood with micro-sampling devices provides an attractive alternative to routine phlebotomy. However, concentrations of certain analytes may differ significantly from those in venous samples, and factors including user proficiency, temperature control and time lags between specimen collection and processing need to be considered for their effect on sample quality and reproducibility.
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Affiliation(s)
- Joost Brandsma
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
- * E-mail:
| | - Josh G. Chenoweth
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
| | - Melissa K. Gregory
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
| | - Subramaniam Krishnan
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
| | - Paul W. Blair
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
- Department of Pathology, School of Medicine, Uniformed Services University, Bethesda, Maryland, United States of America
| | - Deborah A. Striegel
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
| | - Rittal Mehta
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
| | - Kevin L. Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Frederick, Maryland, United States of America
| | - J. Stephen Dumler
- Department of Pathology, School of Medicine, Uniformed Services University, Bethesda, Maryland, United States of America
| | | | - Kelsey O’Connor
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
- Tripler Army Medical Center, Honolulu, Hawaii, United States of America
| | - Susan A. Reichert-Scrivner
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
- Tripler Army Medical Center, Honolulu, Hawaii, United States of America
| | | | | | - COL Viseth Ngauy
- Tripler Army Medical Center, Honolulu, Hawaii, United States of America
| | | | - Danielle V. Clark
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, United States of America
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Blair PW, Brandsma J, Epsi NJ, Richard SA, Striegel D, Chenoweth J, Mehta R, Clemens E, Malloy A, Lanteri C, Dumler JS, Tribble D, Burgess T, Pollett S, Agan B, Clark D. 438. Phenotypic Differences Between Distinct Immune Biomarker Clusters During the ‘Hyperinflammatory’ Middle-Phase of COVID-19. Open Forum Infect Dis 2021. [PMCID: PMC8644901 DOI: 10.1093/ofid/ofab466.637] [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] [Indexed: 11/15/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections peak during an inflammatory ‘middle’ phase and lead to severe illness predominately among those with certain comorbid noncommunicable diseases (NCDs). We used network machine learning to identify inflammation biomarker patterns associated with COVID-19 among those with NCDs. Methods SARS-CoV-2 RT-PCR positive subjects who had specimens available within 15-28 days post-symptom onset were selected from the DoD/USU EPICC COVID-19 cohort study. Plasma levels of 15 inflammation protein biomarkers were measured using a broad dynamic range immunoassay on samples collected from individuals with COVID-19 at 8 military hospitals across the United States. A network machine learning algorithm, topological data analysis (TDA), was performed using results from the ‘hyperinflammatory’ middle phase. Backward selection stepwise logistic regression was used to identify analytes associated with each cluster. NCDs with a significant association (0.05 significance level) across clusters using Fisher’s exact test were further evaluated comparing the NCD frequency in each cluster against all other clusters using a Kruskal-Wallis test. A sensitivity analysis excluding mild disease was also performed. Results The analysis population (n=129, 33.3% female, median 41.3 years of age) included 77 ambulatory, 31 inpatient, 16 ICU-level, and 5 fatal cases. TDA identified 5 unique clusters (Figure 1). Stepwise regression with a Bonferroni-corrected cutoff adjusted for severity identified representative analytes for each cluster (Table 1). The frequency of diabetes (p=0.01), obesity (p< 0.001), and chronic pulmonary disease (p< 0.001) differed among clusters. When restricting to hospitalized patients, obesity (8 of 11), chronic pulmonary disease (6 of 11), and diabetes (6 of 11) were more prevalent in cluster C than all other clusters. ![]()
Cluster differences in comorbid diseases and severity by cluster. 1A: bar plot of diabetes prevalence; 1B: bar plot of chronic lung disease ; 1C: bar plot of obesity prevalence; 1D: prevalence of steroid treatment ; 1E: Topologic data analysis network with clusters labeled; 1F: Bar plot of ordinal levels of severity. ![]()
Conclusion Machine learning clustering methods are promising analytical tools for identifying inflammation marker patterns associated with baseline risk factors and severe illness due to COVID-19. These approaches may offer new insights for COVID19 prognosis, therapy, and prevention. Disclosures Simon Pollett, MBBS, Astra Zeneca (Other Financial or Material Support, HJF, in support of USU IDCRP, funded under a CRADA to augment the conduct of an unrelated Phase III COVID-19 vaccine trial sponsored by AstraZeneca as part of USG response (unrelated work))
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Affiliation(s)
- Paul W Blair
- Uniformed Services University, Bethesda, Maryland
| | | | | | - Stephanie A Richard
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD and Henry M. Jackson Foundation, Bethesda, MD, Bethesda, Maryland
| | | | | | | | | | - Allison Malloy
- Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Charlotte Lanteri
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Boyds, Maryland
| | - J Stephen Dumler
- Uniformed Services University of the Health Sciences, Bethesda, MD
| | | | - Timothy Burgess
- Infectious Disease Clinical Research Program, Bethesda, Maryland
| | - Simon Pollett
- Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Brian Agan
- Infectious Disease Clinical Research Program, USU/HJF, Bethesda, Maryland
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7
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Shoemark A, Rubbo B, Legendre M, Fassad MR, Haarman EG, Best S, Bon ICM, Brandsma J, Burgel PR, Carlsson G, Carr SB, Carroll M, Edwards M, Escudier E, Honoré I, Hunt D, Jouvion G, Loebinger MR, Maitre B, Morris-Rosendahl D, Papon JF, Parsons CM, Patel MP, Thomas NS, Thouvenin G, Walker WT, Wilson R, Hogg C, Mitchison HM, Lucas JS. Topological data analysis reveals genotype-phenotype relationships in primary ciliary dyskinesia. Eur Respir J 2021; 58:13993003.02359-2020. [PMID: 33479112 DOI: 10.1183/13993003.02359-2020] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/24/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Primary ciliary dyskinesia (PCD) is a heterogeneous inherited disorder caused by mutations in approximately 50 cilia-related genes. PCD genotype-phenotype relationships have mostly arisen from small case series because existing statistical approaches to investigating relationships have been unsuitable for rare diseases. METHODS We applied a topological data analysis (TDA) approach to investigate genotype-phenotype relationships in PCD. Data from separate training and validation cohorts included 396 genetically defined individuals carrying pathogenic variants in PCD genes. To develop the TDA models, 12 clinical and diagnostic variables were included. TDA-driven hypotheses were subsequently tested using traditional statistics. RESULTS Disease severity at diagnosis, measured by forced expiratory volume in 1 s (FEV1) z-score, was significantly worse in individuals with CCDC39 mutations (compared to other gene mutations) and better in those with DNAH11 mutations; the latter also reported less neonatal respiratory distress. Patients without neonatal respiratory distress had better preserved FEV1 at diagnosis. Individuals with DNAH5 mutations were phenotypically diverse. Cilia ultrastructure and beat pattern defects correlated closely to specific causative gene groups, confirming these tests can be used to support a genetic diagnosis. CONCLUSIONS This large scale, multi-national study presents PCD as a syndrome with overlapping symptoms and variations in phenotype according to genotype. TDA modelling confirmed genotype-phenotype relationships reported by smaller studies (e.g. FEV1 worse with CCDC39 mutation) and identified new relationships, including FEV1 preservation with DNAH11 mutations and diversity of severity with DNAH5 mutations.
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Affiliation(s)
- Amelia Shoemark
- PCD Diagnostic Centre and Dept of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London, UK.,Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK.,Equal first author contribution
| | - Bruna Rubbo
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK.,Equal first author contribution
| | - Marie Legendre
- Département de Génétique Médicale, Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) U933, Hôpital Trousseau, Paris, France
| | - Mahmoud R Fassad
- Genetics and Genomic Medicine Dept, University College London, UCL Great Ormond Street Institute of Child Health, London, UK.,Dept of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Eric G Haarman
- Dept of Pediatric Pulmonology, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sunayna Best
- Genetics and Genomic Medicine Dept, University College London, UCL Great Ormond Street Institute of Child Health, London, UK.,Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Irma C M Bon
- Dept of Pediatric Pulmonology, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joost Brandsma
- School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Pierre-Regis Burgel
- Service de Pneumologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Institut Cochin, Paris, France
| | | | - Siobhan B Carr
- PCD Diagnostic Centre and Dept of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London, UK
| | - Mary Carroll
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Matt Edwards
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Estelle Escudier
- Département de Génétique Médicale, Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) U933, Hôpital Trousseau, Paris, France
| | - Isabelle Honoré
- Service de Pneumologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - David Hunt
- Wessex Clinical Genetics Service, University Hospitals Southampton, Princess Anne Hospital, Southampton, UK
| | - Gregory Jouvion
- Département de Génétique Médicale, Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) U933, Hôpital Trousseau, Paris, France
| | - Michel R Loebinger
- Host Defence Unit, Dept of Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart and Lung Institute (NHLI), Imperial College, London, UK
| | - Bernard Maitre
- Service de Pneumologie, DHU A-TVB, Centre Hospitalier Intercommunal de Créteil, Université Paris Est, Créteil, France.,Université Paris Est, Institut National de la Santé et de la Recherche Médicale (INSERM) U955, Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | | | - Jean-Francois Papon
- Service d'ORL et Chirurgie Cervico-Faciale, Hôpital Kremlin-Bicêtre, Assistance Publique-Hôpitaux de Paris (AP-HP), Le Kremlin-Bicêtre, France.,Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Centre national de la recherche scientifique (CNRS) ERL 7240, Créteil, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U955, Créteil, France
| | - Camille M Parsons
- Medical Research Council (MRC) Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Mitali P Patel
- Genetics and Genomic Medicine Dept, University College London, UCL Great Ormond Street Institute of Child Health, London, UK
| | - N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.,Human Genetics and Genomic Medicine, University of Southampton Faculty of Medicine, Southampton, UK
| | - Guillaume Thouvenin
- School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK.,Service de Pneumologie Pédiatrique, Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) U938, Centre de Recherche Saint-Antoine, Paris, France
| | - Woolf T Walker
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Robert Wilson
- Host Defence Unit, Dept of Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Claire Hogg
- PCD Diagnostic Centre and Dept of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Dept, University College London, UCL Great Ormond Street Institute of Child Health, London, UK.,National Institute for Health Research (NIHR) Great Ormond Street Hospital Biomedical Research Centre, London, UK.,H.M. Mitchison and J.S. Lucas contributed equally to this article as lead authors and supervised the work
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK .,School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK.,H.M. Mitchison and J.S. Lucas contributed equally to this article as lead authors and supervised the work
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8
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Evans C, Brandsma J, Meredith MP, Thomas DN, Venables HJ, Pond DW, Brussaard CPD. Shift from Carbon Flow through the Microbial Loop to the Viral Shunt in Coastal Antarctic Waters during Austral Summer. Microorganisms 2021; 9:460. [PMID: 33672195 PMCID: PMC7927135 DOI: 10.3390/microorganisms9020460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/30/2022] Open
Abstract
The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these processes in the coastal waters of the Antarctic during the productive austral summer months. Throughout the study a general trend towards lower bacterioplankton and heterotrophic nanoflagellate (HNF) abundances was observed, whereas virioplankton concentration increased. A corresponding decline of HNF grazing rates and shift towards viral production, indicative of viral infection, was measured. Carbon flow mediated by HNF grazing decreased by more than half from 5.7 µg C L-1 day-1 on average in December and January to 2.4 µg C L-1 day-1 in February. Conversely, carbon flow through the viral shunt increased substantially over the study from on average 0.9 µg C L-1 day-1 in December to 7.6 µg C L-1 day-1 in February. This study shows that functioning of the coastal Antarctic microbial community varied considerably over the productive summer months. In early summer, the system favors transfer of matter and energy to higher trophic levels via the microbial loop, however towards the end of summer carbon flow is redirected towards the viral shunt, causing a switch towards more recycling and therefore increased respiration and regeneration.
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Affiliation(s)
- Claire Evans
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Ocean BioGeosciences, National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK
| | - Joost Brandsma
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Michael P. Meredith
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David N. Thomas
- Ecosystems & Environment, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Hugh J. Venables
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David W. Pond
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Corina P. D. Brussaard
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
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9
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Perotin JM, Schofield JPR, Wilson SJ, Ward J, Brandsma J, Strazzeri F, Bansal A, Yang X, Rowe A, Corfield J, Lutter R, Shaw DE, Bakke PS, Caruso M, Dahlén B, Fowler SJ, Horváth I, Howarth P, Krug N, Montuschi P, Sanak M, Sandström T, Sun K, Pandis I, Auffray C, De Meulder B, Lefaudeux D, Riley JH, Sousa AR, Dahlen SE, Adcock IM, Chung KF, Sterk PJ, Skipp PJ, Collins JE, Davies DE, Djukanović R. Epithelial dysregulation in obese severe asthmatics with gastro-oesophageal reflux. Eur Respir J 2019; 53:13993003.00453-2019. [PMID: 31023846 DOI: 10.1183/13993003.00453-2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/20/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Jeanne-Marie Perotin
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James P R Schofield
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, UK
| | - Susan J Wilson
- The Histochemistry Research Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jonathan Ward
- The Histochemistry Research Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Joost Brandsma
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Fabio Strazzeri
- Mathematical Sciences, University of Southampton, Southampton, UK
| | | | - Xian Yang
- Data Science Institute, Imperial College London, London, UK
| | - Anthony Rowe
- Janssen Research and Development, High Wycombe, UK
| | | | - Rene Lutter
- Amsterdam UMC, Dept of Experimental Immunology (Amsterdam Infection and Immunity Institute), University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, Dept of Respiratory Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Dominick E Shaw
- NIHR Biomedical Respiratory Research Centre, University of Nottingham, Nottingham, UK
| | - Per S Bakke
- Institute of Medicine, University of Bergen, Bergen, Norway
| | - Massimo Caruso
- Dept of Clinical and Experimental Medicine Hospital University, University of Catania, Catania, Italy.,Dept of Biomedical and Biotechnological Sciences (Biometec), University of Catania, Catania, Italy
| | - Barbro Dahlén
- Dept of Respiratory Diseases and Allergy, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Stephen J Fowler
- Respiratory and Allergy Research Group, University of Manchester, Manchester, UK
| | - Ildikó Horváth
- Dept of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Peter Howarth
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine Hannover, Hannover, Germany
| | - Paolo Montuschi
- Faculty of Medicine, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario, Agostino Gemelli IRCCS, Rome, Italy
| | - Marek Sanak
- Laboratory of Molecular Biology and Clinical Genetics, Medical College, Jagiellonian University, Krakow, Poland
| | - Thomas Sandström
- Dept of Medicine, Dept of Public Health and Clinical Medicine Respiratory Medicine Unit, Umeå University, Umeå, Sweden
| | - Kai Sun
- Janssen Research and Development, High Wycombe, UK
| | | | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyons, France
| | - Bertrand De Meulder
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyons, France
| | - Diane Lefaudeux
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyons, France
| | | | - Ana R Sousa
- Respiratory Therapeutic Unit, GSK, Uxbridge, UK
| | - Sven-Erik Dahlen
- The Centre for Allergy Research, The Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ian M Adcock
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Kian Fan Chung
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Peter J Sterk
- NIHR Biomedical Respiratory Research Centre, University of Nottingham, Nottingham, UK
| | - Paul J Skipp
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, UK
| | - Jane E Collins
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Donna E Davies
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ratko Djukanović
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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10
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Schofield JPR, Burg D, Nicholas B, Strazzeri F, Brandsma J, Staykova D, Folisi C, Bansal AT, Xian Y, Guo Y, Rowe A, Corfield J, Wilson S, Ward J, Lutter R, Shaw DE, Bakke PS, Caruso M, Dahlen SE, Fowler SJ, Horváth I, Howarth P, Krug N, Montuschi P, Sanak M, Sandström T, Sun K, Pandis I, Riley J, Auffray C, De Meulder B, Lefaudeux D, Sousa AR, Adcock IM, Chung KF, Sterk PJ, Skipp PJ, Djukanović R. Stratification of asthma phenotypes by airway proteomic signatures. J Allergy Clin Immunol 2019; 144:70-82. [PMID: 30928653 DOI: 10.1016/j.jaci.2019.03.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/14/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Stratification by eosinophil and neutrophil counts increases our understanding of asthma and helps target therapy, but there is room for improvement in our accuracy in prediction of treatment responses and a need for better understanding of the underlying mechanisms. OBJECTIVE We sought to identify molecular subphenotypes of asthma defined by proteomic signatures for improved stratification. METHODS Unbiased label-free quantitative mass spectrometry and topological data analysis were used to analyze the proteomes of sputum supernatants from 246 participants (206 asthmatic patients) as a novel means of asthma stratification. Microarray analysis of sputum cells provided transcriptomics data additionally to inform on underlying mechanisms. RESULTS Analysis of the sputum proteome resulted in 10 clusters (ie, proteotypes) based on similarity in proteomic features, representing discrete molecular subphenotypes of asthma. Overlaying granulocyte counts onto the 10 clusters as metadata further defined 3 of these as highly eosinophilic, 3 as highly neutrophilic, and 2 as highly atopic with relatively low granulocytic inflammation. For each of these 3 phenotypes, logistic regression analysis identified candidate protein biomarkers, and matched transcriptomic data pointed to differentially activated underlying mechanisms. CONCLUSION This study provides further stratification of asthma currently classified based on quantification of granulocytic inflammation and provided additional insight into their underlying mechanisms, which could become targets for novel therapies.
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Affiliation(s)
- James P R Schofield
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom; NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Dominic Burg
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom; NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ben Nicholas
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Fabio Strazzeri
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom; Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Joost Brandsma
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Doroteya Staykova
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Caterina Folisi
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Yang Xian
- Data Science Institute, Imperial College, London, United Kingdom
| | - Yike Guo
- Data Science Institute, Imperial College, London, United Kingdom
| | - Anthony Rowe
- Janssen Research & Development, High Wycombe, United Kingdom
| | | | - Susan Wilson
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan Ward
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Rene Lutter
- AMC, Department of Experimental Immunology, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Dominick E Shaw
- Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom
| | - Per S Bakke
- Institute of Medicine, University of Bergen, Bergen, Norway
| | - Massimo Caruso
- Department of Clinical and Experimental Medicine Hospital University, University of Catania, Catania, Italy
| | - Sven-Erik Dahlen
- Centre for Allergy Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stephen J Fowler
- Respiratory and Allergy Research Group, University of Manchester, Manchester, United Kingdom
| | - Ildikó Horváth
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Peter Howarth
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine Hannover, Hannover, Germany
| | - Paolo Montuschi
- Faculty of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Marek Sanak
- Laboratory of Molecular Biology and Clinical Genetics, Medical College, Jagiellonian University, Krakow, Poland
| | - Thomas Sandström
- Department of Medicine, Department of Public Health and Clinical Medicine Respiratory Medicine Unit, Umeå University, Umeå, Sweden
| | - Kai Sun
- Data Science Institute, Imperial College, London, United Kingdom
| | - Ioannis Pandis
- Data Science Institute, Imperial College, London, United Kingdom
| | - John Riley
- Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyon, France
| | - Bertrand De Meulder
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyon, France
| | - Diane Lefaudeux
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyon, France
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | - Ian M Adcock
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Peter J Sterk
- Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul J Skipp
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Ratko Djukanović
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
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11
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Tariq K, Schofield JPR, Nicholas BL, Burg D, Brandsma J, Bansal AT, Wilson SJ, Lutter R, Fowler SJ, Bakke, Caruso M, Dahlen B, Horváth I, Krug N, Montuschi P, Sanak M, Sandström T, Geiser T, Pandis I, Sousa AR, Adcock IM, Shaw DE, Auffray C, Howarth PH, Sterk PJ, Chung KF, Skipp PJ, Dimitrov B, Djukanović R. Sputum proteomic signature of gastro-oesophageal reflux in patients with severe asthma. Respir Med 2019; 150:66-73. [PMID: 30961953 DOI: 10.1016/j.rmed.2019.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 01/08/2023]
Abstract
Gastro-oesophageal reflux disease (GORD) has long been associated with poor asthma control without an established cause-effect relationship. 610 asthmatics (421 severe/88 mild-moderate) and 101 healthy controls were assessed clinically and a subset of 154 severe asthmatics underwent proteomic analysis of induced sputum using untargeted mass spectrometry, LC-IMS-MSE. Univariate and multiple logistic regression analyses (MLR) were conducted to identify proteins associated with GORD in this cohort. When compared to mild/moderate asthmatics and healthy individuals, respectively, GORD was three- and ten-fold more prevalent in severe asthmatics and was associated with increased asthma symptoms and oral corticosteroid use, poorer quality of life, depression/anxiety, obesity and symptoms of sino-nasal disease. Comparison of sputum proteomes in severe asthmatics with and without active GORD showed five differentially abundant proteins with described roles in anti-microbial defences, systemic inflammation and epithelial integrity. Three of these were associated with active GORD by multiple linear regression analysis: Ig lambda variable 1-47 (p = 0·017) and plasma protease C1 inhibitor (p = 0·043), both in lower concentrations, and lipocalin-1 (p = 0·034) in higher concentrations in active GORD. This study provides evidence which suggests that reflux can cause subtle perturbation of proteins detectable in the airways lining fluid and that severe asthmatics with GORD may represent a distinct phenotype of asthma.
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Affiliation(s)
- K Tariq
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Clinical Experimental Sciences Unit, Faculty of Medicine, University of Southampton, University Hospital Southampton, South Academic Block, Southampton, UK
| | - J P R Schofield
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Centre for Proteomic Research, University of Southampton, Highfield, Southampton, UK
| | - B L Nicholas
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Clinical Experimental Sciences Unit, Faculty of Medicine, University of Southampton, University Hospital Southampton, South Academic Block, Southampton, UK
| | - D Burg
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Centre for Proteomic Research, University of Southampton, Highfield, Southampton, UK
| | - J Brandsma
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | | | - S J Wilson
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - R Lutter
- AMC, Department of Experimental Immunology, University of Amsterdam, Amsterdam, the Netherlands; AMC, Department of Respiratory Medicine, University of Amsterdam, Amsterdam, the Netherlands
| | - S J Fowler
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester and University Hospital of South Manchester, NHS Foundation Trust, Manchester, UK
| | - Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - M Caruso
- Dept. of Clinical and Experimental Medicine Hospital University, Policlinico-Vittorio Emanuele, University of Catania, Catania, Italy
| | - B Dahlen
- Division of Respiratory Medicine and Allergy, Department of Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - I Horváth
- Dept. of Pulmonology, Semmelweis University, Budapest, Hungary
| | - N Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine Hannover, Hannover, Germany
| | - P Montuschi
- Dept. of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - M Sanak
- Division of Molecular Biology and Clinical Genetics, Medical College, Jagiellonian University Medical College, Krakow, Poland
| | - T Sandström
- Dept. of Medicine, Dept of Public Health and Clinical Medicine Respiratory Medicine Unit, Umeå University, Umeå, Sweden
| | - T Geiser
- University Hospital Bern, Bern, Switzerland
| | - I Pandis
- Data Science Institute, Imperial College, London, UK
| | - A R Sousa
- Respiratory Therapeutic Unit, GSK, Stockley Park, UK
| | - I M Adcock
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, UK
| | - D E Shaw
- Respiratory Research Unit, University of Nottingham, Nottingham, UK
| | - C Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - P H Howarth
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Clinical Experimental Sciences Unit, Faculty of Medicine, University of Southampton, University Hospital Southampton, South Academic Block, Southampton, UK
| | - P J Sterk
- AMC, Department of Respiratory Medicine, University of Amsterdam, Amsterdam, the Netherlands
| | - K F Chung
- Airways Disease, National Heart and Lung Institute, Imperial College, London & Royal Brompton NIHR Biomedical Research Unit, London, United Kingdom
| | - P J Skipp
- Centre for Proteomic Research, University of Southampton, Highfield, Southampton, UK
| | - B Dimitrov
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - R Djukanović
- NIHR Southampton Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Clinical Experimental Sciences Unit, Faculty of Medicine, University of Southampton, University Hospital Southampton, South Academic Block, Southampton, UK.
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12
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Brandsma J, Goss VM, Yang X, Bakke PS, Caruso M, Chanez P, Dahlén SE, Fowler SJ, Horvath I, Krug N, Montuschi P, Sanak M, Sandström T, Shaw DE, Chung KF, Singer F, Fleming LJ, Sousa AR, Pandis I, Bansal AT, Sterk PJ, Djukanović R, Postle AD. Lipid phenotyping of lung epithelial lining fluid in healthy human volunteers. Metabolomics 2018; 14:123. [PMID: 30830396 PMCID: PMC6153688 DOI: 10.1007/s11306-018-1412-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/12/2018] [Indexed: 01/20/2023]
Abstract
BACKGROUND Lung epithelial lining fluid (ELF)-sampled through sputum induction-is a medium rich in cells, proteins and lipids. However, despite its key role in maintaining lung function, homeostasis and defences, the composition and biology of ELF, especially in respect of lipids, remain incompletely understood. OBJECTIVES To characterise the induced sputum lipidome of healthy adult individuals, and to examine associations between different ELF lipid phenotypes and the demographic characteristics within the study cohort. METHODS Induced sputum samples were obtained from 41 healthy non-smoking adults, and their lipid compositions analysed using a combination of untargeted shotgun and liquid chromatography mass spectrometry methods. Topological data analysis (TDA) was used to group subjects with comparable sputum lipidomes in order to identify distinct ELF phenotypes. RESULTS The induced sputum lipidome was diverse, comprising a range of different molecular classes, including at least 75 glycerophospholipids, 13 sphingolipids, 5 sterol lipids and 12 neutral glycerolipids. TDA identified two distinct phenotypes differentiated by a higher total lipid content and specific enrichments of diacyl-glycerophosphocholines, -inositols and -glycerols in one group, with enrichments of sterols, glycolipids and sphingolipids in the other. Subjects presenting the lipid-rich ELF phenotype also had significantly higher BMI, but did not differ in respect of other demographic characteristics such as age or gender. CONCLUSIONS We provide the first evidence that the ELF lipidome varies significantly between healthy individuals and propose that such differences are related to weight status, highlighting the potential impact of (over)nutrition on lung lipid metabolism.
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Affiliation(s)
- Joost Brandsma
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
| | - Victoria M Goss
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Xian Yang
- Data Science Institute, Imperial College, London, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Massimo Caruso
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Pascal Chanez
- Department of Respiratory Diseases, Aix-Marseille University, Marseille, France
| | - Sven-Erik Dahlén
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Stephen J Fowler
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, University Hospital of South Manchester, Manchester, UK
| | - Ildiko Horvath
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Paolo Montuschi
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Marek Sanak
- Department of Medicine, Jagiellonian University, Krakow, Poland
| | - Thomas Sandström
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Dominick E Shaw
- Respiratory Research Unit, University of Nottingham, Nottingham, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College, London, UK
| | | | | | - Ana R Sousa
- Respiratory Therapy Unit, GlaxoSmithKline, London, UK
| | | | - Aruna T Bansal
- Acclarogen Ltd, St John's Innovation Centre, Cambridge, UK
| | - Peter J Sterk
- Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ratko Djukanović
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health Research Southampton Biomedical Research Centre, Southampton, UK
| | - Anthony D Postle
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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13
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Burg D, Schofield JPR, Brandsma J, Staykova D, Folisi C, Bansal A, Nicholas B, Xian Y, Rowe A, Corfield J, Wilson S, Ward J, Lutter R, Fleming L, Shaw DE, Bakke PS, Caruso M, Dahlen SE, Fowler SJ, Hashimoto S, Horváth I, Howarth P, Krug N, Montuschi P, Sanak M, Sandström T, Singer F, Sun K, Pandis I, Auffray C, Sousa AR, Adcock IM, Chung KF, Sterk PJ, Djukanović R, Skipp PJ, The U-Biopred Study Group. Large-Scale Label-Free Quantitative Mapping of the Sputum Proteome. J Proteome Res 2018; 17:2072-2091. [PMID: 29737851 DOI: 10.1021/acs.jproteome.8b00018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of induced sputum supernatant is a minimally invasive approach to study the epithelial lining fluid and, thereby, provide insight into normal lung biology and the pathobiology of lung diseases. We present here a novel proteomics approach to sputum analysis developed within the U-BIOPRED (unbiased biomarkers predictive of respiratory disease outcomes) international project. We present practical and analytical techniques to optimize the detection of robust biomarkers in proteomic studies. The normal sputum proteome was derived using data-independent HDMSE applied to 40 healthy nonsmoking participants, which provides an essential baseline from which to compare modulation of protein expression in respiratory diseases. The "core" sputum proteome (proteins detected in ≥40% of participants) was composed of 284 proteins, and the extended proteome (proteins detected in ≥3 participants) contained 1666 proteins. Quality control procedures were developed to optimize the accuracy and consistency of measurement of sputum proteins and analyze the distribution of sputum proteins in the healthy population. The analysis showed that quantitation of proteins by HDMSE is influenced by several factors, with some proteins being measured in all participants' samples and with low measurement variance between samples from the same patient. The measurement of some proteins is highly variable between repeat analyses, susceptible to sample processing effects, or difficult to accurately quantify by mass spectrometry. Other proteins show high interindividual variance. We also highlight that the sputum proteome of healthy individuals is related to sputum neutrophil levels, but not gender or allergic sensitization. We illustrate the importance of design and interpretation of disease biomarker studies considering such protein population and technical measurement variance.
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Affiliation(s)
- Dominic Burg
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K.,NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - James P R Schofield
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K.,NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Joost Brandsma
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Doroteya Staykova
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K
| | - Caterina Folisi
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K
| | | | - Ben Nicholas
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Yang Xian
- Data Science Institute , Imperial College London , London SW7 2AZ , U.K
| | - Anthony Rowe
- Janssen Research & Development , Buckinghamshire HP12 4DP , U.K
| | | | - Susan Wilson
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Jonathan Ward
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Rene Lutter
- AMC, Department of Experimental Immunology , University of Amsterdam , 1012 WX Amsterdam , The Netherlands.,AMC, Department of Respiratory Medicine , University of Amsterdam , 1012 WX Amsterdam , The Netherlands
| | - Louise Fleming
- Airways Disease , National Heart and Lung Institute, Imperial College, London & Royal Brompton NIHR Biomedical Research Unit , London SW7 2AZ , United Kingdom
| | - Dominick E Shaw
- Respiratory Research Unit , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Per S Bakke
- Institute of Medicine , University of Bergen , 5007 Bergen , Norway
| | - Massimo Caruso
- Department of Clinical and Experimental Medicine Hospital University , University of Catania , 95124 Catania , Italy
| | - Sven-Erik Dahlen
- The Centre for Allergy Research , The Institute of Environmental Medicine, Karolinska Institutet , SE-171 77 Stockholm , Sweden
| | - Stephen J Fowler
- Respiratory and Allergy Research Group , University of Manchester , Manchester M13 9PL , U.K
| | - Simone Hashimoto
- Department of Respiratory Medicine, Academic Medical Centre , University of Amsterdam , 1012 WX Amsterdam , The Netherlands
| | - Ildikó Horváth
- Department of Pulmonology , Semmelweis University , Budapest 1085 , Hungary
| | - Peter Howarth
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine Hannover , 30625 Hannover , Germany
| | - Paolo Montuschi
- Faculty of Medicine , Catholic University of the Sacred Heart , 00168 Rome , Italy
| | - Marek Sanak
- Laboratory of Molecular Biology and Clinical Genetics, Medical College , Jagiellonian University , 31-007 Krakow , Poland
| | - Thomas Sandström
- Department of Medicine, Department of Public Health and Clinical Medicine Respiratory Medicine Unit , Umeå University , 901 87 Umeå , Sweden
| | - Florian Singer
- University Children's Hospital Zurich , 8032 Zurich , Switzerland
| | - Kai Sun
- Data Science Institute , Imperial College London , London SW7 2AZ , U.K
| | - Ioannis Pandis
- Data Science Institute , Imperial College London , London SW7 2AZ , U.K
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM , Université de Lyon , 69007 Lyon , France
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GSK , Stockley Park , Uxbridge UB11 1BT , U.K
| | - Ian M Adcock
- Cell and Molecular Biology Group, Airways Disease Section , National Heart and Lung Institute, Imperial College London , Dovehouse Street , London SW3 6LR , U.K
| | - Kian Fan Chung
- Airways Disease , National Heart and Lung Institute, Imperial College, London & Royal Brompton NIHR Biomedical Research Unit , London SW7 2AZ , United Kingdom
| | - Peter J Sterk
- AMC, Department of Experimental Immunology , University of Amsterdam , 1012 WX Amsterdam , The Netherlands
| | - Ratko Djukanović
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Paul J Skipp
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K
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14
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Bowden JA, Heckert A, Ulmer CZ, Jones CM, Koelmel JP, Abdullah L, Ahonen L, Alnouti Y, Armando AM, Asara JM, Bamba T, Barr JR, Bergquist J, Borchers CH, Brandsma J, Breitkopf SB, Cajka T, Cazenave-Gassiot A, Checa A, Cinel MA, Colas RA, Cremers S, Dennis EA, Evans JE, Fauland A, Fiehn O, Gardner MS, Garrett TJ, Gotlinger KH, Han J, Huang Y, Neo AH, Hyötyläinen T, Izumi Y, Jiang H, Jiang H, Jiang J, Kachman M, Kiyonami R, Klavins K, Klose C, Köfeler HC, Kolmert J, Koal T, Koster G, Kuklenyik Z, Kurland IJ, Leadley M, Lin K, Maddipati KR, McDougall D, Meikle PJ, Mellett NA, Monnin C, Moseley MA, Nandakumar R, Oresic M, Patterson R, Peake D, Pierce JS, Post M, Postle AD, Pugh R, Qiu Y, Quehenberger O, Ramrup P, Rees J, Rembiesa B, Reynaud D, Roth MR, Sales S, Schuhmann K, Schwartzman ML, Serhan CN, Shevchenko A, Somerville SE, St John-Williams L, Surma MA, Takeda H, Thakare R, Thompson JW, Torta F, Triebl A, Trötzmüller M, Ubhayasekera SJK, Vuckovic D, Weir JM, Welti R, Wenk MR, Wheelock CE, Yao L, Yuan M, Zhao XH, Zhou S. Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J Lipid Res 2017; 58:2275-2288. [PMID: 28986437 DOI: 10.1194/jlr.m079012] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/02/2017] [Indexed: 12/22/2022] Open
Abstract
As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a commercially available reference material. The interlaboratory study comprised 31 diverse laboratories, with each laboratory using a different lipidomics workflow. A total of 1,527 unique lipids were measured across all laboratories and consensus location estimates and associated uncertainties were determined for 339 of these lipids measured at the sum composition level by five or more participating laboratories. These evaluated lipids detected in SRM 1950 serve as community-wide benchmarks for intra- and interlaboratory quality control and method validation. These analyses were performed using nonstandardized laboratory-independent workflows. The consensus locations were also compared with a previous examination of SRM 1950 by the LIPID MAPS consortium. While the central theme of the interlaboratory study was to provide values to help harmonize lipids, lipid mediators, and precursor measurements across the community, it was also initiated to stimulate a discussion regarding areas in need of improvement.
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Affiliation(s)
- John A Bowden
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Alan Heckert
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| | - Candice Z Ulmer
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Christina M Jones
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Jeremy P Koelmel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Linda Ahonen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Yazen Alnouti
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - Aaron M Armando
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA
| | - Takeshi Bamba
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Gerald Bronfman Department of Oncology McGill University, Montreal, Quebec, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Joost Brandsma
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Tomas Cajka
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Antonio Checa
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michelle A Cinel
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Romain A Colas
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Serge Cremers
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Edward A Dennis
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | | | - Alexander Fauland
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA.,Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Michael S Gardner
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Katherine H Gotlinger
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | | | - Aveline Huipeng Neo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | | | - Yoshihiro Izumi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Hongfeng Jiang
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Houli Jiang
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jiang Jiang
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Maureen Kachman
- Metabolomics Core, BRCF, University of Michigan, Ann Arbor, MI
| | | | | | | | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Johan Kolmert
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Grielof Koster
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Zsuzsanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Irwin J Kurland
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Michael Leadley
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Karen Lin
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Krishna Rao Maddipati
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
| | - Danielle McDougall
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | | | - Cian Monnin
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Renu Nandakumar
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Matej Oresic
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rainey Patterson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Jason S Pierce
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Martin Post
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Anthony D Postle
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Rebecca Pugh
- Chemical Sciences Division, Environmental Specimen Bank Group, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Oswald Quehenberger
- Departments of Medicine and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Parsram Ramrup
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jon Rees
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Barbara Rembiesa
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Denis Reynaud
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Mary R Roth
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Charles N Serhan
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stephen E Somerville
- Hollings Marine Laboratory, Medical University of South Carolina, Charleston, SC
| | - Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | | | - Hiroaki Takeda
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Rhishikesh Thakare
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | | | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jacquelyn M Weir
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Ruth Welti
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Libin Yao
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Xueqing Heather Zhao
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Senlin Zhou
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
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15
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Evans C, Brandsma J, Pond DW, Venables HJ, Meredith MP, Witte HJ, Stammerjohn S, Wilson WH, Clarke A, Brussaard CPD. Drivers of interannual variability in virioplankton abundance at the coastal western Antarctic peninsula and the potential effects of climate change. Environ Microbiol 2017; 19:740-755. [PMID: 27902869 DOI: 10.1111/1462-2920.13627] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An 8-year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive interannual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Their findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus, the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling.
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Affiliation(s)
- Claire Evans
- Department of Biological Oceanography, Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Joost Brandsma
- Department of Biological Oceanography, Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - David W Pond
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Hugh J Venables
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Michael P Meredith
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Harry J Witte
- Department of Biological Oceanography, Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Sharon Stammerjohn
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
| | - William H Wilson
- The Laboratory, Sir Alister Hardy Foundation for Ocean Science, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Andrew Clarke
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Corina P D Brussaard
- Department of Biological Oceanography, Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands.,Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, Amsterdam, 1090 GE, The Netherlands
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16
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Lefaudeux D, De Meulder B, Loza MJ, Peffer N, Rowe A, Baribaud F, Bansal AT, Lutter R, Sousa AR, Corfield J, Pandis I, Bakke PS, Caruso M, Chanez P, Dahlén SE, Fleming LJ, Fowler SJ, Horvath I, Krug N, Montuschi P, Sanak M, Sandstrom T, Shaw DE, Singer F, Sterk PJ, Roberts G, Adcock IM, Djukanovic R, Auffray C, Chung KF, Adriaens N, Ahmed H, Aliprantis A, Alving K, Badorek P, Balgoma D, Barber C, Bautmans A, Behndig AF, Bel E, Beleta J, Berglind A, Berton A, Bigler J, Bisgaard H, Bochenek G, Boedigheimer MJ, Bøonnelykke K, Brandsma J, Braun A, Brinkman P, Burg D, Campagna D, Carayannopoulos L, Carvalho da Purfição Rocha JP, Chaiboonchoe A, Chaleckis R, Coleman C, Compton C, D'Amico A, Dahlén B, De Alba J, de Boer P, De Lepeleire I, Dekker T, Delin I, Dennison P, Dijkhuis A, Draper A, Edwards J, Emma R, Ericsson M, Erpenbeck V, Erzen D, Faulenbach C, Fichtner K, Fitch N, Flood B, Frey U, Gahlemann M, Galffy G, Gallart H, Garret T, Geiser T, Gent J, Gerhardsson de Verdier M, Gibeon D, Gomez C, Gove K, Gozzard N, Guo YK, Hashimoto S, Haughney J, Hedlin G, Hekking PP, Henriksson E, Hewitt L, Higgenbottam T, Hoda U, Hohlfeld J, Holweg C, Howarth P, Hu R, Hu S, Hu X, Hudson V, James AJ, Kamphuis J, Kennington EJ, Kerry D, Klüglich M, Knobel H, Knowles R, Knox A, Kolmert J, Konradsen J, Kots M, Krueger L, Kuo S, Kupczyk M, Lambrecht B, Lantz AS, Larsson L, Lazarinis N, Lone-Satif S, Marouzet L, Martin J, Masefield S, Mathon C, Matthews JG, Mazein A, Meah S, Maiser A, Menzies-Gow A, Metcalf L, Middelveld R, Mikus M, Miralpeix M, Monk P, Mores N, Murray CS, Musial J, Myles D, Naz S, Nething K, Nicholas B, Nihlen U, Nilsson P, Nordlund B, Östling J, Pacino A, Pahus L, Palkonnen S, Pavlidis S, Pennazza G, Petrén A, Pink S, Postle A, Powel P, Rahman-Amin M, Rao N, Ravanetti L, Ray E, Reinke S, Reynolds L, Riemann K, Riley J, Robberechts M, Roberts A, Rossios C, Russell K, Rutgers M, Santini G, Sentoninco M, Schoelch C, Schofield JP, Seibold W, Sigmund R, Sjödin M, Skipp PJ, Smids B, Smith C, Smith J, Smith KM, Söderman P, Sogbesan A, Staykova D, Strandberg K, Sun K, Supple D, Szentkereszty M, Tamasi L, Tariq K, Thörngren JO, Thornton B, Thorsen J, Valente S, van Aalderenm W, van de Pol M, van Drunen K, van Geest M, Versnel J, Vestbo J, Vink A, Vissing N, von Garnier C, Wagerner A, Wagers S, Wald F, Walker S, Ward J, Weiszhart Z, Wetzel K, Wheelock CE, Wiegman C, Williams S, Wilson SJ, Woosdcock A, Yang X, Yeyashingham E, Yu W, Zetterquist W, Zwinderman K. U-BIOPRED clinical adult asthma clusters linked to a subset of sputum omics. J Allergy Clin Immunol 2017; 139:1797-1807. [DOI: 10.1016/j.jaci.2016.08.048] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 07/23/2016] [Accepted: 08/08/2016] [Indexed: 01/20/2023]
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17
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Brandsma J, Postle AD. Analysis of the regulation of surfactant phosphatidylcholine metabolism using stable isotopes. Ann Anat 2017; 211:176-183. [PMID: 28351529 DOI: 10.1016/j.aanat.2017.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 01/22/2023]
Abstract
The pathways and mechanisms that regulate pulmonary surfactant synthesis, processing, secretion and catabolism have been extensively characterised using classical biochemical and analytical approaches. These have constructed a model, largely in experimental animals, for surfactant phospholipid metabolism in the alveolar epithelial cell whereby phospholipid synthesised on the endoplasmic reticulum is selectively transported to lamellar body storage vesicles, where it is subsequently processed before secretion into the alveolus. Surfactant phospholipid is a complex mixture of individual molecular species defined by the combination of esterified fatty acid groups and a comprehensive description of surfactant phospholipid metabolism requires consideration of the interactions between such molecular species. However, until recently, lipid analytical techniques have not kept pace with the considerable advances in understanding of the enzymology and molecular biology of surfactant metabolism. Refinements in electrospray ionisation mass spectrometry (ESI-MS) can now provide very sensitive platforms for the rapid characterisation of surfactant phospholipid composition in molecular detail. The combination of ESI-MS and administration of phospholipid substrates labelled with stable isotopes extends this analytical approach to the quantification of synthesis and turnover of individual molecular species of surfactant phospholipid. As this methodology does not involve radioactivity, it is ideally suited to application in clinical studies. This review will provide an overview of the metabolic processes that regulate the molecular specificity of surfactant phosphatidylcholine together with examples of how the application of stable isotope technologies in vivo has, for the first time, begun to explore regulation of the molecular specificity of surfactant synthesis in human subjects.
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Affiliation(s)
- Joost Brandsma
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom
| | - Anthony D Postle
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom.
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Brandsma J, Bailey AP, Koster G, Gould AP, Postle AD. Stable isotope analysis of dynamic lipidomics. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:792-796. [PMID: 28302590 DOI: 10.1016/j.bbalip.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 12/16/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 11/28/2022]
Abstract
Metabolic pathway flux is a fundamental element of biological activity, which can be quantified using a variety of mass spectrometric techniques to monitor incorporation of stable isotope-labelled substrates into metabolic products. This article contrasts developments in electrospray ionisation mass spectrometry (ESI-MS) for the measurement of lipid metabolism with more established gas chromatography mass spectrometry and isotope ratio mass spectrometry methodologies. ESI-MS combined with diagnostic tandem MS/MS scans permits the sensitive and specific analysis of stable isotope-labelled substrates into intact lipid molecular species without the requirement for lipid hydrolysis and derivatisation. Such dynamic lipidomic methodologies using non-toxic stable isotopes can be readily applied to quantify lipid metabolic fluxes in clinical and metabolic studies in vivo. However, a significant current limitation is the absence of appropriate software to generate kinetic models of substrate incorporation into multiple products in the time domain. Finally, we discuss the future potential of stable isotope-mass spectrometry imaging to quantify the location as well as the extent of lipid synthesis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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Affiliation(s)
- Joost Brandsma
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andrew P Bailey
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
| | - Grielof Koster
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; National Institute of Health Research Biomedical Research Unit in Respiratory Medicine, University Hospitals Southampton NHS Foundation Trust, United Kingdom
| | - Alex P Gould
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
| | - Anthony D Postle
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
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Van Leuken J, Swart A, Brandsma J, Terink W, Van de Kassteele J, Droogers P, Sauter F, Havelaar A, Van der Hoek W. Human Q fever incidence is associated to spatiotemporal environmental conditions. One Health 2016; 2:77-87. [PMID: 28616479 PMCID: PMC5441340 DOI: 10.1016/j.onehlt.2016.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 02/04/2016] [Accepted: 03/14/2016] [Indexed: 11/26/2022] Open
Abstract
Airborne pathogenic transmission from sources to humans is characterised by atmospheric dispersion and influence of environmental conditions on deposition and reaerosolisation. We applied a One Health approach using human, veterinary and environmental data regarding the 2009 epidemic in The Netherlands, and investigated whether observed human Q fever incidence rates were correlated to environmental risk factors. We identified 158 putative sources (dairy goat and sheep farms) and included 2339 human cases. We performed a high-resolution (1 × 1 km) zero-inflated regression analysis to predict incidence rates by Coxiella burnetii concentration (using an atmospheric dispersion model and meteorological data), and environmental factors - including vegetation density, soil moisture, soil erosion sensitivity, and land use data - at a yearly and monthly time-resolution. With respect to the annual data, airborne concentration was the most important predictor variable (positively correlated to incidence rate), followed by vegetation density (negatively). The other variables were also important, but to a less extent. High erosion sensitive soils and the land-use fractions "city" and "forest" were positively correlated. Soil moisture and land-use "open nature" were negatively associated. The geographical prediction map identified the largest Q fever outbreak areas. The hazard map identified highest hazards in a livestock dense area. We conclude that environmental conditions are correlated to human Q fever incidence rate. Similar research with data from other outbreaks would be needed to more firmly establish our findings. This could lead to better estimations of the public health risk of a C. burnetii outbreak, and to more detailed and accurate hazard maps that could be used for spatial planning of livestock operations.
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Affiliation(s)
- J.P.G. Van Leuken
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - A.N. Swart
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - W. Terink
- Future Water, Wageningen, The Netherlands
| | - J. Van de Kassteele
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - F. Sauter
- Environmental Safety (M&V), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - A.H. Havelaar
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Emerging Pathogens Institute, University of Floriday, Gainesville, Florida, United States
| | - W. Van der Hoek
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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20
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Brandsma J. Phytoplankton phenotype plasticity induced by phosphorus starvation may play a significant role in marine microbial ecology and biogeochemistry. New Phytol 2016; 211:765-766. [PMID: 27397523 DOI: 10.1111/nph.14085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Joost Brandsma
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
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21
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Sebastián M, Smith AF, González JM, Fredricks HF, Van Mooy B, Koblížek M, Brandsma J, Koster G, Mestre M, Mostajir B, Pitta P, Postle AD, Sánchez P, Gasol JM, Scanlan DJ, Chen Y. Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency. ISME J 2016; 10:968-78. [PMID: 26565724 PMCID: PMC4796936 DOI: 10.1038/ismej.2015.172] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022]
Abstract
Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.
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Affiliation(s)
- Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | | | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Benjamin Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Michal Koblížek
- Institute of Microbiology, Center Algatech, Třeboň, Czech Republic
| | - Joost Brandsma
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Grielof Koster
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Mireia Mestre
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Behzad Mostajir
- Center of Marine Biodiversity, Exploitation and Conservation (MARBEC), UMR 9190, CNRS – Université de Montpellier – IRD – IFREMER, Place Eugène Bataillon, Université de Montpellier, Case 93, Montpellier, France
| | - Paraskevi Pitta
- Hellenic Centre for Marine Research, Oceanography Institute, Heraklion, Greece
| | - Anthony D Postle
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
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22
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Wheelock CE, Goss VM, Balgoma D, Nicholas B, Brandsma J, Skipp PJ, Snowden S, Burg D, D'Amico A, Horvath I, Chaiboonchoe A, Ahmed H, Ballereau S, Rossios C, Chung KF, Montuschi P, Fowler SJ, Adcock IM, Postle AD, Dahlén SE, Rowe A, Sterk PJ, Auffray C, Djukanovic R. Application of 'omics technologies to biomarker discovery in inflammatory lung diseases. Eur Respir J 2013; 42:802-25. [PMID: 23397306 DOI: 10.1183/09031936.00078812] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Inflammatory lung diseases are highly complex in respect of pathogenesis and relationships between inflammation, clinical disease and response to treatment. Sophisticated large-scale analytical methods to quantify gene expression (transcriptomics), proteins (proteomics), lipids (lipidomics) and metabolites (metabolomics) in the lungs, blood and urine are now available to identify biomarkers that define disease in terms of combined clinical, physiological and patho-biological abnormalities. The aspiration is that these approaches will improve diagnosis, i.e. define pathological phenotypes, and facilitate the monitoring of disease and therapy, and also, unravel underlying molecular pathways. Biomarker studies can either select predefined biomarker(s) measured by specific methods or apply an "unbiased" approach involving detection platforms that are indiscriminate in focus. This article reviews the technologies presently available to study biomarkers of lung disease within the 'omics field. The contributions of the individual 'omics analytical platforms to the field of respiratory diseases are summarised, with the goal of providing background on their respective abilities to contribute to systems medicine-based studies of lung disease.
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Affiliation(s)
- Craig E Wheelock
- Division of Physiological Chemistry II, Karolinska Institutet, Stockholm
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23
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Brandsma J, van de Vossenberg J, Risgaard-Petersen N, Schmid MC, Engström P, Eurenius K, Hulth S, Jaeschke A, Abbas B, Hopmans EC, Strous M, Schouten S, Jetten MSM, Damsté JSS. A multi-proxy study of anaerobic ammonium oxidation in marine sediments of the Gullmar Fjord, Sweden. Environ Microbiol Rep 2011; 3:360-366. [PMID: 23761282 DOI: 10.1111/j.1758-2229.2010.00233.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is an important process for nitrogen removal in marine pelagic and benthic environments and represents a major sink in the global nitrogen cycle. We applied a suite of complementary methods for the detection and enumeration of anammox activity and anammox bacteria in marine sediments of the Gullmar Fjord, and compared the results obtained with each technique. (15) N labelling experiments showed that nitrogen removal through N2 production was essentially limited to the upper 2 cm of the sediment, where anammox contributed 23-47% of the total production. The presence of marine anammox bacteria belonging to the genus 'Candidatus Scalindua' was shown by 16S rRNA gene sequence comparison. FISH counts of anammox bacteria correlated well with anammox activity, while quantitative PCR may have underestimated the number of anammox bacterial 16S rRNA gene copies at this site. Potential nitrogen conversion by anammox ranged from 0.6 to 4.8 fmol N cell(-1) day(-1) , in agreement with previous measurements in the marine environment and in bioreactors. Finally, intact ladderane glycerophospholipid concentrations better reflected anammox activity and abundance than ladderane core lipid concentrations, most likely because the core lipid fraction contained a substantial fossil component, especially deeper in the sediment.
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Affiliation(s)
- Joost Brandsma
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands. Radboud University Nijmegen, IWWR, Department of Microbiology, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands. Aarhus University, National Environmental Research Institute, Velsøvej 25, DK-8600 Silkeborg, Denmark. University of Gothenburg, Department of Chemistry, SE-412 96 Göteborg, Sweden
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Kocken P, Voorham T, Brandsma J, Swart W. Effects of peer-led AIDS education aimed at Turkish and Moroccan male immigrants in The Netherlands. A randomised controlled evaluation study. Eur J Public Health 2001; 11:153-9. [PMID: 11420801 DOI: 10.1093/eurpub/11.2.153] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND An evaluation study was conducted in The Netherlands into acquired immune deficiency syndrome (AIDS) education for immigrants given in their native language by peers. Turkish and Moroccan men were trained to educate people from their own ethnic group. The effect of peer education on the perceived threat of AIDS and beliefs about condom use were studied. METHODS Places where male immigrants met, i.e. coffee houses, mosques and bars, were matched and randomly assigned to experimental and control groups. The experimental group filled out a short questionnaire at the end of the education session (post-test), whereas the control group was pre-tested and had the opportunity of following the AIDS education after participation in the questionnaire. RESULTS Using multilevel logistic regression analysis, an effect could be established on misunderstandings regarding human immunodeficiency virus (HIV) transmission (OR = 5.9 and 95% CI: 2.3-15.3) and risk appraisal for HIV infection (OR = 2.9 and 95% CI: 1.3-6.3). The perceived benefits of the protective effect of condom use were affected in men 30 years and older, the perceived barrier of diminished satisfaction if using condoms was changed among unmarried men, condom self-efficacy was affected in men who valued peer education as important and an effect on intention to use condoms was found among Moroccans. CONCLUSION Continuation of peer-led AIDS education for immigrants and adaption of the message to the needs of specific target groups is recommended.
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Affiliation(s)
- P Kocken
- Municipal Health Service of Rotterdam area, Department of Health Promotion, P.O. Box 70032, 3000 LP Rotterdam, The Netherlands.
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Abstract
Interest in dissociation has been renewed, and its relationship to Post-traumatic Stress Disorder is especially intriguing. In this study 57 consecutively admitted chronic, combat-related Posttraumatic Stress Disorder sufferers were grouped by scores on a dissociative scale (Dissociative Experiences Scale). The three groups (high, medium, and low) were compared on personality measures (MMPI basic scales and subscales, and Millon's MCMI), Posttraumatic Stress Disorder measures, and a psychophysiological index of heart rate under baseline trauma conditions. The results showed that the survivors with more dissociative experiences show distinctive and higher symptom levels--excessive fearfulness, symptoms of strange experiences, and high tonic psychophysiological states--as well as greater severity of ratings of Posttraumatic Stress Disorder (on the Mississippi Scale). The discussion addressed the possible role of dissociation in Posttraumatic Stress Disorder.
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Affiliation(s)
- L A Hyer
- Veterans Affairs Medical Center, Augusta, GA 30910
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Abstract
Hairy leukoplakia has been defined and confirmed as a specific oral mucosal marker for human immunodeficiency virus infection. Light microscopic findings include alteration of spinous layer cells, which contain nuclear chromatin abnormalities. Enlargement of spinous cells with ballooning degeneration is also characteristic. Ultrastructural morphology has defined the presence of large numbers of herpes-type virus particles within the intranuclear, cytoplasmic, and intercellular regions. Morphologically, the criteria of Epstein-Barr virus are satisfied. Southern blot analysis has confirmed the virus to be Epstein-Barr virus. Further hybridization analyses failed to show any evidence of human immunodeficiency virus or human papillomavirus in the lesions themselves. We conclude that hairy leukoplakia may represent an epithelial opportunistic Epstein-Barr virus infection. Finally, the production and shedding of Epstein-Barr virions into the oral cavity from the sites of hairy leukoplakia can occur separate from the usual tonsillar and oropharyngeal sites.
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Affiliation(s)
- J Sciubba
- Department of Dentistry, Long Island Jewish Medical Center, New Hyde Park, NY 11042
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Brandsma J, Burk RD, Lancaster WD, Pfister H, Schiffman MH. Inter-laboratory variation as an explanation for varying prevalence estimates of human papillomavirus infection. Int J Cancer 1989; 43:260-2. [PMID: 2537262 DOI: 10.1002/ijc.2910430216] [Citation(s) in RCA: 43] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human papillomavirus (HPV) infection has been strongly implicated as a cause of genital neoplasia. Although Southern blot DNA hybridization techniques are regarded as the most accurate means of identifying HPV infection, studies using this technique to measure infection have provided varying estimates of the prevalence of HPV among healthy and diseased groups. This investigation provides a possible explanation for study-to-study differences, by demonstrating inter-laboratory variability in the detection and typing of HPV by Southern blot. Four experienced laboratories tested 40 identical, masked samples of DNA extracted from presumed infected and non-infected tissues. The pairwise percentage agreement between the laboratories in judging samples as HPV-positive or negative ranged from 66 to 97%. Among samples judged to contain HPV, agreement as to type ranged from 77 to 96%. We conclude that inter-laboratory differences are an important consideration in any discussion of HPV prevalence estimates.
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Affiliation(s)
- J Brandsma
- Long Island Jewish Medical Center, New Hyde Park, NY
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29
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Abstract
Photodynamic activation of hematoporphyrin derivative was originally developed for the treatment of cancer. This article demonstrates that it may also be an effective therapy for papillomavirus infections of the larynx. Seventy-two hours prior to surgery, hematoporphyrin derivative (6 mg/kg) was given intravenously to two patients with the adult-onset form of this disease. Three days later, endoscopic surgery was performed and 32 J/cm2 was delivered to the endolarynx via an argon pump dye laser with a red light output of 630 nm. No significant complications such as swelling or hemorrhage occurred. At follow-up (13 months) there has been no recurrence of the laryngeal papilloma in either of these patients. The surgical technique, molecular biology, and clinical implications of this work to control laryngeal papillomatosis are described.
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Affiliation(s)
- A L Abramson
- Department of Otolaryngology and Communicative Disorders, Long Island Jewish Medical Center, New Hyde Park, NY 11042
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Affiliation(s)
- N Kamani
- Division of Allergy-Immunology, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine 19104
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Schuldiner S, Agmon V, Brandsma J, Cohen A, Friedman E, Padan E. Induction of SOS functions by alkaline intracellular pH in Escherichia coli. J Bacteriol 1986; 168:936-9. [PMID: 3096964 PMCID: PMC213574 DOI: 10.1128/jb.168.2.936-939.1986] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Alkalinization of intracellular pH (pHi) causes an increase in UV resistance in wild-type and pH-sensitive mutant (DZ3) cells of Escherichia coli. Utilizing cells transformed with a plasmid (pA7) which bears the uvrA promoter fused to galK galactokinase structural gene, it was shown that alkaline pHi leads to an increase in the specific activity of galactokinase. This effect was not displayed in a mutant bearing a recA-insensitive lexA gene, nor in cells harboring a plasmid (pA8) in which the galK is fused to a lexA-insensitive uvrA promoter. Hence, the effects of pHi on cells functions may involve the lexA product of the SOS system.
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Abstract
Verrucous carcinoma of the larynx is a distinct and uncommon variant of well-differentiated squamous cell carcinoma. By DNA hybridization techniques, we clearly demonstrated human papillomavirus (HPV-16-related) sequences in five patients with this neoplasm. In addition, HPV-16-related sequences were found in adjacent normal tissues. The DNAs from squamous cell carcinomas of the larynx were negative when hybridized to HPV-6, -11, or -16. Postirradiation anaplastic transformation of verrucous carcinoma has been described. We believe that radiotherapy should not be given unless the potential consequences are fully explained because of its potential to activate or alter HPV-16-related sequences.
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Abstract
A chimeric gene consisting of DNA coding for the 15-amino acid signal peptide of influenza virus hemagglutinin and the C-terminal 694 amino acids of SV40 large T antigen was inserted into a bovine papilloma virus (BPV) expression vector and introduced into NIH-3T3 cells. Cell lines were obtained that express high levels (approximately 5 X 10(6) molecules/cell) of the chimeric protein (HA-T antigen). The biochemical properties and intracellular localization of HA-T antigens were compared with those of wild-type T antigen. Wild-type T antigen. Wild-type T antigen is located chiefly in the cell nucleus, although a small fraction is detected on the cell surface. By contrast, HA-T antigen is found exclusively in the endoplasmic reticulum (ER). During biosynthesis, HA-T antigen is co-translationally translocated across the membrane of the ER, the signal peptide is cleaved and a mannose-rich oligosaccharide is attached to the polypeptide (T antigen contains one potential N-linked glycosylation site at Asn154). HA-T antigen does not become terminally glycosylated or acylated and little or none reaches the cell surface. These results suggest that T antigen is incapable of being transported along the exocytotic pathway. To explain the presence of wild-type T antigen on the surface of SV40-transformed cells, an alternative route is proposed involving transport of T antigen from the nucleus to the cell surface.
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Fischer DK, Miller G, Gradoville L, Heston L, Westrate MW, Maris W, Wright J, Brandsma J, Summers WC. Genome of a mononucleosis Epstein-Barr virus contains DNA fragments previously regarded to be unique to Burkitt's lymphoma isolates. Cell 1981; 24:543-53. [PMID: 6263500 DOI: 10.1016/0092-8674(81)90345-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We wished to learn whether the genomes of strains of EMB isolated from patients with infectious mononucleosis are consistently distinguishable from those of strains from Burkitt's lymphoma. The genome of a new transforming strains (FF41) of EBV isolated from saliva of a patient with uncomplicated infectious mononucleosis was compared with the DNA of B95-8, the only other available virus from mononucleosis. It had been found previously that B95-8 has a deletion of about 8 Md in the region of the physical map represented by the Eco RI C, Hind III D, and Bam HI I fragments. The W91 and HR-1 isolates for Burkitt's lymphoma are not deleted in this region and it had been proposed that additional information was characteristic of EBV isolates from Burkitt's lymphoma. By means of restriction enzyme analysis, blot hybridization experiments and molecular cloning of FF41 DNA we demonstrate that the deletion found in B95-8 is not present in the new mononucleosis isolate. The FF41 genome contains an extra 8 Md of DNA, represented by Bam HI fragments B', W' and I', which are located in a larger Eco RI C fragment. Thus the genome of this salivary isolate contains DNA that had previously been regarded to be unique to strains from Burkitt's lymphoma. It is therefore unlikely that major insertions or deletions in the EBV genome account for differences in disease manifestation following EBV infection.
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Brandsma J, Miller G. Nucleic acid spot hybridization: rapid quantitative screening of lymphoid cell lines for Epstein-Barr viral DNA. Proc Natl Acad Sci U S A 1980; 77:6851-5. [PMID: 6256764 PMCID: PMC350388 DOI: 10.1073/pnas.77.11.6851] [Citation(s) in RCA: 142] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A simple nucleic acid hybridization method to screen numerous samples of eukaryotic cells rapidly for their Epstein-Barr virus (EBV) DNA content is described. Whole cells are spotted on nitrocellulose filters and their DNA is denatured and fixed to the filter. The resultant DNA spots are hybridized to nick-translated EBV DNA and the extent of hybridization is monitored by autoradiography and scintillation counting. Statistical analysis of serial dilutions of cells permits their viral genome content to be estimated quantitatively by reference to a known standard, such as Raji cells or an artificial mixture of pure viral DNA and uninfected lymphocytes. The sensitivity of the method is between 5 and 50 pg of viral DNA. With this method we are able to select subclones that are high produces of EBV DNA and to identify the optimal time for harvest of EBV DNA from cultured cells. Spot hybridization should permit any cell population or fluid to be screened for the presence of a DNA sequence for which a radioisotopically labeled probe is available.
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Coope D, Heston L, Brandsma J, Miller G. Cross-neutralization of infectious mononucleosis and Burkitt lymphoma strains of Epstein-Barr virus with hyperimmune rabbit antisera. J Immunol 1979; 123:232-8. [PMID: 221591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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St George TD, Standfast HA, Doherty RL, Carley JG, Fillipich C, Brandsma J. The isolation of Saumarez Reef virus, a new flavivirus, from bird ticks Ornithodoros capensis and Ixodes eudyptidis in Australia. Aust J Exp Biol Med Sci 1977; 55:493-9. [PMID: 75000 DOI: 10.1038/icb.1977.49] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Strains of a new flavivirus, for which the name Saumarez Reef Virus is proposed, were isolated from seabird ticks collected from four localities. Two strains were isolated from ticks of the species Ornithodoros capensis Neumann 1901 collected from the nests of Sooty Terns, Sterna fuscata Linnaeus 1766 on coral cays off the east coast of Queensland, Australia. The other three strains were isolated from ticks of the species Ixodes eudyptidis Maskell 1885 taken from two dead Silver Gulls Larus novaehollandiae Stephens 1826 in northern Tasmania. The new virus was compared serologically with 50 other flaviviruses at the Yale Arbovirus Research Unit and was found to be most closely related to Tyuleniy virus.
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