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Leacy EJ, Teh JW, O’Rourke AM, Brady G, Gargan S, Conlon N, Scott J, Dunne J, Phelan T, Griffin MD, Power J, Mooney A, Naughton A, Kiersey R, Gardiner M, O’Brien C, Mullan R, Flood R, Clarkson M, Townsend L, O’Shaughnessy M, Dyer AH, Moran B, Fletcher JM, Zgaga L, Little MA. Effect of Immunosuppression on the Immune Response to SARS-CoV-2 Infection and Vaccination. Int J Mol Sci 2024; 25:5239. [PMID: 38791279 PMCID: PMC11120762 DOI: 10.3390/ijms25105239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Immunosuppressive treatment in patients with rheumatic diseases can maintain disease remission but also increase risk of infection. Their response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is frequently blunted. In this study we evaluated the effect of immunosuppression exposure on humoral and T cell immune responses to SARS-CoV-2 infection and vaccination in two distinct cohorts of patients; one during acute SARS-CoV-2 infection and 3 months later during convalescence, and another prior to SARS-CoV-2 vaccination, with follow up sampling 6 weeks after vaccination. Results were compared between rituximab-exposed (in previous 6 months), immunosuppression-exposed (in previous 3 months), and non-immunosuppressed groups. The immune cell phenotype was defined by flow cytometry and ELISA. Antigen specific T cell responses were estimated using a whole blood stimulation interferon-γ release assay. A focused post-vaccine assessment of rituximab-treated patients using high dimensional spectral cytometry was conducted. Acute SARS-CoV-2 infection was characterised by T cell lymphopenia, and a reduction in NK cells and naïve CD4 and CD8 cells, without any significant differences between immunosuppressed and non-immunosuppressed patient groups. Conversely, activated CD4 and CD8 cell counts increased in non-immunosuppressed patients with acute SARS-CoV-2 infection but this response was blunted in the presence of immunosuppression. In rituximab-treated patients, antigen-specific T cell responses were preserved in SARS-CoV-2 vaccination, but patients were unable to mount an appropriate humoral response.
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Affiliation(s)
- Emma J. Leacy
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Jia Wei Teh
- Department of Nephrology, Galway University Hospital, H91 YR71 Galway, Ireland
| | - Aoife M. O’Rourke
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (A.M.O.)
| | - Gareth Brady
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Siobhan Gargan
- Department of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Niall Conlon
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Jennifer Scott
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Jean Dunne
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Thomas Phelan
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Matthew D. Griffin
- Department of Nephrology, Galway University Hospital, H91 YR71 Galway, Ireland
- Regenerative Medicine Institute (REMEDI) at CÚRAM SFI Research Centre for Medical Devices, School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Julie Power
- Vasculitis Ireland Awareness, Belfast & Dublin, Ireland
| | - Aoife Mooney
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Aifric Naughton
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Rachel Kiersey
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Mary Gardiner
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Caroline O’Brien
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Ronan Mullan
- Department of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Department of Rheumatology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
| | - Rachael Flood
- Department of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Department of Rheumatology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
| | - Michael Clarkson
- Department of Nephrology, Cork University Hospital, T12 DC4A Cork, Ireland
| | - Liam Townsend
- Department of Infectious Diseases, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Michelle O’Shaughnessy
- Department of Nephrology, Galway University Hospital, H91 YR71 Galway, Ireland
- Department of Nephrology, Cork University Hospital, T12 DC4A Cork, Ireland
| | - Adam H. Dyer
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Barry Moran
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (A.M.O.)
| | - Jean M. Fletcher
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (A.M.O.)
| | - Lina Zgaga
- Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Mark A. Little
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
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Scott J, White A, Walsh C, Aslett L, Rutherford MA, Ng J, Judge C, Sebastian K, O'Brien S, Kelleher J, Power J, Conlon N, Moran SM, Luqmani RA, Merkel PA, Tesar V, Hruskova Z, Little MA. Computable phenotype for real-world, data-driven retrospective identification of relapse in ANCA-associated vasculitis. RMD Open 2024; 10:e003962. [PMID: 38688690 PMCID: PMC11086371 DOI: 10.1136/rmdopen-2023-003962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
OBJECTIVE ANCA-associated vasculitis (AAV) is a relapsing-remitting disease, resulting in incremental tissue injury. The gold-standard relapse definition (Birmingham Vasculitis Activity Score, BVAS>0) is often missing or inaccurate in registry settings, leading to errors in ascertainment of this key outcome. We sought to create a computable phenotype (CP) to automate retrospective identification of relapse using real-world data in the research setting. METHODS We studied 536 patients with AAV and >6 months follow-up recruited to the Rare Kidney Disease registry (a national longitudinal, multicentre cohort study). We followed five steps: (1) independent encounter adjudication using primary medical records to assign the ground truth, (2) selection of data elements (DEs), (3) CP development using multilevel regression modelling, (4) internal validation and (5) development of additional models to handle missingness. Cut-points were determined by maximising the F1-score. We developed a web application for CP implementation, which outputs an individualised probability of relapse. RESULTS Development and validation datasets comprised 1209 and 377 encounters, respectively. After classifying encounters with diagnostic histopathology as relapse, we identified five key DEs; DE1: change in ANCA level, DE2: suggestive blood/urine tests, DE3: suggestive imaging, DE4: immunosuppression status, DE5: immunosuppression change. F1-score, sensitivity and specificity were 0.85 (95% CI 0.77 to 0.92), 0.89 (95% CI 0.80 to 0.99) and 0.96 (95% CI 0.93 to 0.99), respectively. Where DE5 was missing, DE2 plus either DE1/DE3 were required to match the accuracy of BVAS. CONCLUSIONS This CP accurately quantifies the individualised probability of relapse in AAV retrospectively, using objective, readily accessible registry data. This framework could be leveraged for other outcomes and relapsing diseases.
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Affiliation(s)
- Jennifer Scott
- Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Arthur White
- School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
- ADAPT SFI centre, Trinity College Dublin, Dublin, Ireland
| | - Cathal Walsh
- Department of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
- National Centre for Pharmacoeconomics, St James's Hospital, Dublin, Ireland
| | - Louis Aslett
- Department of Mathematical Science, University of Durham, Durham, UK
| | | | - James Ng
- School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
| | - Conor Judge
- School of Medicine, College of Medicine, Nursing and Health Science, University of Galway, Galway, Ireland
| | - Kuruvilla Sebastian
- Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Sorcha O'Brien
- Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - John Kelleher
- Department of Statistics, Dublin Institute of Technology, Dublin, Ireland
| | - Julie Power
- Vasculitis Ireland Awareness, Dublin, Ireland
| | - Niall Conlon
- Department of Immunology, St James's Hospital, Dublin, Ireland
| | - Sarah M Moran
- Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Department of Nephrology, Cork University Hospital, Cork, Ireland
| | - Raashid Ahmed Luqmani
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science (NDORMs), University of Oxford, Oxford, UK
| | - Peter A Merkel
- Division of Rheumatology, Department of Medicine, Division of Epidemiology, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vladimir Tesar
- Department of Nephrology, General University Hospital, Prague, Czech Republic
- 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Zdenka Hruskova
- 1st Faculty of Medicine, Charles University, Prague, Czech Republic
- General University Hospital, Prague, Czech Republic
| | - Mark A Little
- Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- ADAPT SFI centre, Trinity College Dublin, Dublin, Ireland
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Gisslander K, Rutherford M, Aslett L, Basu N, Dradin F, Hederman L, Hruskova Z, Kardaoui H, Lamprecht P, Lichołai S, Musial J, O'Sullivan D, Puechal X, Scott J, Segelmark M, Straka R, Terrier B, Tesar V, Tesi M, Vaglio A, Wandrei D, White A, Wójcik K, Yaman B, Little MA, Mohammad AJ. Data quality and patient characteristics in European ANCA-associated vasculitis registries: data retrieval by federated querying. Ann Rheum Dis 2024; 83:112-120. [PMID: 37907255 PMCID: PMC10804071 DOI: 10.1136/ard-2023-224571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/16/2023] [Indexed: 11/02/2023]
Abstract
OBJECTIVES This study aims to describe the data structure and harmonisation process, explore data quality and define characteristics, treatment, and outcomes of patients across six federated antineutrophil cytoplasmic antibody-associated vasculitis (AAV) registries. METHODS Through creation of the vasculitis-specific Findable, Accessible, Interoperable, Reusable, VASCulitis ontology, we harmonised the registries and enabled semantic interoperability. We assessed data quality across the domains of uniqueness, consistency, completeness and correctness. Aggregated data were retrieved using the semantic query language SPARQL Protocol and Resource Description Framework Query Language (SPARQL) and outcome rates were assessed through random effects meta-analysis. RESULTS A total of 5282 cases of AAV were identified. Uniqueness and data-type consistency were 100% across all assessed variables. Completeness and correctness varied from 49%-100% to 60%-100%, respectively. There were 2754 (52.1%) cases classified as granulomatosis with polyangiitis (GPA), 1580 (29.9%) as microscopic polyangiitis and 937 (17.7%) as eosinophilic GPA. The pattern of organ involvement included: lung in 3281 (65.1%), ear-nose-throat in 2860 (56.7%) and kidney in 2534 (50.2%). Intravenous cyclophosphamide was used as remission induction therapy in 982 (50.7%), rituximab in 505 (17.7%) and pulsed intravenous glucocorticoid use was highly variable (11%-91%). Overall mortality and incidence rates of end-stage kidney disease were 28.8 (95% CI 19.7 to 42.2) and 24.8 (95% CI 19.7 to 31.1) per 1000 patient-years, respectively. CONCLUSIONS In the largest reported AAV cohort-study, we federated patient registries using semantic web technologies and highlighted concerns about data quality. The comparison of patient characteristics, treatment and outcomes was hampered by heterogeneous recruitment settings.
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Affiliation(s)
- Karl Gisslander
- Clinical Sciences, Rheumatology, Lund University, Lund, Sweden
| | | | - Louis Aslett
- Department of Mathematical Science, University of Durham, Durham, UK
| | - Neil Basu
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | | | - Lucy Hederman
- ADAPT SFI Centre, School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
| | - Zdenka Hruskova
- Department of Nephrology, General University Hospital, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Hicham Kardaoui
- National Referral Center for Rare Systemic Autoimmune Diseases, Hospital Cochin, Paris, France
- Université Paris Cité, Paris, France
| | - Peter Lamprecht
- Department of Rheumatology and Clinical Immunology, Universitat zu Lubeck, Lubeck, Germany
| | - Sabina Lichołai
- Division of Molecular Biology and Clinical Genetics, Jagiellonian University Medical College, Krakow, Poland
| | - Jacek Musial
- 2nd Department of Internal Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Declan O'Sullivan
- ADAPT SFI Centre, School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
| | - Xavier Puechal
- National Referral Center for Rare Systemic Autoimmune Diseases, Hospital Cochin, Paris, France
- French Vasculitis Study Group, Paris, France
| | - Jennifer Scott
- ADAPT SFI Centre, School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
- Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Mårten Segelmark
- Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Endocrinology, Nephrology and Rheumatology, Skåne University Hospital, Lund, Sweden
| | - Richard Straka
- General University Hospital in Prague, Praha, Czech Republic
| | - Benjamin Terrier
- National Referral Center for Rare Systemic Autoimmune Diseases, Hospital Cochin, Paris, France
- French Vasculitis Study Group, Paris, France
| | - Vladimir Tesar
- Department of Nephrology, General University Hospital, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Michelangelo Tesi
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Firenze, Italy
| | - Augusto Vaglio
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Firenze, Italy
| | - Dagmar Wandrei
- Clinical Trials Unit, Medical Center, University of Freiburg Faculty of Medicine, Freiburg, Germany
| | - Arthur White
- School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
| | - Krzysztof Wójcik
- 2nd Department of Internal Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Beyza Yaman
- ADAPT SFI Centre, School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
| | - Mark A Little
- ADAPT SFI Centre, School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland
- Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Aladdin J Mohammad
- Clinical Sciences, Rheumatology, Lund University, Lund, Sweden
- Department of Medicine, University of Cambridge, Cambridge, UK
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