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Kidwai S, Barbiero P, Meijerman I, Tonda A, Perez‐Pardo P, Lio ´ P, van der Maitland‐Zee AH, Oberski DL, Kraneveld AD, Lopez‐Rincon A. A robust mRNA signature obtained via recursive ensemble feature selection predicts the responsiveness of omalizumab in moderate-to-severe asthma. Clin Transl Allergy 2023; 13:e12306. [PMID: 38006387 PMCID: PMC10655633 DOI: 10.1002/clt2.12306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 09/01/2023] [Accepted: 10/11/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Not being well controlled by therapy with inhaled corticosteroids and long-acting β2 agonist bronchodilators is a major concern for severe-asthma patients. The current treatment option for these patients is the use of biologicals such as anti-IgE treatment, omalizumab, as an add-on therapy. Despite the accepted use of omalizumab, patients do not always benefit from it. Therefore, there is a need to identify reliable biomarkers as predictors of omalizumab response. METHODS Two novel computational algorithms, machine-learning based Recursive Ensemble Feature Selection (REFS) and rule-based algorithm Logic Explainable Networks (LEN), were used on open accessible mRNA expression data from moderate-to-severe asthma patients to identify genes as predictors of omalizumab response. RESULTS With REFS, the number of features was reduced from 28,402 genes to 5 genes while obtaining a cross-validated accuracy of 0.975. The 5 responsiveness predictive genes encode the following proteins: Coiled-coil domain- containing protein 113 (CCDC113), Solute Carrier Family 26 Member 8 (SLC26A), Protein Phosphatase 1 Regulatory Subunit 3D (PPP1R3D), C-Type lectin Domain Family 4 member C (CLEC4C) and LOC100131780 (not annotated). The LEN algorithm found 4 identical genes with REFS: CCDC113, SLC26A8 PPP1R3D and LOC100131780. Literature research showed that the 4 identified responsiveness predicting genes are associated with mucosal immunity, cell metabolism, and airway remodeling. CONCLUSION AND CLINICAL RELEVANCE Both computational methods show 4 identical genes as predictors of omalizumab response in moderate-to-severe asthma patients. The obtained high accuracy indicates that our approach has potential in clinical settings. Future studies in relevant cohort data should validate our computational approach.
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Affiliation(s)
- Sarah Kidwai
- Division of PharmacologyUtrecht Institute for Pharmaceutical ScienceFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
| | - Pietro Barbiero
- Department of Computer Science and TechnologyUniversity of CambridgeCambridgeUK
| | - Irma Meijerman
- Division of PharmacologyUtrecht Institute for Pharmaceutical ScienceFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
| | | | - Paula Perez‐Pardo
- Division of PharmacologyUtrecht Institute for Pharmaceutical ScienceFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
| | - Pietro Lio ´
- Department of Computer Science and TechnologyUniversity of CambridgeCambridgeUK
| | | | - Daniel L. Oberski
- Department of Data ScienceUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Aletta D. Kraneveld
- Division of PharmacologyUtrecht Institute for Pharmaceutical ScienceFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
| | - Alejandro Lopez‐Rincon
- Division of PharmacologyUtrecht Institute for Pharmaceutical ScienceFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
- Department of Data ScienceUniversity Medical Center UtrechtUtrechtThe Netherlands
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Plattner K, Augusto G, Muerner L, von Gunten S, Jörg L, Engeroff P, Bachmann MF, Vogel M. IgE glycosylation is essential for the function of omalizumab. Allergy 2023; 78:2546-2549. [PMID: 37073887 DOI: 10.1111/all.15748] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 04/20/2023]
Affiliation(s)
- Kevin Plattner
- Department of Immunology, University Clinic for Rheumatology and Immunology, University of Bern, Bern, Switzerland
- Department of Biomedical Research Bern (DBMR), University of Bern, Bern, Switzerland
| | - Gilles Augusto
- Department of Immunology, University Clinic for Rheumatology and Immunology, University of Bern, Bern, Switzerland
- Department of Biomedical Research Bern (DBMR), University of Bern, Bern, Switzerland
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, UK
| | - Lukas Muerner
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | | | - Lukas Jörg
- Division of Allergology and Clinical Immunology, Department of Pneumology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Paul Engeroff
- Department of Immunology, University Clinic for Rheumatology and Immunology, University of Bern, Bern, Switzerland
- Department of Biomedical Research Bern (DBMR), University of Bern, Bern, Switzerland
| | - Martin F Bachmann
- Department of Immunology, University Clinic for Rheumatology and Immunology, University of Bern, Bern, Switzerland
- Department of Biomedical Research Bern (DBMR), University of Bern, Bern, Switzerland
| | - Monique Vogel
- Department of Immunology, University Clinic for Rheumatology and Immunology, University of Bern, Bern, Switzerland
- Department of Biomedical Research Bern (DBMR), University of Bern, Bern, Switzerland
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Khaleva E, Rattu A, Brightling C, Bush A, Bourdin A, Bossios A, Chung KF, Chaudhuri R, Coleman C, Djukanovic R, Dahlén SE, Exley A, Fleming L, Fowler SJ, Gupta A, Hamelmann E, Koppelman GH, Melén E, Mahler V, Seddon P, Singer F, Porsbjerg C, Ramiconi V, Rusconi F, Yasinska V, Roberts G. Definitions of non-response and response to biological therapy for severe asthma: a systematic review. ERJ Open Res 2023; 9:00444-2022. [PMID: 37143849 PMCID: PMC10152254 DOI: 10.1183/23120541.00444-2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/06/2022] [Indexed: 01/27/2023] Open
Abstract
Background Biologics have proven efficacy for patients with severe asthma but there is lack of consensus on defining response. We systematically reviewed and appraised methodologically developed, defined and evaluated definitions of non-response and response to biologics for severe asthma. Methods We searched four bibliographic databases from inception to 15 March 2021. Two reviewers screened references, extracted data, and assessed methodological quality of development, measurement properties of outcome measures and definitions of response based on COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN). A modified GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach and narrative synthesis were undertaken. Results 13 studies reported three composite outcome measures, three asthma symptoms measures, one asthma control measure and one quality of life measure. Only four measures were developed with patient input; none were composite measures. Studies utilised 17 definitions of response: 10 out of 17 (58.8%) were based on minimal clinically important difference (MCID) or minimal important difference (MID) and 16 out of 17 (94.1%) had high-quality evidence. Results were limited by poor methodology for the development process and incomplete reporting of psychometric properties. Most measures rated "very low" to "low" for quality of measurement properties and none met all quality standards. Conclusions This is the first review to synthesise evidence about definitions of response to biologics for severe asthma. While high-quality definitions are available, most are MCIDs or MIDs, which may be insufficient to justify continuation of biologics in terms of cost-effectiveness. There remains an unmet need for universally accepted, patient-centred, composite definitions to aid clinical decision making and comparability of responses to biologics.
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Affiliation(s)
- Ekaterina Khaleva
- Clinical and Experimental Sciences and Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Anna Rattu
- Clinical and Experimental Sciences and Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Chris Brightling
- Institute for Lung Health, Leicester NIHR BRC, University of Leicester, UK
| | - Andrew Bush
- Centre for Paediatrics and Child Health and National Heart and Lung Institute, Imperial College, Royal Brompton Hospital, London, UK
| | - Arnaud Bourdin
- PhyMedExp, University of Montpellier, Montpellier, France
| | - Apostolos Bossios
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital and Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Rekha Chaudhuri
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | | | - Ratko Djukanovic
- Clinical and Experimental Sciences and Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sven-Erik Dahlén
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital and Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Louise Fleming
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Stephen J. Fowler
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, NIHR Manchester Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester, UK
| | - Atul Gupta
- Department of Paediatric Respiratory Medicine, King's College Hospital, London, UK
| | - Eckard Hamelmann
- Children's Center Bethel, Department of Pediatrics, University Bielefeld, Bielefeld, Germany
| | - Gerard H. Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Erik Melén
- Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Vera Mahler
- Division of Allergology, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Paul Seddon
- Respiratory Care, Royal Alexandra Children's Hospital, Brighton, UK
| | - Florian Singer
- Department of Respiratory Medicine, University Children's Hospital Zurich and Childhood Research Center, Zurich, Switzerland
- Division of Paediatric Pulmonology and Allergology, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Celeste Porsbjerg
- Department of Respiratory Medicine, Respiratory Research Unit, Bispebjerg Hospital, Copenhagen, Denmark
| | - Valeria Ramiconi
- European Federation of Allergy and Airways Diseases Patients’ Associations, Brussels, Belgium
| | - Franca Rusconi
- Department of Mother and Child Health, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Valentyna Yasinska
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital and Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Graham Roberts
- Clinical and Experimental Sciences and Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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Kardas G, Panek M, Kuna P, Damiański P, Kupczyk M. Monoclonal antibodies in the management of asthma: Dead ends, current status and future perspectives. Front Immunol 2022; 13:983852. [PMID: 36561741 PMCID: PMC9763885 DOI: 10.3389/fimmu.2022.983852] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022] Open
Abstract
Patients with moderate-to-severe asthma may now be treated using a variety of monoclonal antibodies that target key inflammatory cytokines involved in disease pathogenesis. Existing clinical data on anti-IgE, anti-IL-5 and other immunological pathways indicate these therapies to offer reduced exacerbation rates, improved lung function, greater asthma control and better quality of life. However, as several patients still do not achieve satisfactory clinical response with the antibodies available, many more biologics, aiming different immunological pathways, are under evaluation. This review summarizes recent data on existing and potential monoclonal antibodies in asthma. Recent advances have resulted in the registration of a new antibody targeting TSLP (tezepelumab), with others being under development. Some of the researched monoclonal antibodies (e.g. anti-IL-13 tralokinumab and lebrikizumab or anti-IL-17A secukinumab) have shown optimistic results in preliminary research; however, these have been discontinued in asthma clinical research. In addition, as available monoclonal antibody treatments have shown little benefit among patients with T2-low asthma, research continues in this area, with several antibodies in development. This article summarizes the available pre-clinical and clinical data on new and emerging drugs for treating severe asthma, discusses discontinued treatments and outlines future directions in this area.
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Effects of Therapeutic Antibodies on Gene and Protein Signatures in Asthma Patients: A Comparative Systematic Review. Biomedicines 2022; 10:biomedicines10020293. [PMID: 35203504 PMCID: PMC8869456 DOI: 10.3390/biomedicines10020293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
Several biologic therapies that target inflammatory modulators are now used for treating patients with uncontrolled, severe asthma. Knowledge about how this type of treatment modifies the molecular milieu is rapidly increasing. Thus, this systematic review aimed to compile the reported effects of therapeutic antibodies on the transcriptome or proteome of asthma patients. Studies of asthmatic patients under biological treatment describing transcriptomic or proteomic changes upon treatment were included. Preclinical or single gene/protein studies were not considered. PubMed and Scopus search was performed in August and September 2021. Following PRISMA guidelines and GRADE recommendations, we selected 12 studies on gene or protein expression changes in patients treated with the antibodies currently approved by EMA and the FDA. All studies were at low risk of bias as per the RoB2 tool. Different gene clusters have been identified to change upon omalizumab treatment, found a reduction in eosinophil-associated gene signatures after benralizumab treatment, and protein profiles were different in patients treated with mepolizumab and in those treated with benralizumab. The main potential biomarkers proposed by the selected studies are shown. These results may contribute to discovering biomarkers of response and selecting the best therapy for each patient.
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Boyle RJ, Shamji MH. Developments in the field of allergy in 2020 through the eyes of Clinical and Experimental Allergy. Clin Exp Allergy 2021; 51:1531-1537. [PMID: 34750898 DOI: 10.1111/cea.14046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
While 2020 will be remembered for the global coronavirus pandemic, there were also important advances in the field of allergy. In this review article, we summarize key findings reported in Clinical and Experimental Allergy during 2020. We hope this provides readers with an accessible snapshot of the work published in our journal during this time.
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Affiliation(s)
- Robert J Boyle
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mohamed H Shamji
- National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Imperial Biomedical Research Centre, London, UK
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