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Shannon CP, Lee AH, Tebbutt SJ, Singh A. A Commentary on Multi-omics Data Integration in Systems Vaccinology. J Mol Biol 2024; 436:168522. [PMID: 38458605 DOI: 10.1016/j.jmb.2024.168522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Affiliation(s)
| | - Amy Hy Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Scott J Tebbutt
- PROOF Centre of Excellence, Vancouver, Canada; Department of Medicine, The University of British Columbia, Vancouver, Canada; Centre for Heart Lung Innovation, Vancouver, Canada
| | - Amrit Singh
- Centre for Heart Lung Innovation, Vancouver, Canada; Department of Anesthesiology, Pharmacology and Therapeutics, The University of British Columbia, Vancouver, Canada.
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2
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Yang C, Shannon CP, Tebbutt SJ. Unravelling long COVID: insights from proteomics and considerations for comprehensive understanding. EBioMedicine 2024; 101:105023. [PMID: 38377796 PMCID: PMC10884337 DOI: 10.1016/j.ebiom.2024.105023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/22/2024] Open
Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada; Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada; Providence Research, Providence Health Care, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada; Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada; Providence Research, Providence Health Care, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada; Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada; Providence Research, Providence Health Care, Vancouver, BC, Canada.
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Yang C, Lapp L, Tebbutt SJ. Overcoming COVID-19 vaccine hesitancy hurdles. Lancet 2023; 402:1129-1130. [PMID: 37777327 DOI: 10.1016/s0140-6736(23)01425-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/05/2023] [Indexed: 10/02/2023]
Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Linda Lapp
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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4
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Yang C, Lapp L, Tebbutt SJ. Vaccination After SARS-CoV-2 Infection and Post-COVID-19 Condition. JAMA Intern Med 2023; 183:1035-1036. [PMID: 37486686 DOI: 10.1001/jamainternmed.2023.3033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, Canada
- Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, University of British Columbia, Vancouver, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Linda Lapp
- Prevention of Organ Failure Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, Canada
- Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, University of British Columbia, Vancouver, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, Canada
- Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, University of British Columbia, Vancouver, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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5
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Kim JYV, Assadian S, Hollander Z, Burns P, Shannon CP, Lam K, Toma M, Ignaszewski A, Davies RA, Delgado D, Haddad H, Isaac D, Kim D, Mui A, Rajda M, West L, White M, Zieroth S, Keown PA, McMaster WR, Ng RT, McManus BM, Levings MK, Tebbutt SJ. Regulatory T Cell Biomarkers Identify Patients at Risk of Developing Acute Cellular Rejection in the First Year Following Heart Transplantation. Transplantation 2023; 107:1810-1819. [PMID: 37365692 DOI: 10.1097/tp.0000000000004607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
BACKGROUND Acute cellular rejection (ACR), an alloimmune response involving CD4+ and CD8+ T cells, occurs in up to 20% of patients within the first year following heart transplantation. The balance between a conventional versus regulatory CD4+ T cell alloimmune response is believed to contribute to developing ACR. Therefore, tracking these cells may elucidate whether changes in these cell populations could signal ACR risk. METHODS We used a CD4+ T cell gene signature (TGS) panel that tracks CD4+ conventional T cells (Tconv) and regulatory T cells (Treg) on longitudinal samples from 94 adult heart transplant recipients. We evaluated combined diagnostic performance of the TGS panel with a previously developed biomarker panel for ACR diagnosis, HEARTBiT, while also investigating TGS' prognostic utility. RESULTS Compared with nonrejection samples, rejection samples showed decreased Treg- and increased Tconv-gene expression. The TGS panel was able to discriminate between ACR and nonrejection samples and, when combined with HEARTBiT, showed improved specificity compared with either model alone. Furthermore, the increased risk of ACR in the TGS model was associated with lower expression of Treg genes in patients who later developed ACR. Reduced Treg gene expression was positively associated with younger recipient age and higher intrapatient tacrolimus variability. CONCLUSIONS We demonstrated that expression of genes associated with CD4+ Tconv and Treg could identify patients at risk of ACR. In our post hoc analysis, complementing HEARTBiT with TGS resulted in an improved classification of ACR. Our study suggests that HEARTBiT and TGS may serve as useful tools for further research and test development.
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Affiliation(s)
- Ji-Young V Kim
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
- Providence Research, Providence Health Care Research Institute, Vancouver, BC, Canada
| | - Sara Assadian
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
- Providence Research, Providence Health Care Research Institute, Vancouver, BC, Canada
| | - Zsuzsanna Hollander
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
- Providence Research, Providence Health Care Research Institute, Vancouver, BC, Canada
| | - Paloma Burns
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
- Providence Research, Providence Health Care Research Institute, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
- Providence Research, Providence Health Care Research Institute, Vancouver, BC, Canada
| | - Karen Lam
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
- Providence Research, Providence Health Care Research Institute, Vancouver, BC, Canada
| | - Mustafa Toma
- Department of Cardiology, University of British Columbia, Vancouver, BC, Canada
| | - Andrew Ignaszewski
- Department of Cardiology, University of British Columbia, Vancouver, BC, Canada
| | - Ross A Davies
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - Diego Delgado
- University Health Network/Mount Sinai Hospital, Toronto, ON, Canada
| | - Haissam Haddad
- Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Debra Isaac
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Daniel Kim
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Alice Mui
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Miroslaw Rajda
- Department of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Lori West
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Michel White
- Institut de Cardiologie de Montréal, Montréal, QC, Canada
| | - Shelley Zieroth
- Department of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Paul A Keown
- Department of Medicine, Division of Nephrology, University of British Columbia, Vancouver, BC, Canada
| | - W Robert McMaster
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Raymond T Ng
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
| | - Bruce M McManus
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Megan K Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
- Providence Research, Providence Health Care Research Institute, Vancouver, BC, Canada
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6
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Castro-Rodriguez JA, Fish EN, Montgomery ST, Kollmann TR, Iturriaga C, Shannon C, Karpievitch Y, Ho J, Chen V, Balshaw R, Ben-Othman R, Aniba R, Gidi-Yunge F, Hartnell L, Hancock DG, Pérez-Mateluna G, Urzúa M, Tebbutt SJ, García-Huidobro D, Perret C, Borzutzky A, Stick SM. Interferon β-1a ring prophylaxis to reduce household transmission of SARS-CoV-2: a cluster randomised clinical trial. EClinicalMedicine 2023; 62:102082. [PMID: 37538539 PMCID: PMC10393621 DOI: 10.1016/j.eclinm.2023.102082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 08/05/2023] Open
Abstract
Background Accumulating evidence indicates that an early, robust type 1 interferon (IFN) response to SARS-CoV-2 is important in determining COVID-19 outcomes, with an inadequate IFN response associated with disease severity. Our objective was to examine the prophylactic potential of IFN administration to limit viral transmission. Methods A cluster randomised open label clinical trial was undertaken to determine the effects of pegylated IFNβ-1a administration on SARS-CoV-2 household transmission between December 3rd, 2020 and June 29th, 2021. Index cases were identified from databases of confirmed SARS-CoV-2 individuals in Santiago, Chile. Households were cluster randomised (stratified by household size and age of index cases) to receive 3 doses of 125 μg subcutaneous pegylated IFNβ-1a (172 households, 607 participants), or standard care (169 households, 565 participants). The statistical team was blinded to treatment assignment until the analysis plan was finalised. Analyses were undertaken to determine effects of treatment on viral shedding and viral transmission. Safety analyses included incidence and severity of adverse events in all treatment eligible participants in the standard care arm, or in the treatment arm with at least one dose administered. Clinicaltrials.gov identifier: NCT04552379. Findings 5154 index cases were assessed for eligibility, 1372 index cases invited to participate, and 341 index cases and their household contacts (n = 831) enrolled. 1172 participants in 341 households underwent randomisation, with 607 assigned to receive IFNβ-1a and 565 to standard care. Based on intention to treat (ITT) and per protocol (PP) analyses for the primary endpoints, IFNβ-1a treatment did not affect duration of viral shedding in index cases (absolute risk reduction = -0.2%, 95% CI = -8.46% to 8.06%) and transmission of SARS-CoV-2 to household contacts (absolute risk reduction = 3.87%, 95% CI = -3.6% to 11.3%). Treatment with IFNβ-1a resulted in significantly more treatment-related adverse events, but no increase in overall adverse events or serious adverse events. Interpretation Based upon the primary analyses, IFNβ-1a treatment did not affect duration of viral shedding or the probability of SARS-CoV-2 transmission to uninfected contacts within a household. Funding Biogen PTY Ltd. Supply of interferon as 'Plegridy (peginterferon beta-1a).' The study was substantially funded by BHP Holdings Pty Ltd.
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Affiliation(s)
| | - Eleanor N. Fish
- Toronto General Hospital Research Institute, University Health Network & Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Samuel T. Montgomery
- Telethon Kids Institute, Perth, Australia
- School of Population Health, Curtin University, Bentley, Australia
| | | | - Carolina Iturriaga
- Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Casey Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | | | - Joseph Ho
- Telethon Kids Institute, Perth, Australia
| | - Virginia Chen
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- Centre for Healthcare Innovation, University of Manitoba, Manitoba, Canada
| | | | | | | | | | | | | | - Marcela Urzúa
- Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Scott J. Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Diego García-Huidobro
- Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Family and Community Medicine, University of Minnesota, MN, USA
| | - Cecilia Perret
- Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Arturo Borzutzky
- Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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Randhawa GK, Orach J, Black A, Chan V, Potter N, Brinkman J, Côté H, Worfolk L, Knight D, Leversage I, Tebbutt SJ. Design, delivery, and evaluation of a knowledge translation intervention for multi-stakeholders. Implement Sci Commun 2023; 4:85. [PMID: 37488655 PMCID: PMC10364428 DOI: 10.1186/s43058-023-00465-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/30/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Knowledge translation (KT) is a key competency for trainees (graduate students and post-doctoral fellows), the new generation of researchers who must learn how to synthesize, disseminate, exchange, and ethically apply knowledge to improve patient and health system services, products, and outcomes. KT training is a key enabler to support KT competency development. Yet, there is a dearth of research on the design, delivery, and evaluation of KT training for trainees. METHODS The study applied a QUAN(qual) mixed methods approach with an embedded experimental model design. A heart and lung patient was also recruited to participate as a partner and researcher in the study. A multi-faceted KT intervention for trainees was designed, delivered, and evaluated. Data were collected using surveys and focus groups. Quantitative data were analyzed using descriptive and inferential statistics in R Studio and MS Excel. Qualitative data were analyzed in NVivo using thematic analysis. RESULTS Participation in each KT intervention varied, with 8-42 participants attending KT webinars, 61 attendees in the Three Minute Thesis (3MT) Competition Heat, and 31 participants in the Patient & Public Forum. In total, 27 trainees and 4 faculty participated in at least one of the KT webinars. Trainee participants reported satisfaction, as well as statistically significant increases in 10/13 KT competencies after receiving one or more components of the KT intervention. Additionally, participating faculty, patients, and the public were satisfied with the intervention components they participated in. Several challenges and facilitators were also identified to improve the KT intervention. CONCLUSIONS The KT intervention is a promising initiative that can be adopted and adapted across various post-secondary settings to support trainees' competency development in KT. This evaluation demonstrates that trainees will respond to opportunities for KT training and that capacity for KT competencies can be advanced through a multi-faceted intervention that involves trainees, faculty, patients, and health system collaborators in its design and delivery. This evaluation study contributes the design and results of a novel KT intervention for multi-stakeholders. TRIAL REGISTRATION N/A.
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Affiliation(s)
- Gurprit Kaur Randhawa
- University of British Columbia, Vancouver, BC, Canada.
- University of Victoria, Victoria, BC, Canada.
| | - Juma Orach
- University of British Columbia, Vancouver, BC, Canada
| | - Agnes Black
- Providence Health Care, Vancouver, BC, Canada
| | - Vivienne Chan
- University of British Columbia, Vancouver, BC, Canada
| | - Naomi Potter
- University of British Columbia, Vancouver, BC, Canada
| | | | - Hélène Côté
- University of British Columbia, Vancouver, BC, Canada
| | - Larry Worfolk
- University of British Columbia, Vancouver, BC, Canada
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8
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Yang C, Zhao H, Espín E, Tebbutt SJ. Association of SARS-CoV-2 infection and persistence with long COVID. Lancet Respir Med 2023:S2213-2600(23)00142-X. [PMID: 37178694 PMCID: PMC10171832 DOI: 10.1016/s2213-2600(23)00142-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/27/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023]
Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Hedi Zhao
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Estefanía Espín
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada.
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Espín E, Yang C, Shannon CP, Assadian S, He D, Tebbutt SJ. Cellular and molecular biomarkers of long COVID: a scoping review. EBioMedicine 2023; 91:104552. [PMID: 37037165 PMCID: PMC10082390 DOI: 10.1016/j.ebiom.2023.104552] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 12/01/2022] [Revised: 03/01/2023] [Accepted: 03/17/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Long-COVID (LC) encompasses diverse symptoms lasting months after the initial SARS-CoV-2 infection. Symptoms can be debilitating and affect the quality of life of individuals with LC and their families. Although the symptoms of LC are well described, the aetiology of LC remains unclear, and consequently, patients may be underdiagnosed. Identification of LC specific biomarkers is therefore paramount for the diagnosis and clinical management of the syndrome. This scoping review describes the molecular and cellular biomarkers that have been identified to date with potential use for diagnosis or prediction of LC. METHODS This review was conducted using the Joanna Briggs Institute (JBI) Methodology for Scoping Reviews. A search was executed in the MEDLINE and EMBASE databases, as well as in the grey literature for original studies, published until October 5th, 2022, reporting biomarkers identified in participants with LC symptoms (from all ages, ethnicities, and sex), with a previous infection of SARS-CoV-2. Non-English studies, cross-sectional studies, studies without a control group, and pre-prints were excluded. Two reviewers independently evaluated the studies, extracted population data and associated biomarkers. FINDINGS 23 cohort studies were identified, involving 2163 LC patients [median age 51.8 years, predominantly female sex (61.10%), white (75%), and non-vaccinated (99%)]. A total of 239 candidate biomarkers were identified, consisting mainly of immune cells, immunoglobulins, cytokines, and other plasma proteins. 19 of the 239 candidate biomarkers identified were evaluated by the authors, by means of receiver operating characteristic (ROC) curves. INTERPRETATION Diverse cellular and molecular biomarkers for LC have been proposed. Validation of candidate biomarkers in independent samples should be prioritized. Modest reported performance (particularly in larger studies) suggests LC may encompass many distinct aetiologies, which should be explored e.g., by stratifying by symptom clusters and/or sex. FUNDING Dr. Tebbutt has received funding from the Canadian Institutes of Health Research (177747) to conduct this work. The funding source was not involved in this scoping review, or in the decision to submit this manuscript for publication.
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Affiliation(s)
- Estefanía Espín
- Prevention of Organ Failure (PROOF) Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; UBC Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
| | - Chengliang Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; UBC Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; UBC Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
| | - Sara Assadian
- Prevention of Organ Failure (PROOF) Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; UBC Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
| | - Daniel He
- Prevention of Organ Failure (PROOF) Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; UBC Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; UBC Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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10
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Yang C, Tebbutt SJ. Long COVID: the next public health crisis is already on its way. Lancet Reg Health Eur 2023; 28:100612. [PMID: 37131860 PMCID: PMC10006728 DOI: 10.1016/j.lanepe.2023.100612] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/13/2023] Open
Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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11
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Yang C, Zhao H, Shannon CP, Tebbutt SJ. Omicron variants of SARS-CoV-2 and long COVID. Front Immunol 2022; 13:1061686. [PMID: 36569883 PMCID: PMC9780375 DOI: 10.3389/fimmu.2022.1061686] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Understanding the epidemiology of long COVID and emerging variants has significant public-health implications as physical interventions and restrictions that help limit viral spread are eased globally. Here, we provide rationales for the necessity of updating current vaccines to improve protection against omicron and emerging variants, as well as more research into understanding the epidemiology and mechanisms of long COVID.
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Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada,Centre for Heart Lung Innovation, Providence Research, St. Paul’s Hospital, Vancouver, BC, Canada,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Hedi Zhao
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Casey P. Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada,Centre for Heart Lung Innovation, Providence Research, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Scott J. Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada,Centre for Heart Lung Innovation, Providence Research, St. Paul’s Hospital, Vancouver, BC, Canada,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada,*Correspondence: Scott J. Tebbutt,
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12
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Prieto MD, Jang J, Franciosi AN, Av-Gay Y, Bach H, Tebbutt SJ, Quon BS. Whole blood RNA-seq demonstrates an increased host immune response in individuals with cystic fibrosis who develop nontuberculous mycobacterial pulmonary disease. PLoS One 2022; 17:e0278296. [PMID: 36480571 PMCID: PMC9731410 DOI: 10.1371/journal.pone.0278296] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Individuals with cystic fibrosis have an elevated lifetime risk of colonization, infection, and disease caused by nontuberculous mycobacteria. A prior study involving non-cystic fibrosis individuals reported a gene expression signature associated with susceptibility to nontuberculous mycobacteria pulmonary disease (NTM-PD). In this study, we determined whether people living with cystic fibrosis who progress to NTM-PD have a gene expression pattern similar to the one seen in the non-cystic fibrosis population. METHODS We evaluated whole blood transcriptomics using bulk RNA-seq in a cohort of cystic fibrosis patients with samples collected closest in timing to the first isolation of nontuberculous mycobacteria. The study population included patients who did (n = 12) and did not (n = 30) develop NTM-PD following the first mycobacterial growth. Progression to NTM-PD was defined by a consensus of two expert clinicians based on reviewing clinical, microbiological, and radiological information. Differential gene expression was determined by DESeq2. RESULTS No differences in demographics or composition of white blood cell populations between groups were identified at baseline. Out of 213 genes associated with NTM-PD in the non-CF population, only two were significantly different in our cystic fibrosis NTM-PD cohort. Gene set enrichment analysis of the differential expression results showed that CF individuals who developed NTM-PD had higher expression levels of genes involved in the interferon (α and γ), tumor necrosis factor, and IL6-STAT3-JAK pathways. CONCLUSION In contrast to the non-cystic fibrosis population, the gene expression signature of patients with cystic fibrosis who develop NTM-PD is characterized by increased innate immune responses.
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Affiliation(s)
- Miguel Dario Prieto
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Jiah Jang
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Alessandro N. Franciosi
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Yossef Av-Gay
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Horacio Bach
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Bradley S. Quon
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
- * E-mail:
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13
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West AG, Digby A, Lear G, Taylor MW, Bromley M, Buckley E, Chatterton J, Cox MP, Cramer RA, Crane J, Dearden PK, Eason D, Fisher MC, Gago S, Gartrell B, Gemmell NJ, Glare TR, Guhlin J, Howard J, Lacap-Bugler D, Le Lec M, Lin XX, Lofgren L, Mackay J, Meis J, Morelli KA, Perrott J, Petterson M, Quinones-Mateu M, Rhodes J, Roberts J, Stajich J, Taylor MW, Tebbutt SJ, Truter-Meyer A, Uddstrom L, Urban L, van Rhijn N, Vercoe D, Vesely E, Weir BS, West AG, Winter DJ, Yeung J, Taylor MW. Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter. Anim Microbiome 2022; 4:55. [PMID: 36175950 PMCID: PMC9523977 DOI: 10.1186/s42523-022-00204-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/29/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial communities to animal health, and increasing appreciation of their potential relevance to threatened species conservation, we sought to better understand the development of this unusual gut microbiota profile. To this end, we conducted a longitudinal analysis of faecal material collected from kākāpō chicks during the 2019 breeding season, in addition to associated nest litter material. RESULTS Using an experimental approach rarely seen in studies of threatened species microbiota, we evaluated the impact of a regular conservation practice on the developing kākāpō microbiota, namely the removal of faecal material from nests. Artificially removing chick faeces from nests had negligible impact on bacterial community diversity for either chicks or nests (p > 0.05). However, the gut microbiota did change significantly over time as chick age increased (p < 0.01), with an increasing relative abundance of Escherichia-Shigella coli over the study period and similar observations for the associated nest litter microbiota (p < 0.01). Supplementary feeding substantially altered gut bacterial diversity of kākāpō chicks (p < 0.01), characterised by a significant increase in Lactobacillus bacteria. CONCLUSIONS Overall, chick age and hand rearing conditions had the most marked impact on faecal bacterial communities. Similarly, the surrounding nest litter microbiota changed significantly over time since a kākāpō chick was first placed in the nest, though we found no evidence that removal of faecal material influenced the bacterial communities of either litter or faecal samples. Taken together, these observations will inform ongoing conservation and management of this most enigmatic of bird species.
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Affiliation(s)
- Annie G. West
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Andrew Digby
- Department of Conservation, Kākāpō Recovery Team, PO Box 743, Invercargill, New Zealand
| | - Gavin Lear
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Kākāpō Recovery Team
- Department of Conservation, Kākāpō Recovery Team, PO Box 743, Invercargill, New Zealand
| | | | - Michael W. Taylor
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
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14
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Yang C, Zhao H, Tebbutt SJ. A glimpse into long COVID and symptoms. The Lancet Respiratory Medicine 2022; 10:e81. [PMID: 35697054 PMCID: PMC9187332 DOI: 10.1016/s2213-2600(22)00217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022]
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15
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Maestre-Batlle D, Nygaard UC, Huff RD, Alexis NE, Tebbutt SJ, Turvey SE, Carlsten C, Kocbach Bølling A. Dibutyl phthalate exposure alters T-cell subsets in blood from allergen-sensitized volunteers. Indoor Air 2022; 32:e13026. [PMID: 35481934 DOI: 10.1111/ina.13026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/04/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Phthalates are ubiquitous environmental contaminants associated with allergic disease in epidemiological and animal studies. This investigation aims to support these associations by interrogating systemic immune effects in allergen-sensitized volunteers after controlled indoor air exposure to a known concentration of dibutyl phthalate (DBP). The phthalate-allergen immune response (PAIR) study enrolled 16 allergen-sensitized participants to a double-blinded, randomized, crossover exposure to two conditions (DBP or control air for 3 hr), each followed immediately by inhaled allergen challenge. Peripheral blood immune cell composition and activation along with inflammatory mediators were measured before and after exposure. DBP exposure prior to the inhaled allergen challenge increased the percentage of CD4+ T helper cells and decreased the percentage of regulatory T cells (3 hr and 20 hr post-exposure), while only modest overall effects were observed for inflammatory mediators. The cells and mediators affected by the phthalate exposure were generally not overlapping with the endpoints affected by allergen inhalation alone. Thus, in distinction to our previously published effects on lung function, DBP appears to alter endpoints in peripheral blood that are not necessarily enhanced by allergen alone. Further studies are needed to clarify the role of phthalate-induced systemic effects in disease pathogenesis.
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Affiliation(s)
- Danay Maestre-Batlle
- Department of Medicine, Air Pollution Exposure Lab and Legacy for Airway Health, University of British Columbia and Vancouver Coastal Health, Vancouver, Canada
| | - Unni C Nygaard
- Department of Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ryan D Huff
- Department of Medicine, Air Pollution Exposure Lab and Legacy for Airway Health, University of British Columbia and Vancouver Coastal Health, Vancouver, Canada
| | - Neil E Alexis
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott J Tebbutt
- Department of Medicine, PROOF Centre of Excellence, & Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Christopher Carlsten
- Department of Medicine, Air Pollution Exposure Lab and Legacy for Airway Health, University of British Columbia and Vancouver Coastal Health, Vancouver, Canada
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16
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Yang C, Zhao H, Tebbutt SJ. Balancing the Risks and Benefits of COVID-19 Vaccination for Pregnant Women and Their Children. Front Immunol 2021; 12:748456. [PMID: 34975839 PMCID: PMC8716367 DOI: 10.3389/fimmu.2021.748456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/23/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Hedi Zhao
- Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Scott J. Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Scott J. Tebbutt,
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17
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Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada
| | - Hedi Zhao
- Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Health Care Research Institute, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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18
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Aevermann BD, Shannon CP, Novotny M, Ben-Othman R, Cai B, Zhang Y, Ye JC, Kobor MS, Gladish N, Lee AHY, Blimkie TM, Hancock RE, Llibre A, Duffy D, Koff WC, Sadarangani M, Tebbutt SJ, Kollmann TR, Scheuermann RH. Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response. Front Immunol 2021; 12:690470. [PMID: 34777332 PMCID: PMC8588842 DOI: 10.3389/fimmu.2021.690470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/25/2021] [Indexed: 01/23/2023] Open
Abstract
Vaccination to prevent infectious disease is one of the most successful public health interventions ever developed. And yet, variability in individual vaccine effectiveness suggests that a better mechanistic understanding of vaccine-induced immune responses could improve vaccine design and efficacy. We have previously shown that protective antibody levels could be elicited in a subset of recipients with only a single dose of the hepatitis B virus (HBV) vaccine and that a wide range of antibody levels were elicited after three doses. The immune mechanisms responsible for this vaccine response variability is unclear. Using single cell RNA sequencing of sorted innate immune cell subsets, we identified two distinct myeloid dendritic cell subsets (NDRG1-expressing mDC2 and CDKN1C-expressing mDC4), the ratio of which at baseline (pre-vaccination) correlated with the immune response to a single dose of HBV vaccine. Our results suggest that the participants in our vaccine study were in one of two different dendritic cell dispositional states at baseline – an NDRG2-mDC2 state in which the vaccine elicited an antibody response after a single immunization or a CDKN1C-mDC4 state in which the vaccine required two or three doses for induction of antibody responses. To explore this correlation further, genes expressed in these mDC subsets were used for feature selection prior to the construction of predictive models using supervised canonical correlation machine learning. The resulting models showed an improved correlation with serum antibody titers in response to full vaccination. Taken together, these results suggest that the propensity of circulating dendritic cells toward either activation or suppression, their “dispositional endotype” at pre-vaccination baseline, could dictate response to vaccination.
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Affiliation(s)
- Brian D Aevermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Bing Cai
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Jamie C Ye
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Michael S Kobor
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Travis M Blimkie
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Robert E Hancock
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Alba Llibre
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Wayne C Koff
- Human Vaccines Project, New York, NY, United States
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States.,Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
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19
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Smolen KK, Plotkin AL, Shannon CP, Idoko OT, Pak J, Darboe A, van Haren S, Amenyogbe N, Tebbutt SJ, Kollmann TR, Kampmann B, Ozonoff A, Levy O, Odumade OA. Ontogeny of plasma cytokine and chemokine concentrations across the first week of human life. Cytokine 2021; 148:155704. [PMID: 34597920 PMCID: PMC8665647 DOI: 10.1016/j.cyto.2021.155704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/30/2022]
Abstract
Introduction/background & aims: Early life is marked by distinct and rapidly evolving immunity and increased susceptibility to infection. The vulnerability of the newborn reflects development of a complex immune system in the face of rapidly changing demands during the transition to extra-uterine life. Cytokines and chemokines contribute to this dynamic immune signaling network and can be altered by many factors, such as infection. Newborns undergo dynamic changes important to health and disease, yet there is limited information regarding human neonatal plasma cytokine and chemokine concentrations over the first week of life. The few available studies are limited by small sample size, cross-sectional study design, or focus on perturbed host states like severe infection or prematurity. To characterize immune ontogeny among healthy full-term newborns, we assessed plasma cytokine and chemokine concentrations across the first week of life in a robust longitudinal cohort of healthy, full-term African newborns. Methods: We analyzed a subgroup of a cohort of healthy newborns at the Medical Research Council Unit in The Gambia (West Africa; N = 608). Peripheral blood plasma was collected from all study participants at birth (day of life (DOL) 0) and at one follow-up time point at DOL 1, 3, or 7. Plasma cytokine and chemokine concentrations were measured by bead-based cytokine multiplex assay. Unsupervised clustering was used to identify patterns in plasma cytokine and chemokine ontogeny during early life. Results: We observed an increase across the first week of life in plasma Th1 cytokines such as IFNγ and CXCL10 and a decrease in Th2 and anti-inflammatory cytokines such as IL-6 and IL-10, and chemokines such as CXCL8. In contrast, other cytokines and chemokines (e.g. IL-4 and CCL5, respectively) remained unchanged during the first week of life. This robust ontogenetic pattern did not appear to be affected by gestational age or sex. Conclusions: Ontogeny is a strong driver of newborn plasma-based levels of cytokines and chemokines throughout the first week of life with a rising IFNγ axis suggesting post-natal upregulation of host defense pathways. Our study will prove useful to the design and interpretation of future studies aimed at understanding the neonatal immune system during health and disease.
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Affiliation(s)
- Kinga K Smolen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Alec L Plotkin
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Casey P Shannon
- PROOF Centre of Excellence, 10th Floor, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada
| | - Olubukola T Idoko
- Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia; The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London UK
| | - Jensen Pak
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Alansana Darboe
- Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia; The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London UK
| | - Simon van Haren
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Nelly Amenyogbe
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Scott J Tebbutt
- PROOF Centre of Excellence, 10th Floor, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada; UBC Centre for Heart and Lung Innovation, Vancouver, V6T1Z4 BC, Canada; Department of Medicine, Division of Respiratory Medicine, UBC, Vancouver, V6T1Z4 BC, Canada
| | - Tobias R Kollmann
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Beate Kampmann
- Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia; The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London UK
| | - Al Ozonoff
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT & Harvard, Cambridge, USA
| | - Oludare A Odumade
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Medicine Critical Care, Boston Children's Hospital, Boston, MA, USA.
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20
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Hernandez Cordero AI, Yang CX, Milne S, Li X, Hollander Z, Chen V, Ng R, Tebbutt SJ, Leung JM, Sin DD. Epigenetic blood biomarkers of ageing and mortality in COPD. Eur Respir J 2021; 58:13993003.01890-2021. [PMID: 34561282 DOI: 10.1183/13993003.01890-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/09/2021] [Indexed: 01/05/2023]
Affiliation(s)
- Ana I Hernandez Cordero
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Stephen Milne
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada.,Sydney Medical School, Faculty of Medicine and Health Sciences, University of Sydney, Sydney, Australia
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Zsuzsanna Hollander
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada.,PROOF Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada
| | - Virginia Chen
- PROOF Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada
| | - Raymond Ng
- PROOF Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada.,PROOF Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada
| | - Janice M Leung
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
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21
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Samra SK, Rajasekaran A, Sandford AJ, Ellis AK, Tebbutt SJ. Cholinergic Synapse Pathway Gene Polymorphisms Associated With Late-Phase Responses in Allergic Rhinitis. Front Allergy 2021; 2:724328. [PMID: 35387037 PMCID: PMC8974783 DOI: 10.3389/falgy.2021.724328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 07/26/2021] [Indexed: 01/25/2023] Open
Abstract
Allergic rhinitis (AR) is characterized by an early-phase response (EPR), and in a subgroup of individuals, a late-phase response (LPR). We sought to investigate polymorphisms in cholinergic synapse pathway genes, previously associated with late-asthmatic responses, in the LPR. Twenty healthy participants and 74 participants with AR underwent allergen exposure using the Environmental Exposure Unit. Allergic participants were sub-phenotyped using self-reported nasal congestion scores; congestion is the predominant symptom experienced during the LPR. Acute congestion (AC, n = 36) participants developed only an EPR, while persistent congestion (PC, n = 38) participants developed both allergic responses. We interrogated blood samples collected before allergen exposure with genotyping and gene expression assays. Twenty-five SNPs located in ADCY3, AKT3, CACNA1S, CHRM3, CHRNB2, GNG4, and KCNQ4 had significantly different allele frequencies (P < 0.10) between PC and AC participants. PC participants had increased minor allele content (P = 0.009) in the 25 SNPs compared to AC participants. Two SNPs in AKT3 were associated with gene expression differences (FDR < 0.01) in PC participants. This study identified an association between the LPR and polymorphisms in the cholinergic synapse pathway genes, and developed a novel method to sub-phenotype AR using self-reported nasal congestion scores.
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Affiliation(s)
- Simranjit K. Samra
- Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Ashwini Rajasekaran
- Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Andrew J. Sandford
- Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Anne K. Ellis
- Departments of Medicine and Biomedical & Molecular Science, Queen's University, Kingston, ON, Canada
- Allergy Research Unit, Kingston General Hospital, Kingston, ON, Canada
| | - Scott J. Tebbutt
- Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Scott J. Tebbutt
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22
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Brook B, Harbeson DJ, Shannon CP, Cai B, He D, Ben-Othman R, Francis F, Huang J, Varankovich N, Liu A, Bao W, Bjerregaard-Andersen M, Schaltz-Buchholzer F, Sanca L, Golding CN, Larsen KL, Levy O, Kampmann B, Tan R, Charles A, Wynn JL, Shann F, Aaby P, Benn CS, Tebbutt SJ, Kollmann TR, Amenyogbe N. BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis. Sci Transl Med 2021; 12:12/542/eaax4517. [PMID: 32376769 DOI: 10.1126/scitranslmed.aax4517] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 03/13/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022]
Abstract
Death from sepsis in the neonatal period remains a serious threat for millions. Within 3 days of administration, bacille Calmette-Guérin (BCG) vaccination can reduce mortality from neonatal sepsis in human newborns, but the underlying mechanism for this rapid protection is unknown. We found that BCG was also protective in a mouse model of neonatal polymicrobial sepsis, where it induced granulocyte colony-stimulating factor (G-CSF) within hours of administration. This was necessary and sufficient to drive emergency granulopoiesis (EG), resulting in a marked increase in neutrophils. This increase in neutrophils was directly and quantitatively responsible for protection from sepsis. Rapid induction of EG after BCG administration also occurred in three independent cohorts of human neonates.
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Affiliation(s)
- Byron Brook
- Department of Experimental Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor, Room 10117, Vancouver, BC V5Z 1M9, Canada
| | - Danny J Harbeson
- Department of Experimental Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor, Room 10117, Vancouver, BC V5Z 1M9, Canada
| | - Casey P Shannon
- PROOF Centre of Excellence, British Columbia, 10th floor, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada.,UBC Centre for Heart Lung Innovation, St. Paul's Hospital, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Bing Cai
- Department of Pediatrics, University of British Columbia, and BC Children's Hospital, 4480 Oak Street, Vancouver, BC V6H 3V4, Canada
| | - Daniel He
- Department of Experimental Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor, Room 10117, Vancouver, BC V5Z 1M9, Canada.,PROOF Centre of Excellence, British Columbia, 10th floor, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada.,UBC Centre for Heart Lung Innovation, St. Paul's Hospital, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, and BC Children's Hospital, 4480 Oak Street, Vancouver, BC V6H 3V4, Canada
| | - Freddy Francis
- Department of Experimental Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor, Room 10117, Vancouver, BC V5Z 1M9, Canada
| | - Joe Huang
- Department of Pediatrics, University of British Columbia, and BC Children's Hospital, 4480 Oak Street, Vancouver, BC V6H 3V4, Canada
| | - Natallia Varankovich
- Department of Pediatrics, University of British Columbia, and BC Children's Hospital, 4480 Oak Street, Vancouver, BC V6H 3V4, Canada
| | - Aaron Liu
- Department of Experimental Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor, Room 10117, Vancouver, BC V5Z 1M9, Canada
| | - Winnie Bao
- Department of Pediatrics, University of British Columbia, and BC Children's Hospital, 4480 Oak Street, Vancouver, BC V6H 3V4, Canada
| | - Morten Bjerregaard-Andersen
- Bandim Health Project, Indepth Network, Apartado 861, 1004 Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines (CVIVA), Statens Serum Institut (SSI), Artillerivej 5, 2300 Copenhagen S, Denmark.,Department of Endocrinology, Odense University Hospital, Kløvervænget 6, 5000 Odense C, Denmark
| | - Frederik Schaltz-Buchholzer
- Bandim Health Project, Indepth Network, Apartado 861, 1004 Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines (CVIVA), Statens Serum Institut (SSI), Artillerivej 5, 2300 Copenhagen S, Denmark.,OPEN, Institute of Clinical Research and Danish Institute for Advanced Science, University of Southern Denmark, and Odense University Hospital, J.B. Winsløws Vej, 5000 Odense C, Denmark
| | - Lilica Sanca
- Bandim Health Project, Indepth Network, Apartado 861, 1004 Bissau, Guinea-Bissau
| | - Christian N Golding
- Bandim Health Project, Indepth Network, Apartado 861, 1004 Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines (CVIVA), Statens Serum Institut (SSI), Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Kristina Lindberg Larsen
- Bandim Health Project, Indepth Network, Apartado 861, 1004 Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines (CVIVA), Statens Serum Institut (SSI), Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, P.O. Box 273, Banjul, The Gambia.,Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | | | - Rusung Tan
- Department of Pathology, Sidra Medicine and Weill Cornell Medicine, Doha, Qatar
| | - Adrian Charles
- Department of Pathology, Sidra Medicine and Weill Cornell Medicine, Doha, Qatar
| | - James L Wynn
- Department of Paediatrics and Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, P.O. Box 100296, Gainesville, FL 32610-0296, USA
| | - Frank Shann
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Peter Aaby
- Bandim Health Project, Indepth Network, Apartado 861, 1004 Bissau, Guinea-Bissau
| | - Christine S Benn
- Bandim Health Project, Indepth Network, Apartado 861, 1004 Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines (CVIVA), Statens Serum Institut (SSI), Artillerivej 5, 2300 Copenhagen S, Denmark.,OPEN, Institute of Clinical Research and Danish Institute for Advanced Science, University of Southern Denmark, and Odense University Hospital, J.B. Winsløws Vej, 5000 Odense C, Denmark
| | - Scott J Tebbutt
- PROOF Centre of Excellence, British Columbia, 10th floor, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada.,UBC Centre for Heart Lung Innovation, St. Paul's Hospital, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Tobias R Kollmann
- Department of Experimental Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor, Room 10117, Vancouver, BC V5Z 1M9, Canada. .,Department of Pediatrics, University of British Columbia, and BC Children's Hospital, 4480 Oak Street, Vancouver, BC V6H 3V4, Canada.,Telethon Kids Institute, 100 Roberts Road, Subiaco, Western Australia 6008, Australia
| | - Nelly Amenyogbe
- Department of Experimental Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor, Room 10117, Vancouver, BC V5Z 1M9, Canada. .,Telethon Kids Institute, 100 Roberts Road, Subiaco, Western Australia 6008, Australia
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23
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Kim YW, Tonti E, Hickey P, Ellis AK, Neighbour H, Larché M, Tebbutt SJ. Immunological changes in peripheral blood following nasal allergen challenge in subjects with allergic rhinitis pre- and post-peptide immunotherapy: An open-label clinical study. Allergy 2021; 76:1907-1911. [PMID: 33320968 DOI: 10.1111/all.14710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/27/2020] [Accepted: 12/09/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Young Woong Kim
- Experimental Medicine University of British Columbia Vancouver BC Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence Vancouver BC Canada
- Centre for Heart Lung Innovation St. Paul’s Hospital Vancouver BC Canada
| | - Elena Tonti
- Department of Medicine McMaster University Hamilton ON Canada
| | | | - Anne K. Ellis
- Departments of Medicine and Biomedical & Molecular Science Queen’s University Kingston ON Canada
- Allergy Research Unit Kingston General Hospital Kingston ON Canada
| | - Helen Neighbour
- Department of Medicine McMaster University Hamilton ON Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare Hamilton ON Canada
| | - Mark Larché
- Department of Medicine McMaster University Hamilton ON Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare Hamilton ON Canada
| | - Scott J. Tebbutt
- Experimental Medicine University of British Columbia Vancouver BC Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence Vancouver BC Canada
- Centre for Heart Lung Innovation St. Paul’s Hospital Vancouver BC Canada
- Department of Medicine (Respiratory Division) University of British Columbia Vancouver BC Canada
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24
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Kim JYV, Lee B, Koitsopoulos P, Shannon CP, Chen V, Hollander Z, Assadian S, Lam K, Ritchie G, McManus J, McMaster WR, Ng RT, McManus BM, Tebbutt SJ. Analytical Validation of HEARTBiT: A Blood-Based Multiplex Gene Expression Profiling Assay for Exclusionary Diagnosis of Acute Cellular Rejection in Heart Transplant Patients. Clin Chem 2021; 66:1063-1071. [PMID: 32705124 DOI: 10.1093/clinchem/hvaa123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/04/2019] [Accepted: 05/15/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND HEARTBiT is a whole blood-based gene profiling assay using the nucleic acid counting NanoString technology for the exclusionary diagnosis of acute cellular rejection in heart transplant patients. The HEARTBiT score measures the risk of acute cellular rejection in the first year following heart transplant, distinguishing patients with stable grafts from those at risk for acute cellular rejection. Here, we provide the analytical performance characteristics of the HEARTBiT assay and the results on pilot clinical validation. METHODS We used purified RNA collected from PAXgene blood samples to evaluate the characteristics of a 12-gene panel HEARTBiT assay, for its linearity range, quantitative bias, precision, and reproducibility. These parameters were estimated either from serial dilutions of individual samples or from repeated runs on pooled samples. RESULTS We found that all 12 genes showed linear behavior within the recommended assay input range of 125 ng to 500 ng of purified RNA, with most genes showing 3% or lower quantitative bias and around 5% coefficient of variation. Total variation resulting from unique operators, reagent lots, and runs was less than 0.02 units standard deviation (SD). The performance of the analytically validated assay (AUC = 0.75) was equivalent to what we observed in the signature development dataset. CONCLUSION The analytical performance of the assay within the specification input range demonstrated reliable quantification of the HEARTBiT score within 0.02 SD units, measured on a 0 to 1 unit scale. This assay may therefore be of high utility in clinical validation of HEARTBiT in future biomarker observational trials.
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Affiliation(s)
- Ji-Young V Kim
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada.,Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Brandon Lee
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Pavlos Koitsopoulos
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Virginia Chen
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Zsuzsanna Hollander
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Sara Assadian
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Karen Lam
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Gordon Ritchie
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janet McManus
- netCAD Canadian Blood Services, Vancouver, BC, Canada
| | - W Robert McMaster
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Raymond T Ng
- Department of Computer Science, University of British Columbia
| | - Bruce M McManus
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada.,Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada.,Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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25
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Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao KA, Scheuermann RH, Tebbutt SJ, Hancock RE, Koff WC, Kollmann TR, Sadarangani M, Lee AHY. Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort. Front Immunol 2020; 11:578801. [PMID: 33329547 PMCID: PMC7734088 DOI: 10.3389/fimmu.2020.578801] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background Vaccination remains one of the most effective means of reducing the burden of infectious diseases globally. Improving our understanding of the molecular basis for effective vaccine response is of paramount importance if we are to ensure the success of future vaccine development efforts. Methods We applied cutting edge multi-omics approaches to extensively characterize temporal molecular responses following vaccination with hepatitis B virus (HBV) vaccine. Data were integrated across cellular, epigenomic, transcriptomic, proteomic, and fecal microbiome profiles, and correlated to final HBV antibody titres. Results Using both an unsupervised molecular-interaction network integration method (NetworkAnalyst) and a data-driven integration approach (DIABLO), we uncovered baseline molecular patterns and pathways associated with more effective vaccine responses to HBV. Biological associations were unravelled, with signalling pathways such as JAK-STAT and interleukin signalling, Toll-like receptor cascades, interferon signalling, and Th17 cell differentiation emerging as important pre-vaccination modulators of response. Conclusion This study provides further evidence that baseline cellular and molecular characteristics of an individual's immune system influence vaccine responses, and highlights the utility of integrating information across many parallel molecular datasets.
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Affiliation(s)
- Casey P. Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Travis M. Blimkie
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Nicole Gladish
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Nelly Amenyogbe
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rachel D. Edgar
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Queenie Chan
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - William W. Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ryan R. Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Kim-Anh Le Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, CA, United States
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Scott J. Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Robert E.W. Hancock
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | | | - Tobias R. Kollmann
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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26
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Maestre-Batlle D, Huff RD, Schwartz C, Alexis NE, Tebbutt SJ, Turvey S, Bølling AK, Carlsten C. Dibutyl Phthalate Augments Allergen-induced Lung Function Decline and Alters Human Airway Immunology. A Randomized Crossover Study. Am J Respir Crit Care Med 2020; 202:672-680. [PMID: 32320637 DOI: 10.1164/rccm.201911-2153oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Rationale: Phthalates are a group of chemicals used in common commercial products. Epidemiological studies suggest that phthalate exposure is associated with development or worsening of allergic diseases such as asthma. However, effects of dibutyl phthalate (DBP) or other phthalates found in high concentrations in indoor air have never been examined in allergic individuals in a controlled exposure setting.Objectives: To investigate the airway effects in humans caused by inhalation of a known concentration of a single phthalate, DBP.Methods: In a randomized crossover study, 16 allergen-sensitized participants were exposed to control air or DBP for 3 hours in an environmental chamber followed immediately by an allergen inhalation challenge. Bronchoalveolar wash and lavage were obtained 24 hours after exposure. Lung function, early allergic response, airway responsiveness, inflammation, immune mediators, and immune cell phenotypes were assessed after DBP exposure.Measurements and Main Results: DBP exposure increased the early allergic response (21.4% decline in FEV1 area under the curve, P = 0.03). Airway responsiveness was increased by 48.1% after DBP exposure in participants without baseline hyperresponsiveness (P = 0.01). DBP increased the recruitment of BAL total macrophages by 4.6% (P = 0.07), whereas the M2 macrophage phenotype increased by 46.9% (P = 0.04). Airway immune mediator levels were modestly affected by DBP.Conclusions: DBP exposure augmented allergen-induced lung function decline, particularly in those without baseline hyperresponsiveness, and exhibited immunomodulatory effects in the airways of allergic individuals. This is the first controlled human exposure study providing biological evidence for phthalate-induced effects in the airways.Clinical trial registered with www.clinicaltrials.gov (NCT02688478).
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Affiliation(s)
| | | | | | - Neil E Alexis
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | | | - Stuart Turvey
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anette K Bølling
- Department of Air Pollution and Noise, Norwegian Institute of Public Health, Oslo, Norway
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27
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Ben-Othman R, Cai B, Liu AC, Varankovich N, He D, Blimkie TM, Lee AH, Gill EE, Novotny M, Aevermann B, Drissler S, Shannon CP, McCann S, Marty K, Bjornson G, Edgar RD, Lin DTS, Gladish N, Maclsaac J, Amenyogbe N, Chan Q, Llibre A, Collin J, Landais E, Le K, Reiss SM, Koff WC, Havenar-Daughton C, Heran M, Sangha B, Walt D, Krajden M, Crotty S, Sok D, Briney B, Burton DR, Duffy D, Foster LJ, Mohn WW, Kobor MS, Tebbutt SJ, Brinkman RR, Scheuermann RH, Hancock REW, Kollmann TR, Sadarangani M. Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults. Front Immunol 2020; 11:580373. [PMID: 33250895 PMCID: PMC7672042 DOI: 10.3389/fimmu.2020.580373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022] Open
Abstract
Conventional vaccine design has been based on trial-and-error approaches, which have been generally successful. However, there have been some major failures in vaccine development and we still do not have highly effective licensed vaccines for tuberculosis, HIV, respiratory syncytial virus, and other major infections of global significance. Approaches at rational vaccine design have been limited by our understanding of the immune response to vaccination at the molecular level. Tools now exist to undertake in-depth analysis using systems biology approaches, but to be fully realized, studies are required in humans with intensive blood and tissue sampling. Methods that support this intensive sampling need to be developed and validated as feasible. To this end, we describe here a detailed approach that was applied in a study of 15 healthy adults, who were immunized with hepatitis B vaccine. Sampling included ~350 mL of blood, 12 microbiome samples, and lymph node fine needle aspirates obtained over a ~7-month period, enabling comprehensive analysis of the immune response at the molecular level, including single cell and tissue sample analysis. Samples were collected for analysis of immune phenotyping, whole blood and single cell gene expression, proteomics, lipidomics, epigenetics, whole blood response to key immune stimuli, cytokine responses, in vitro T cell responses, antibody repertoire analysis and the microbiome. Data integration was undertaken using different approaches-NetworkAnalyst and DIABLO. Our results demonstrate that such intensive sampling studies are feasible in healthy adults, and data integration tools exist to analyze the vast amount of data generated from a multi-omics systems biology approach. This will provide the basis for a better understanding of vaccine-induced immunity and accelerate future rational vaccine design.
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Affiliation(s)
- Rym Ben-Othman
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Bing Cai
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Aaron C Liu
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Natallia Varankovich
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Daniel He
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Travis M Blimkie
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Amy H Lee
- Simon Fraser University, Burnaby, BC, Canada
| | - Erin E Gill
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute (La Jolla), La Jolla, CA, United States
| | - Brian Aevermann
- Department of Informatics, J. Craig Venter Institute (La Jolla), La Jolla, CA, United States
| | | | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Sarah McCann
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kim Marty
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gordean Bjornson
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Rachel D Edgar
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David Tse Shen Lin
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Julia Maclsaac
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Nelly Amenyogbe
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Queenie Chan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alba Llibre
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Joyce Collin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Khoa Le
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Samantha M Reiss
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Wayne C Koff
- Human Vaccines Project, New York, NY, United States
| | - Colin Havenar-Daughton
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Manraj Heran
- Department of Radiology, BC Children's Hospital, Vancouver, BC, Canada
| | - Bippan Sangha
- Department of Radiology, BC Children's Hospital, Vancouver, BC, Canada
| | - David Walt
- Wyss Institute at Harvard University, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ryan R Brinkman
- Terry Fox Laboratory, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute (La Jolla), La Jolla, CA, United States.,Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
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28
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Zhou Q, Chen V, Shannon CP, Wei XS, Xiang X, Wang X, Wang ZH, Tebbutt SJ, Kollmann TR, Fish EN. Corrigendum: Interferon-α2b Treatment for COVID-19. Front Immunol 2020; 11:615275. [PMID: 33193462 PMCID: PMC7653513 DOI: 10.3389/fimmu.2020.615275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 11/21/2022] Open
Affiliation(s)
- Qiong Zhou
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Virginia Chen
- Prevention of Organ Failure (PROOF) Centre of Excellence & Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence & Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Xiao-Shan Wei
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Xiang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xu Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-Hao Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence & Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Systems Vaccinology, Center for Precision Health, Telethon Kids Institute, Nedlands, WA, Australia
| | - Eleanor N Fish
- Toronto General Hospital Research Institute, University Health Network & Department of Immunology, University of Toronto, Toronto, ON, Canada
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29
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Bennike TB, Fatou B, Angelidou A, Diray-Arce J, Falsafi R, Ford R, Gill EE, van Haren SD, Idoko OT, Lee AH, Ben-Othman R, Pomat WS, Shannon CP, Smolen KK, Tebbutt SJ, Ozonoff A, Richmond PC, van den Biggelaar AHJ, Hancock REW, Kampmann B, Kollmann TR, Levy O, Steen H. Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life. Front Immunol 2020; 11:578505. [PMID: 33329546 PMCID: PMC7732455 DOI: 10.3389/fimmu.2020.578505] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/22/2020] [Indexed: 01/05/2023] Open
Abstract
Neonates have heightened susceptibility to infections. The biological mechanisms are incompletely understood but thought to be related to age-specific adaptations in immunity due to resource constraints during immune system development and growth. We present here an extended analysis of our proteomics study of peripheral blood-plasma from a study of healthy full-term newborns delivered vaginally, collected at the day of birth and on day of life (DOL) 1, 3, or 7, to cover the first week of life. The plasma proteome was characterized by LC-MS using our established 96-well plate format plasma proteomics platform. We found increasing acute phase proteins and a reduction of respective inhibitors on DOL1. Focusing on the complement system, we found increased plasma concentrations of all major components of the classical complement pathway and the membrane attack complex (MAC) from birth onward, except C7 which seems to have near adult levels at birth. In contrast, components of the lectin and alternative complement pathways mainly decreased. A comparison to whole blood messenger RNA (mRNA) levels enabled characterization of mRNA and protein levels in parallel, and for 23 of the 30 monitored complement proteins, the whole blood transcript information by itself was not reflective of the plasma protein levels or dynamics during the first week of life. Analysis of immunoglobulin (Ig) mRNA and protein levels revealed that IgM levels and synthesis increased, while the plasma concentrations of maternally transferred IgG1-4 decreased in accordance with their in vivo half-lives. The neonatal plasma ratio of IgG1 to IgG2-4 was increased compared to adult values, demonstrating a highly efficient IgG1 transplacental transfer process. Partial compensation for maternal IgG degradation was achieved by endogenous synthesis of the IgG1 subtype which increased with DOL. The findings were validated in a geographically distinct cohort, demonstrating a consistent developmental trajectory of the newborn's immune system over the first week of human life across continents. Our findings indicate that the classical complement pathway is central for newborn immunity and our approach to characterize the plasma proteome in parallel with the transcriptome will provide crucial insight in immune ontogeny and inform new approaches to prevent and treat diseases.
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Affiliation(s)
- Tue Bjerg Bennike
- Department of Pathology, Boston Children’s Hospital, Boston, MA, United States
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Benoit Fatou
- Department of Pathology, Boston Children’s Hospital, Boston, MA, United States
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Asimenia Angelidou
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Reza Falsafi
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Rebecca Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Erin E. Gill
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Simon D. van Haren
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Olubukola T. Idoko
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Amy H. Lee
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, and BC Children’s Hospital, Vancouver, BC, Canada
| | - William S. Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | - Kinga K. Smolen
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Scott J. Tebbutt
- PROOF Centre of Excellence, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Al Ozonoff
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | | | | | - Robert E. W. Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia
- Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tobias R. Kollmann
- Department of Pediatrics, University of British Columbia, and BC Children’s Hospital, Vancouver, BC, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT & Harvard, Cambridge, MA, United States
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital, Boston, MA, United States
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
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30
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Amenyogbe N, Dimitriu P, Cho P, Ruck C, Fortuno ES, Cai B, Alimenti A, Côté HCF, Maan EJ, Slogrove AL, Esser M, Marchant A, Goetghebuer T, Shannon CP, Tebbutt SJ, Kollmann TR, Mohn WW, Smolen KK. Innate Immune Responses and Gut Microbiomes Distinguish HIV-Exposed from HIV-Unexposed Children in a Population-Specific Manner. J Immunol 2020; 205:2618-2628. [PMID: 33067377 DOI: 10.4049/jimmunol.2000040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022]
Abstract
In both high- and low-income countries, HIV-negative children born to HIV-positive mothers (HIV exposed, uninfected [HEU]) are more susceptible to severe infection than HIV-unexposed, uninfected (HUU) children, with altered innate immunity hypothesized to be a cause. Both the gut microbiome and systemic innate immunity differ across biogeographically distinct settings, and the two are known to influence each other. And although the gut microbiome is influenced by HIV infection and may contribute to altered immunity, the biogeography of immune-microbiome correlations among HEU children have not been investigated. To address this, we compared the innate response and the stool microbiome of 2-y-old HEU and HUU children from Belgium, Canada, and South Africa to test the hypothesis that region-specific immune alterations directly correlate to differences in their stool microbiomes. We did not detect a universal immune or microbiome signature underlying differences between HEU versus HUU that was applicable to all children. But as hypothesized, population-specific differences in stool microbiomes were readily detected and included reduced abundances of short-chain fatty acid-producing bacteria in Canadian HEU children. Furthermore, we did not identify innate immune-microbiome associations that distinguished HEU from HUU children in any population. These findings suggest that maternal HIV infection is independently associated with differences in both innate immunity and the stool microbiome in a biogeographical population-specific way.
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Affiliation(s)
- Nelly Amenyogbe
- Department of Experimental Medicine, The University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada; .,Telethon Kids Institute, Perth, Western Australia 6009, Australia
| | - Pedro Dimitriu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Patricia Cho
- Department of Experimental Medicine, The University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Candice Ruck
- Department of Experimental Medicine, The University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Edgardo S Fortuno
- Division of Infectious Diseases, Department of Pediatrics, The University of British Columbia, Vancouver, British Columbia V6H 3V4, Canada.,Division of Palliative, Rehabilitation, and Integrative Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Bing Cai
- Division of Infectious Diseases, Department of Pediatrics, The University of British Columbia, Vancouver, British Columbia V6H 3V4, Canada
| | - Ariane Alimenti
- Department of Pediatrics, BC Women's Hospital and Health Centre, The University of British Columbia, Vancouver, British Columbia V6H 3V4, Canada
| | - Hélène C F Côté
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
| | - Evelyn J Maan
- Oak Tree Clinic, BC Women's Hospital, Vancouver, British Columbia V5Z 0A7, Canada
| | - Amy L Slogrove
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Worcester 6849, South Africa
| | - Monika Esser
- The Immunology Unit, Division of Medical Microbiology, Department of Pathology, National Health Laboratory Service, Stellenbosch University, Cape Town 7505, South Africa
| | - Arnaud Marchant
- Institut d'Immunologie Médicale, Université Libre de Bruxelles, Charleroi B-6041, Belgium
| | - Tessa Goetghebuer
- Département de Pédiatrie, Centre Hospitalier Universitaire St Pierre, Université Libre de Bruxelles, B-1000, Belgium
| | - Casey P Shannon
- Prevention of Organ Failure Centre of Excellence, Centre for Heart Lung Innovation, St. Paul's Hospital, The University of British Columbia, Vancouver, British Columbia V6Z 2K5, Canada.,Centre for Heart Lung Innovation, St. Paul's Hospital, The University of British Columbia, Vancouver, British Columbia V6Z 1Y6, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure Centre of Excellence, Centre for Heart Lung Innovation, St. Paul's Hospital, The University of British Columbia, Vancouver, British Columbia V6Z 2K5, Canada.,Department of Medicine, Division of Respiratory Medicine, The University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Tobias R Kollmann
- Telethon Kids Institute, Perth, Western Australia 6009, Australia.,Division of Infectious Diseases, Department of Pediatrics, The University of British Columbia, Vancouver, British Columbia V6H 3V4, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada;
| | - Kinga K Smolen
- Department of Experimental Medicine, The University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada.,Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115; and.,Harvard Medical School, Boston, MA 02115
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31
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Vignolo SM, Diray-Arce J, McEnaney K, Rao S, Shannon CP, Idoko OT, Cole F, Darboe A, Cessay F, Ben-Othman R, Tebbutt SJ, Kampmann B, Levy O, Ozonoff A. A cloud-based bioinformatic analytic infrastructure and Data Management Core for the Expanded Program on Immunization Consortium. J Clin Transl Sci 2020; 5:e52. [PMID: 33948273 PMCID: PMC8057481 DOI: 10.1017/cts.2020.546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/21/2020] [Revised: 08/06/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
The Expanded Program for Immunization Consortium - Human Immunology Project Consortium study aims to employ systems biology to identify and characterize vaccine-induced biomarkers that predict immunogenicity in newborns. Key to this effort is the establishment of the Data Management Core (DMC) to provide reliable data and bioinformatic infrastructure for centralized curation, storage, and analysis of multiple de-identified "omic" datasets. The DMC established a cloud-based architecture using Amazon Web Services to track, store, and share data according to National Institutes of Health standards. The DMC tracks biological samples during collection, shipping, and processing while capturing sample metadata and associated clinical data. Multi-omic datasets are stored in access-controlled Amazon Simple Storage Service (S3) for data security and file version control. All data undergo quality control processes at the generating site followed by DMC validation for quality assurance. The DMC maintains a controlled computing environment for data analysis and integration. Upon publication, the DMC deposits finalized datasets to public repositories. The DMC architecture provides resources and scientific expertise to accelerate translational discovery. Robust operations allow rapid sharing of results across the project team. Maintenance of data quality standards and public data deposition will further benefit the scientific community.
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Affiliation(s)
- Sofia M. Vignolo
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Kerry McEnaney
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, USA
| | - Shun Rao
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, USA
| | | | - Olubukola T. Idoko
- Vaccines & Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
- Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Fatoumata Cole
- Vaccines & Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Alansana Darboe
- Vaccines & Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
- Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Fatoumatta Cessay
- Vaccines & Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | | | - Scott J. Tebbutt
- PROOF Centre of Excellence, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Beate Kampmann
- Vaccines & Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
- Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Al Ozonoff
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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32
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Zhou Q, Chen V, Shannon CP, Wei XS, Xiang X, Wang X, Wang ZH, Tebbutt SJ, Kollmann TR, Fish EN. Interferon-α2b Treatment for COVID-19. Front Immunol 2020; 11:1061. [PMID: 32574262 PMCID: PMC7242746 DOI: 10.3389/fimmu.2020.01061] [Citation(s) in RCA: 251] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/04/2020] [Indexed: 11/13/2022] Open
Abstract
The global pandemic of COVID-19 cases caused by infection with SARS-CoV-2 is ongoing, with no approved antiviral intervention. We describe here the effects of treatment with interferon (IFN)-α2b in a cohort of confirmed COVID-19 cases in Wuhan, China. In this uncontrolled, exploratory study, 77 adults hospitalized with confirmed COVID-19 were treated with either nebulized IFN-α2b (5 mU b.i.d.), arbidol (200 mg t.i.d.) or a combination of IFN-α2b plus arbidol. Serial SARS-CoV-2 testing along with hematological measurements, including cell counts, blood biochemistry and serum cytokine levels, and temperature and blood oxygen saturation levels, were recorded for each patient during their hospital stay. Treatment with IFN-α2b with or without arbidol significantly reduced the duration of detectable virus in the upper respiratory tract and in parallel reduced duration of elevated blood levels for the inflammatory markers IL-6 and CRP. These findings suggest that IFN-α2b should be further investigated as a therapy in COVID-19 cases.
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Affiliation(s)
- Qiong Zhou
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Virginia Chen
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Xiao-Shan Wei
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Xiang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xu Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-Hao Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Systems Vaccinology, Center for Precision Health, Telethon Kids Institute, Nedlands, WA, Australia
| | - Eleanor N Fish
- Toronto General Hospital Research Institute, University Health Network and Department of Immunology, University of Toronto, Toronto, ON, Canada
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33
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Idoko OT, Smolen KK, Wariri O, Imam A, Shannon CP, Dibassey T, Diray-Arce J, Darboe A, Strandmark J, Ben-Othman R, Odumade OA, McEnaney K, Amenyogbe N, Pomat WS, van Haren S, Sanchez-Schmitz G, Brinkman RR, Steen H, Hancock REW, Tebbutt SJ, Richmond PC, van den Biggelaar AHJ, Kollmann TR, Levy O, Ozonoff A, Kampmann B. Corrigendum: Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front Pediatr 2020; 8:610461. [PMID: 33313031 PMCID: PMC7707081 DOI: 10.3389/fped.2020.610461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fped.2020.00197.].
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Affiliation(s)
- Olubukola T Idoko
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia.,Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,CIH LMU Center for International Health, Medical Center of the University of Munich (LMU), Munich, Germany.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kinga K Smolen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Oghenebrume Wariri
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Abdulazeez Imam
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | | | - Tida Dibassey
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Alansana Darboe
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Julia Strandmark
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Rym Ben-Othman
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Oludare A Odumade
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Division of Medicine Critical Care, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Kerry McEnaney
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Cardiology, Boston Children's Hospital, Boston, MA, United States
| | - Nelly Amenyogbe
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - William S Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Simon van Haren
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Guzmán Sanchez-Schmitz
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Ryan R Brinkman
- BC Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Hanno Steen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Department of Pathology, Boston Children's Hospital, Boston, MA, United States
| | - Robert E W Hancock
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- PROOF Centre of Excellence, Vancouver, BC, Canada.,Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Department of Medicine, UBC, Vancouver, BC, Canada
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia.,Division of Pediatrics, School of Medicine, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Anita H J van den Biggelaar
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Tobias R Kollmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT & Harvard, Cambridge, MA, United States
| | - Al Ozonoff
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Idoko OT, Smolen KK, Wariri O, Imam A, Shannon CP, Dibassey T, Diray-Arce J, Darboe A, Strandmark J, Ben-Othman R, Odumade OA, McEnaney K, Amenyogbe N, Pomat WS, van Haren S, Sanchez-Schmitz G, Brinkman RR, Steen H, Hancock REW, Tebbutt SJ, Richmond PC, van den Biggelaar AHJ, Kollmann TR, Levy O, Ozonoff A, Kampmann B. Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front Pediatr 2020; 8:197. [PMID: 32426309 PMCID: PMC7205022 DOI: 10.3389/fped.2020.00197] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/01/2020] [Indexed: 01/30/2023] Open
Abstract
Background: Infection contributes to significant morbidity and mortality particularly in the very young and in low- and middle-income countries. While vaccines are a highly cost-effective tool against infectious disease little is known regarding the cellular and molecular pathways by which vaccines induce protection at an early age. Immunity is distinct in early life and greater precision is required in our understanding of mechanisms of early life protection to inform development of new pediatric vaccines. Methods and Analysis: We will apply transcriptomic, proteomic, metabolomic, multiplex cytokine/chemokine, adenosine deaminase, and flow cytometry immune cell phenotyping to delineate early cellular and molecular signatures that correspond to vaccine immunogenicity. This approach will be applied to a neonatal cohort in The Gambia (N ~ 720) receiving at birth: (1) Hepatitis B (HepB) vaccine alone, (2) Bacille Calmette Guerin (BCG) vaccine alone, or (3) HepB and BCG vaccines, (4) HepB and BCG vaccines delayed till day 10 at the latest. Each study participant will have a baseline peripheral blood sample drawn at DOL0 and a second blood sample at DOL1,-3, or-7 as well as late timepoints to assess HepB vaccine immunogenicity. Blood will be fractionated via a "small sample big data" standard operating procedure that enables multiple downstream systems biology assays. We will apply both univariate and multivariate frameworks and multi-OMIC data integration to identify features associated with anti-Hepatitis B (anti-HB) titer, an established correlate of protection. Cord blood sample collection from a subset of participants will enable human in vitro modeling to test mechanistic hypotheses identified in silico regarding vaccine action. Maternal anti-HB titer and the infant microbiome will also be correlated with our findings which will be validated in a smaller cohort in Papua New Guinea (N ~ 80). Ethics and Dissemination: The study has been approved by The Gambia Government/MRCG Joint Ethics Committee and The Boston Children's Hospital Institutional Review Board. Ethics review is ongoing with the Papua New Guinea Medical Research Advisory Committee. All de-identified data will be uploaded to public repositories following submission of study output for publication. Feedback meetings will be organized to disseminate output to the study communities. Clinical Trial Registration: Clinicaltrials.gov Registration Number: NCT03246230.
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Affiliation(s)
- Olubukola T Idoko
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia.,Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,CIH LMU Center for International Health, Medical Center of the University of Munich (LMU), Munich, Germany.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kinga K Smolen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Oghenebrume Wariri
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Abdulazeez Imam
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | | | - Tida Dibassey
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Alansana Darboe
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Julia Strandmark
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Rym Ben-Othman
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Oludare A Odumade
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Division of Medicine Critical Care, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Kerry McEnaney
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Cardiology, Boston Children's Hospital, Boston, MA, United States
| | - Nelly Amenyogbe
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - William S Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Simon van Haren
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Guzmán Sanchez-Schmitz
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Ryan R Brinkman
- BC Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Hanno Steen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Department of Pathology, Boston Children's Hospital, Boston, MA, United States
| | - Robert E W Hancock
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- PROOF Centre of Excellence, Vancouver, BC, Canada.,Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Department of Medicine, UBC, Vancouver, BC, Canada
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia.,Division of Pediatrics, School of Medicine, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Anita H J van den Biggelaar
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Tobias R Kollmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT & Harvard, Cambridge, MA, United States
| | - Al Ozonoff
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Shannon CP, Hollander Z, Dai DLY, Chen V, Assadian S, Lam KK, McManus JE, Zarzycki M, Kim Y, Kim JYV, Balshaw R, Gidlöf O, Öhman J, Smith JG, Toma M, Ignaszewski A, Davies RA, Delgado D, Haddad H, Isaac D, Kim D, Mui A, Rajda M, West L, White M, Zieroth S, Tebbutt SJ, Keown PA, McMaster WR, Ng RT, McManus BM. HEARTBiT: A Transcriptomic Signature for Excluding Acute Cellular Rejection in Adult Heart Allograft Patients. Can J Cardiol 2019; 36:1217-1227. [PMID: 32553820 DOI: 10.1016/j.cjca.2019.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Nine mRNA transcripts associated with acute cellular rejection (ACR) in previous microarray studies were ported to the clinically amenable NanoString nCounter platform. Here we report the diagnostic performance of the resulting blood test to exclude ACR in heart allograft recipients: HEARTBiT. METHODS Blood samples for transcriptomic profiling were collected during routine post-transplantation monitoring in 8 Canadian transplant centres participating in the Biomarkers in Transplantation initiative, a large (n = 1622) prospective observational study conducted between 2009 and 2014. All adult cardiac transplant patients were invited to participate (median age = 56 [17 to 71]). The reference standard for rejection status was histopathology grading of tissue from endomyocardial biopsy (EMB). All locally graded ISHLT ≥ 2R rejection samples were selected for analysis (n = 36). ISHLT 1R (n = 38) and 0R (n = 86) samples were randomly selected to create a cohort approximately matched for site, age, sex, and days post-transplantation, with a focus on early time points (median days post-transplant = 42 [7 to 506]). RESULTS ISHLT ≥ 2R rejection was confirmed by EMB in 18 and excluded in 92 samples in the test set. HEARTBiT achieved 47% specificity (95% confidence interval [CI], 36%-57%) given ≥ 90% sensitivity, with a corresponding area under the receiver operating characteristic curve of 0.69 (95% CI, 0.56-0.81). CONCLUSIONS HEARTBiT's diagnostic performance compares favourably to the only currently approved minimally invasive diagnostic test to rule out ACR, AlloMap (CareDx, Brisbane, CA) and may be used to inform care decisions in the first 2 months post-transplantation, when AlloMap is not approved, and most ACR episodes occur.
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Affiliation(s)
- Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada.
| | - Zsuzsanna Hollander
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Darlene L Y Dai
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Virginia Chen
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Sara Assadian
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Karen K Lam
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada; Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janet E McManus
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Marek Zarzycki
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - YoungWoong Kim
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ji-Young V Kim
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada; Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Olof Gidlöf
- Department of Cardiology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Jenny Öhman
- Department of Cardiology, Skåne University Hospital, Lund University, Lund, Sweden
| | - J Gustav Smith
- Department of Cardiology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Mustafa Toma
- Department of Cardiology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Ignaszewski
- Department of Cardiology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ross A Davies
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Diego Delgado
- University Health Network/Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Haissam Haddad
- Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Debra Isaac
- Department of Medicine, University of Alberta, Calgary, Aberta, Canada
| | - Daniel Kim
- Department of Medicine, University of Alberta, Calgary, Aberta, Canada
| | - Alice Mui
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Miroslaw Rajda
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lori West
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Michel White
- Institut de Cardiologie de Montréal, Montréal, Québec, Canada
| | - Shelley Zieroth
- Department of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul A Keown
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - W Robert McMaster
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raymond T Ng
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce M McManus
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada; Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada.
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Giles LV, Tebbutt SJ, Carlsten C, Koehle MS. Effects of low-intensity and high-intensity cycling with diesel exhaust exposure on soluble P-selectin, E-selectin, I-CAM-1, VCAM-1 and complete blood count. BMJ Open Sport Exerc Med 2019; 5:e000625. [PMID: 31803496 PMCID: PMC6887503 DOI: 10.1136/bmjsem-2019-000625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Exposure to particulate matter 2.5 μm or less (PM2.5) that contains transition metals may play a role in systemic oxidative stress and inflammation. Exposure to diesel exhaust (DE) can increase adhesion molecules, which are important in the inflammatory response; however, it is unclear how exercising in DE affects adhesion molecules and how exercise intensity modulates this response. AIM To determine how DE exposure during exercise of varying intensities affects adhesion molecules and markers of systemic inflammation. METHODS Eighteen males performed 30 min cycling bouts at low intensity and high intensity (30% and 60% of power at VO2peak (peak oxygen consumption) and a control condition (rest)). Each trial was performed once breathing filtered air (FA) and once breathing DE (300 μg/m3 of PM2.5, six trials in total). Prior to, immediately post, 1 and 2 hours post exposure, blood was drawn to measure parameters of a complete blood count and soluble (s) platelet-Selectin, endothelin-Selectin, intracellular cell adhesion molecule (sICAM)-1 and vascular cell adhesion molecule (sVCAM)-1. Data were analysed using repeated-measures analysis of variance. RESULTS Two hours following high-intensity exercise, sICAM-1 was significantly less in DE compared with FA (p=0.008). Immediately following rest (p=0.013) and high-intensity exercise (p=0.042) in DE, sICAM-1 was significantly greater than immediately following low-intensity exercise in DE. There were no significant differences in other markers between DE and FA. CONCLUSIONS Based on this study, healthy individuals may not experience an acute increase in adhesion molecules and systemic inflammatory markers from exercising in DE compared with FA, and higher exercise intensities do not appear to increase the likelihood that DE will affect adhesion molecules and systemic inflammatory markers.
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Affiliation(s)
- Luisa V Giles
- Sport Science Department, Douglas College, New Westminster, British Columbia, Canada
- School of Kinesiology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J Tebbutt
- Department of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Christopher Carlsten
- Department of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Koehle
- Division of Sport & Exercise Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
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He D, Yang CX, Sahin B, Singh A, Shannon CP, Oliveria JP, Gauvreau GM, Tebbutt SJ. Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma. Allergy Asthma Clin Immunol 2019; 15:67. [PMID: 31832069 PMCID: PMC6873413 DOI: 10.1186/s13223-019-0382-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/04/2019] [Indexed: 12/15/2022] Open
Abstract
Background Blood has proven to be a useful resource for molecular analysis in numerous biomedical studies, with peripheral blood mononuclear cells (PBMCs) and whole blood being the major specimen types. However, comparative analyses between these two major compartments (PBMCs and whole blood) are few and far between. In this study, we compared gene expression profiles of PBMCs and whole blood samples obtained from research subjects with or without mild allergic asthma. Methods Whole blood (PAXgene) and PBMC samples were obtained from 5 mild allergic asthmatics and 5 healthy controls. RNA from both sample types was measured for expression of 730 immune-related genes using the NanoString nCounter platform. Results We identified 64 uniquely expressed transcripts in whole blood that reflected a variety of innate, humoral, and adaptive immune processes, and 13 uniquely expressed transcripts in PBMCs which were representative of T-cell and monocyte-mediated processes. Furthermore, analysis of mild allergic asthmatics versus non-asthmatics revealed 47 differentially expressed transcripts in whole blood compared to 1 differentially expressed transcript in PBMCs (FDR < 0.25). Finally, through simultaneous measurement of PBMC proteins on the nCounter assay, we identified CD28 and OX40 (TNFRSF4), both of which are critical co-stimulatory molecules during T-cell activation, as significantly upregulated in asthmatics. Conclusions Whole blood RNA preserved in PAXgene tubes is excellent for producing gene expression data with minimal variability and good sensitivity, suggesting its utility in multi-centre studies requiring measurement of blood gene expression.
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Affiliation(s)
- Daniel He
- 1Centre for Heart Lung Innovation, University of British Columbia, Room 166, 1081 Burrard Street, Vancouver, BC V6Z1Y6 Canada.,2Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC V6Z2K5 Canada
| | - Chen Xi Yang
- 1Centre for Heart Lung Innovation, University of British Columbia, Room 166, 1081 Burrard Street, Vancouver, BC V6Z1Y6 Canada.,2Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC V6Z2K5 Canada
| | - Basak Sahin
- 1Centre for Heart Lung Innovation, University of British Columbia, Room 166, 1081 Burrard Street, Vancouver, BC V6Z1Y6 Canada
| | - Amrit Singh
- 1Centre for Heart Lung Innovation, University of British Columbia, Room 166, 1081 Burrard Street, Vancouver, BC V6Z1Y6 Canada.,2Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC V6Z2K5 Canada
| | - Casey P Shannon
- 2Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC V6Z2K5 Canada
| | - John-Paul Oliveria
- 3Department of Medicine, McMaster University, Hamilton, ON L8N3Z5 Canada.,4Department of Pathology, Stanford University, Palo Alto, CA 94043 USA
| | - Gail M Gauvreau
- 3Department of Medicine, McMaster University, Hamilton, ON L8N3Z5 Canada
| | - Scott J Tebbutt
- 1Centre for Heart Lung Innovation, University of British Columbia, Room 166, 1081 Burrard Street, Vancouver, BC V6Z1Y6 Canada.,2Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC V6Z2K5 Canada.,5Department of Medicine (Division of Respiratory Medicine), University of British Columbia, Vancouver, BC V6Z1Y6 Canada
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Rajasekaran A, He D, Yue A, Singh A, Shannon CP, FitzGerald JM, Boulet LP, O'Byrne PM, Gauvreau GM, Tebbutt SJ. Cholinergic synapse pathway gene polymorphisms associated with allergen-induced late asthmatic responses. ERJ Open Res 2019; 5:00107-2019. [PMID: 31720291 PMCID: PMC6826244 DOI: 10.1183/23120541.00107-2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/25/2019] [Indexed: 01/21/2023] Open
Abstract
Allergen inhalation challenge triggers well-defined airway responses in mild, allergic asthmatics. Some individuals develop only an isolated early response (early responders (ERs)) characterised by acute airway smooth muscle constriction immediately following allergen inhalation. Others develop a late response (dual responders (DRs)) that begins 3–4 h later, resulting in prolonged reduction of airway function, associated with cellular infiltration, inflammation and hyperresponsiveness of the airways [1]. It is not well understood how certain individuals are protected from developing a late response. Our previous research identified novel RNA transcripts in peripheral blood that are predictive of asthmatics who could develop a late response. Our findings pointed towards the presence of inherent differences underlying molecular mechanisms that predispose asthmatic individuals to the late response [2]. Cholinergic synapse pathway gene polymorphisms may play a role in regulating a type of asthmatic airway response triggered upon allergen challengehttp://bit.ly/2lJx1VG
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Affiliation(s)
- Ashwini Rajasekaran
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Daniel He
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Alice Yue
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada.,School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Amrit Singh
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada.,Dept of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Casey P Shannon
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - J Mark FitzGerald
- Vancouver Coastal Health Research Institute, Vancouver General Hospital, Vancouver, BC, Canada.,Dept of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Paul M O'Byrne
- Dept of Medicine, McMaster University, Hamilton, ON, Canada
| | | | - Scott J Tebbutt
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada.,Dept of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
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Singh A, Shannon CP, Gautier B, Rohart F, Vacher M, Tebbutt SJ, Lê Cao KA. DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays. Bioinformatics 2019; 35:3055-3062. [PMID: 30657866 PMCID: PMC6735831 DOI: 10.1093/bioinformatics/bty1054] [Citation(s) in RCA: 352] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/17/2018] [Accepted: 01/14/2019] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION In the continuously expanding omics era, novel computational and statistical strategies are needed for data integration and identification of biomarkers and molecular signatures. We present Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO), a multi-omics integrative method that seeks for common information across different data types through the selection of a subset of molecular features, while discriminating between multiple phenotypic groups. RESULTS Using simulations and benchmark multi-omics studies, we show that DIABLO identifies features with superior biological relevance compared with existing unsupervised integrative methods, while achieving predictive performance comparable to state-of-the-art supervised approaches. DIABLO is versatile, allowing for modular-based analyses and cross-over study designs. In two case studies, DIABLO identified both known and novel multi-omics biomarkers consisting of mRNAs, miRNAs, CpGs, proteins and metabolites. AVAILABILITY AND IMPLEMENTATION DIABLO is implemented in the mixOmics R Bioconductor package with functions for parameters' choice and visualization to assist in the interpretation of the integrative analyses, along with tutorials on http://mixomics.org and in our Bioconductor vignette. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Amrit Singh
- Prevention of Organ Failure (PROOF) Centre of Excellence, University of British Columbia, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, University of British Columbia, Vancouver, BC, Canada
| | - Benoît Gautier
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Florian Rohart
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Michaël Vacher
- Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Queensland, Australia
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, University of British Columbia, Vancouver, BC, Canada
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
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40
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Singh A, Shannon CP, Kim YW, Yang CX, Balshaw R, Cohen Freue GV, Gauvreau GM, FitzGerald JM, Boulet LP, O'Byrne PM, Tebbutt SJ. Novel Blood-based Transcriptional Biomarker Panels Predict the Late-Phase Asthmatic Response. Am J Respir Crit Care Med 2019; 197:450-462. [PMID: 29087730 DOI: 10.1164/rccm.201701-0110oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The allergen inhalation challenge is used in clinical trials to test the efficacy of new treatments in attenuating the late-phase asthmatic response (LAR) and associated airway inflammation in subjects with allergic asthma. However, not all subjects with allergic asthma develop the LAR after allergen inhalation. Blood-based transcriptional biomarkers that can identify such individuals may help in subject recruitment for clinical trials as well as provide novel molecular insights. OBJECTIVES To identify blood-based transcriptional biomarker panels that can predict an individual's response to allergen inhalation challenge. METHODS We applied RNA sequencing to total RNA from whole blood (n = 36) collected before and after allergen challenge and generated both genome-guided and de novo datasets: genes, gene-isoforms (University of California, Santa Cruz, UCSC Genome Browser), Ensembl, and Trinity. Candidate biomarker panels were validated using the NanoString platform in an independent cohort of 33 subjects. MEASUREMENTS AND MAIN RESULTS The Trinity biomarker panel consisting of known and novel biomarker transcripts had an area under the receiver operating characteristic curve of greater than 0.70 in both the discovery and validation cohorts. The Trinity biomarker panel was useful in predicting the response of subjects that elicited different responses (accuracy between 0.65 and 0.71) and subjects that elicit a dual response (accuracy between 0.70 and 0.75) upon repeated allergen inhalation challenges. CONCLUSIONS Interestingly, the biomarker panel containing novel transcripts successfully validated compared with panels with known, well-characterized genes. These biomarker-blood tests may be used to identify subjects with asthma who develop the LAR, and may also represent members of novel molecular mechanisms that can be targeted for therapy.
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Affiliation(s)
- Amrit Singh
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,3 Department of Pathology and Laboratory Medicine.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Casey P Shannon
- 2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Young Woong Kim
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- 4 Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Gail M Gauvreau
- 6 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - J Mark FitzGerald
- 8 Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,7 Vancouver Coastal Health Research Institute, Vancouver General Hospital, Vancouver, British Columbia, Canada; and
| | | | - Paul M O'Byrne
- 6 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Scott J Tebbutt
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,8 Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
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Yang CX, Singh A, Kim YW, Conway EM, Carlsten C, Tebbutt SJ. Diagnosis of Western Red Cedar Asthma Using a Blood-based Gene Expression Biomarker Panel. Am J Respir Crit Care Med 2019; 196:1615-1617. [PMID: 28463537 DOI: 10.1164/rccm.201608-1740le] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Chen Xi Yang
- 1 University of British Columbia Vancouver, British Columbia, Canada and.,2 Prevention of Organ Failure Centre of Excellence Vancouver, British Columbia, Canada
| | - Amrit Singh
- 1 University of British Columbia Vancouver, British Columbia, Canada and.,2 Prevention of Organ Failure Centre of Excellence Vancouver, British Columbia, Canada
| | - Young Woong Kim
- 1 University of British Columbia Vancouver, British Columbia, Canada and.,2 Prevention of Organ Failure Centre of Excellence Vancouver, British Columbia, Canada
| | - Edward M Conway
- 1 University of British Columbia Vancouver, British Columbia, Canada and
| | | | - Scott J Tebbutt
- 1 University of British Columbia Vancouver, British Columbia, Canada and.,2 Prevention of Organ Failure Centre of Excellence Vancouver, British Columbia, Canada
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Pesenacker AM, Chen V, Gillies J, Speake C, Marwaha AK, Sun A, Chow S, Tan R, Elliott T, Dutz JP, Tebbutt SJ, Levings MK. Treg gene signatures predict and measure type 1 diabetes trajectory. JCI Insight 2019; 4:123879. [PMID: 30730852 DOI: 10.1172/jci.insight.123879] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 07/30/2018] [Accepted: 02/05/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Multiple therapeutic strategies to restore immune regulation and slow type 1 diabetes (T1D) progression are in development and testing. A major challenge has been defining biomarkers to prospectively identify subjects likely to benefit from immunotherapy and/or measure intervention effects. We previously found that, compared with healthy controls, Tregs from children with new-onset T1D have an altered Treg gene signature (TGS), suggesting that this could be an immunoregulatory biomarker. METHODS nanoString was used to assess the TGS in sorted Tregs (CD4+CD25hiCD127lo) or peripheral blood mononuclear cells (PBMCs) from individuals with T1D or type 2 diabetes, healthy controls, or T1D recipients of immunotherapy. Biomarker discovery pipelines were developed and applied to various sample group comparisons. RESULTS Compared with controls, the TGS in isolated Tregs or PBMCs was altered in adult new-onset and cross-sectional T1D cohorts, with sensitivity or specificity of biomarkers increased by including T1D-associated SNPs in algorithms. The TGS was distinct in T1D versus type 2 diabetes, indicating disease-specific alterations. TGS measurement at the time of T1D onset revealed an algorithm that accurately predicted future rapid versus slow C-peptide decline, as determined by longitudinal analysis of placebo arms of START and T1DAL trials. The same algorithm stratified participants in a phase I/II clinical trial of ustekinumab (αIL-12/23p40) for future rapid versus slow C-peptide decline. CONCLUSION These data suggest that biomarkers based on measuring TGSs could be a new approach to stratify patients and monitor autoimmune activity in T1D. FUNDING JDRF (1-PNF-2015-113-Q-R, 2-PAR-2015-123-Q-R, 3-SRA-2016-209-Q-R, 3-PDF-2014-217-A-N), the JDRF Canadian Clinical Trials Network, the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (UM1AI109565 and FY15ITN168), and BCCHRI.
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Affiliation(s)
- Anne M Pesenacker
- Department of Surgery, University of British Columbia (UBC), and BC Children's Hospital Research Institute (BCCHRI), Vancouver, British Columbia, Canada
| | - Virginia Chen
- Department of Medicine and Centre for Heart Lung Innovation, UBC, and Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jana Gillies
- Department of Surgery, University of British Columbia (UBC), and BC Children's Hospital Research Institute (BCCHRI), Vancouver, British Columbia, Canada
| | - Cate Speake
- Diabetes Clinical Research Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Ashish K Marwaha
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Annika Sun
- Department of Surgery, University of British Columbia (UBC), and BC Children's Hospital Research Institute (BCCHRI), Vancouver, British Columbia, Canada
| | - Samuel Chow
- Department of Dermatology, UBC, and BCCHRI, Vancouver, British Columbia, Canada
| | - Rusung Tan
- Department of Pathology, Sidra Medicine, Weill Cornell Medicine, Doha, Qatar
| | - Thomas Elliott
- Department of Medicine, UBC, and BCDiabetes, Vancouver, British Columbia, Canada
| | - Jan P Dutz
- Department of Dermatology, UBC, and BCCHRI, Vancouver, British Columbia, Canada
| | - Scott J Tebbutt
- Department of Medicine and Centre for Heart Lung Innovation, UBC, and Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Megan K Levings
- Department of Surgery, University of British Columbia (UBC), and BC Children's Hospital Research Institute (BCCHRI), Vancouver, British Columbia, Canada
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Culibrk L, Croft CA, Toor A, Yang SJ, Singhera GK, Dorscheid DR, Moore MM, Tebbutt SJ. Phagocytosis of Aspergillus fumigatus by Human Bronchial Epithelial Cells Is Mediated by the Arp2/3 Complex and WIPF2. Front Cell Infect Microbiol 2019; 9:16. [PMID: 30792969 PMCID: PMC6375057 DOI: 10.3389/fcimb.2019.00016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 12/01/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen capable of causing severe infection in humans. One of the limitations in our understanding of how A. fumigatus causes infection concerns the initial stages of infection, notably the initial interaction between inhaled spores or conidia and the human airway. Using publicly-available datasets, we identified the Arp2/3 complex and the WAS-Interacting Protein Family Member 2 WIPF2 as being potentially responsible for internalization of conidia by airway epithelial cells. Using a cell culture model, we demonstrate that RNAi-mediated knockdown of WIPF2 significantly reduces internalization of conidia into airway epithelial cells. Furthermore, we demonstrate that inhibition of Arp2/3 by a small molecule inhibitor causes similar effects. Using super-resolution fluorescence microscopy, we demonstrate that WIPF2 is transiently localized to the site of bound conidia. Overall, we demonstrate the active role of the Arp2/3 complex and WIPF2 in mediating the internalization of A. fumigatus conidia into human airway epithelial cells.
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Affiliation(s)
- Luka Culibrk
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada
| | - Carys A Croft
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada
| | - Amreen Toor
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Department of Graduate Studies, Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - S Jasemine Yang
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Department of Graduate Studies, Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gurpreet K Singhera
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Divison of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Delbert R Dorscheid
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Divison of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Divison of Critical Care Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Margo M Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Scott J Tebbutt
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Divison of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada
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44
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Toor A, Culibrk L, Singhera GK, Moon KM, Prudova A, Foster LJ, Moore MM, Dorscheid DR, Tebbutt SJ. Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium. PLoS One 2018; 13:e0209652. [PMID: 30589860 PMCID: PMC6307744 DOI: 10.1371/journal.pone.0209652] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022] Open
Abstract
Aspergillus fumigatus (A. fumigatus) is a wide-spread fungus that is a potent allergen in hypersensitive individuals but also an opportunistic pathogen in immunocompromised patients. It reproduces asexually by releasing airborne conidiospores (conidia). Upon inhalation, fungal conidia are capable of reaching the airway epithelial cells (AECs) in bronchial and alveolar tissues. Previous studies have predominantly used submerged monolayer cultures for studying this host-pathogen interaction; however, these cultures do not recapitulate the mucocililary differentiation phenotype of the in vivo epithelium in the respiratory tract. Thus, the aim of this study was to use well-differentiated primary human bronchial epithelial cells (HBECs) grown at the air-liquid interface (ALI) to determine their transcriptomic and proteomic responses following interaction with A. fumigatus conidia. We visualized conidial interaction with HBECs using confocal laser scanning microscopy (CLSM), and applied NanoString nCounter and shotgun proteomics to assess gene expression changes in the human cells upon interaction with A. fumigatus conidia. Western blot analysis was used to assess the expression of top three differentially expressed proteins, CALR, SET and NUCB2. CLSM showed that, unlike submerged monolayer cultures, well-differentiated ALI cultures of primary HBECs were estimated to internalize less than 1% of bound conidia. Nevertheless, transcriptomic and proteomic analyses revealed numerous differentially expressed host genes; these were enriched for pathways including apoptosis/autophagy, translation, unfolded protein response and cell cycle (up-regulated); complement and coagulation pathways, iron homeostasis, nonsense mediated decay and rRNA binding (down-regulated). CALR and SET were confirmed to be up-regulated in ALI cultures of primary HBECs upon exposure to A. fumigatus via western blot analysis. Therefore, using transcriptomics and proteomics approaches, ALI models recapitulating the bronchial epithelial barrier in the conductive zone of the respiratory tract can provide novel insights to the molecular response of bronchial epithelial cells upon exposure to A. fumigatus conidia.
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Affiliation(s)
- Amreen Toor
- Experimental Medicine, University of British Columbia, Vancouver, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Luka Culibrk
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Gurpreet K. Singhera
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Anna Prudova
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - Delbert R. Dorscheid
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Scott J. Tebbutt
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, Canada
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Giles LV, Tebbutt SJ, Carlsten C, Koehle MS. The effect of low and high-intensity cycling in diesel exhaust on flow-mediated dilation, circulating NOx, endothelin-1 and blood pressure. PLoS One 2018; 13:e0192419. [PMID: 29466393 PMCID: PMC5821322 DOI: 10.1371/journal.pone.0192419] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 04/23/2017] [Accepted: 01/11/2018] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Exposure to air pollution impairs aspects of endothelial function such as flow-mediated dilation (FMD). Outdoor exercisers are frequently exposed to air pollution, but how exercising in air pollution affects endothelial function and how these effects are modified by exercise intensity are poorly understood. OBJECTIVES Therefore, the purpose of this study was to determine the effects of low-intensity and high-intensity cycling with diesel exhaust (DE) exposure on FMD, blood pressure, plasma nitrite and nitrate (NOx) and endothelin-1. METHODS Eighteen males performed 30-minute trials of low or high-intensity cycling (30% and 60% of power at VO2peak) or a resting control condition. For each subject, each trial was performed once while breathing filtered air (FA) and once while breathing DE (300ug/m3 of PM2.5, six trials in total). Preceding exposure, immediately post-exposure, 1 hour and 2 hours post-exposure, FMD, blood pressure and plasma endothelin-1 and NOx concentrations were measured. Data were analyzed using repeated-measures ANOVA and linear mixed model. RESULTS Following exercise in DE, plasma NOx significantly increased and was significantly greater than FA (p<0.05). Two hours following DE exposure, endothelin-1 was significantly less than FA (p = 0.037) but exercise intensity did not modify this response. DE exposure did not affect FMD or blood pressure. CONCLUSION Our results suggest that exercising in DE did not adversely affect plasma NOX, endothelin-1, FMD and blood pressure. Therefore, recommendations for healthy individuals to moderate or avoid exercise during bouts of high pollution appear to have no acute protective effect.
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Affiliation(s)
- Luisa V. Giles
- School of Kinesiology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Christopher Carlsten
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S. Koehle
- School of Kinesiology, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Sports Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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46
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Jamil S, Mousavizadeh R, Roshan-Moniri M, Tebbutt SJ, McCormack RG, Duronio V, Scott A. Angiopoietin-like 4 Enhances the Proliferation and Migration of Tendon Fibroblasts. Med Sci Sports Exerc 2018; 49:1769-1777. [PMID: 28398948 DOI: 10.1249/mss.0000000000001294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE Angiopoietin-like 4 (ANGPTL4) is known to play a variety of roles in the response to exercise, and more recently has been shown to enhance the healing of tendon, a fibrous load-bearing tissue required for efficient movement. The objective of the current study was to further explore the mechanisms of ANGPTL4's effect on tendon cells using a gene array approach. METHODS Human tendon fibroblasts were treated with recANGPTL4 and their global transcriptome response analyzed after 4 and 24 h. We also conducted functional studies using tendon fibroblasts derived from human subjects, cultured in the presence or absence of applied cyclic stretch and/or siRNA for ANGPTL4, and as confirmation we also used tendon cells from wild type (ANGPTL4 +/+) or knockout (ANGPTL4-/-) mice. RESULTS The leading functions of ANGPTL4 predicted by the resulting pathway analysis were cell movement and proliferation. The experiments demonstrated that ANGPTL4 significantly enhanced tendon cell proliferation and the cell cycle progression, as well as adhesion and migration. CONCLUSION Taken together, these findings provide novel molecular insights into the effect of ANGPTL4, a multifunctional protein that regulates the physiological response to exercise, on fundamental tendon cell functions.
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Affiliation(s)
- Sarwat Jamil
- 1Department of Physical Therapy, Centre for Hip Health and Mobility, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, BC, CANADA; 2Department of Medicine, Jack Bell Research Centre, University of British Columbia, Vancouver, BC, CANADA; 3Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, CANADA; 4Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, CANADA; 5Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, CANADA; and 6Department of Orthopaedic Surgery, University of British Columbia, Vancouver, CANADA
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Abstract
RNA sequencing is a powerful technology that allows for unbiased profiling of the entire transcriptome. The analysis of transcriptome profiles from heterogeneous tissues, cell admixtures with relative proportions that can vary several fold across samples, poses a significant challenge. Blood is perhaps the most egregious example. Here, we describe in detail a computational pipeline for RNA-Seq data preparation and statistical analysis, with development of a means of estimating the cell type composition of blood samples from their bulk RNA-Seq profiles. We also illustrate the importance of adjusting for the potential confounding effect of cellular heterogeneity in the context of statistical inference in a whole blood RNA-Seq dataset.
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Affiliation(s)
- Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Vancouver, BC, Canada.
| | - Chen Xi Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence, Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Vancouver, BC, Canada.
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, St. Paul's Hospital, Vancouver, BC, Canada.
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48
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Roberts JM, Dai DLY, Hollander Z, Ng RT, Tebbutt SJ, Wilcox PG, Sin DD, Quon BS. Multiple reaction monitoring mass spectrometry to identify novel plasma protein biomarkers of treatment response in cystic fibrosis pulmonary exacerbations. J Cyst Fibros 2017; 17:333-340. [PMID: 29174082 DOI: 10.1016/j.jcf.2017.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND Systemic inflammation decreases with IV antibiotics during the treatment of CF pulmonary exacerbations (PEx). We used multiple reaction monitoring mass spectrometry and immunoassays to monitor blood proteins during PEx treatment to determine if early changes could be used to predict PEx outcomes following treatment. METHODS Blood samples from 25 PEx (22 unique adults) were collected within 24h of admission, day 5, day 10, and at IV antibiotic completion. Ninety-two blood proteins involved in host immunity and inflammation were measured. RESULTS Levels of several blood proteins changed from admission to end of IV antibiotics, most increasing with treatment. Early changes (admission to day 5) in fibrinogen levels had the strongest correlation with overall improvement in CFRSD-CRISS and FEV1% predicted by the end of treatment. CONCLUSIONS Several plasma proteins changed significantly with IV antibiotics. Future studies will evaluate fibrinogen as an early biomarker of PEx treatment response in CF.
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Affiliation(s)
- James M Roberts
- Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Canada
| | - Darlene L Y Dai
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Zsuzsanna Hollander
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Raymond T Ng
- Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Canada; Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Canada; Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Pearce G Wilcox
- Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Bradley S Quon
- Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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Kim YW, Singh A, Shannon CP, Thiele J, Steacy LM, Ellis AK, Neighbour H, Gliddon DR, Hickey PLC, Larché M, Tebbutt SJ. Investigating Immune Gene Signatures in Peripheral Blood from Subjects with Allergic Rhinitis Undergoing Nasal Allergen Challenge. J I 2017; 199:3395-3405. [DOI: 10.4049/jimmunol.1700378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
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50
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Alsayegh MA, Alshamali H, Khadada M, Ciccolini A, Ellis AK, Quint D, Powley W, Lee L, Fiteih Y, Baksh S, Vliagoftis H, Gerega SK, Millson B, Charland K, Barakat S, Sun X, Jimenez R, Waserman S, FitzGerald MJ, Hébert J, Cognet-Sicé J, Renahan KE, Huq S, Chooniedass R, Sawyer S, Pasterkamp H, Becker A, Smith SG, Zhang S, Jayasundara K, Tacon C, Simidchiev A, Nadeau G, Gunsoy N, Mullerova H, Albers F, Kim YW, Shannon CP, Singh A, Neighbour H, Larché M, Tebbutt SJ, Klopp A, Vehling L, Becker AB, Subbarao P, Mandhane PJ, Turvey SE, Sears MR, Azad MB, Loewen K, Monchka B, Mahmud SM, Jong G‘, Longo C, Bartlett G, Ducharme FM, Schuster T, MacGibbon B, Barnett T, North ML, Brook J, Lee E, Omana V, Thiele J, Steacy LM, Evans G, Diamond M, Sussman GL, Amistani Y, Abiteboul K, Tenn MW, Yang C, Carlsten C, Conway EM, Mack D, Othman Y, Barber CM, Kalicinsky C, Burke AE, Messieh M, Nair P, Che CT, Douglas L, Liem J, Duan L, Miller C, Dupuis P, Connors LA, Fein MN, Shuster J, Hadi H, Polk B, Raje N, Labrosse R, Bégin P, Paradis L, Roches AD, Lacombe-Barrios J, Mishra S, Lacuesta G, Chiasson M, Haroon B, Robertson K, Issekutz T, Leddin D, Couban S, Connors L, Roos A, Kanani A, Chan ES, Schellenberg R, Rosenfield L, Cvetkovic A, Woodward K, Quirt J, Watson WTA, Castilho E, Sullivan JA, Temple B, Martin D, Cook VE, Mills C, Portales-Casamar E, Fu LW, Ho A, Zaltzman J, Chen L, Vadas P, Gabrielli S, Clarke A, Eisman H, Morris J, Joseph L, LaVieille S, Ben-Shoshan M, Graham F, Barnes C, Portnoy J, Stagg V, Simons E, Lefebvre D, Dai D, Mandhane P, Sears M, Tam H, Simons FER, Alotaibi D, Dawod B, Tunis MC, Marshall J, Desjardins M, Béland M, Lejtenyi D, Drolet JP, Lemire M, Tsoukas C, Noya FJ, Alizadehfar R, McCusker CT, Mazer BD, Maestre-Batlle D, Gunawan E, Rider CF, Bølling AK, Pena OM, Suez D, Melamed I, Hussain I, Stein M, Gupta S, Paris K, Fritsch S, Bourgeois C, Leibl H, McCoy B, Noel M, Yel L, Scott O, Reid B, Atkinson A, Kim VHD, Roifman CM, Grunebaum E, AlSelahi E, Aleman F, Oberle A, Trus M, Sussman G, Kanani AS, Chambenoi O, Chiva-Razavi S, Grodecki S, Joshi N, Menikefs P, Holt D, Pun T, Tworek D, Hanna R, Heroux D, Rosenberg E, Stiemsma L, Turvey S, Denburg J, Mill C, Teoh T, Zimmer P, Avinashi V, Paina M, Darwish Hassan AA, Oliveria JP, Olesovsky C, Gauvreau G, Pedder L, Keith PK, Plunkett G, Bolner M, Pourshahnazari P, Stark D, Vostretsova K, Moses A, Wakeman A, Singer A, Gerstner T, Abrams E, Johnson SF, Woodgate RL. Canadian Society of Allergy and Clinical Immunology annual scientific meeting 2016. Allergy Asthma Clin Immunol 2017. [PMCID: PMC5390240 DOI: 10.1186/s13223-017-0192-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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