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. 2024 Nov 21;64(5):2400207.
doi: 10.1183/13993003.00207-2024. Print 2024 Nov.

Radiomultiomics: quantitative CT clusters of severe asthma associated with multiomics

Affiliations

Radiomultiomics: quantitative CT clusters of severe asthma associated with multiomics

Nazanin Zounemat Kermani et al. Eur Respir J. .

Abstract

Background: Lung quantitative computed tomography (qCT) severe asthma clusters have been reported, but their replication and underlying disease mechanisms are unknown. We identified and replicated qCT clusters of severe asthma in two independent asthma cohorts and determined their association with molecular pathways, using radiomultiomics, integrating qCT, multiomics and machine learning/artificial intelligence.

Methods: We used consensus clustering on qCT measurements of airway and lung CT scans, performed in 105 severe asthmatic adults from the U-BIOPRED cohort. The same qCT measurements were used to replicate qCT clusters in a subsample of the ATLANTIS asthma cohort (n=97). We performed integrated enrichment analysis using blood, sputum, bronchial biopsies, bronchial brushings and nasal brushings transcriptomics and blood and sputum proteomics to characterise radiomultiomic-associated clusters (RACs).

Results: qCT clusters and clinical features in U-BIOPRED were replicated in the matched ATLANTIS cohort. In the U-BIOPRED cohort, RAC1 (n=30) was predominantly female with elevated body mass index, mild airflow limitation, decreased CT lung volume and increased lung density and upregulation of the complement pathway. RAC2 (n=34) subjects had airway wall thickness and a mild degree of airflow limitation, with upregulation of proliferative pathways including neurotrophic receptor tyrosine kinase 2/tyrosine kinase receptor B, and downregulation of semaphorin pathways. RAC3 (n=41) showed increased lung attenuation area and air trapping, severe airflow limitation, hyperinflation, and upregulation of cytokine signalling and signalling by interleukin pathways, and matrix metallopeptidase 1, 2 and 9.

Conclusions: U-BIOPRED severe asthma qCT clusters were replicated in a matched independent asthmatic cohort and associated with specific molecular pathways. Radiomultiomics might represent a novel strategy to identify new molecular pathways in asthma pathobiology.

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Conflict of interest statement

Conflict of interest: K.F. Chung reports grants from the MRC, EPSRC, GSK, Merck and NIEHS, payment or honoraria for lectures, presentations, manuscript writing or educational events from GSK, Novartis and AstraZeneca, and participation on a data safety monitoring board or advisory board with GSK, AstraZeneca, Novartis, Roche, Merck, Trevi, Rickett-Beckinson, Nocion, Shionogi and Clean Breathing Institute supported by Haleon. C. Auffray reports support for the present study from the Innovative Medicines Initiative. Y. Badi reports support for the present study from the Innovative Medicines Initiative. P. Bakke reports payment or honoraria for lectures, presentations, manuscript writing or educational events from AstraZeneca, GSK and Sanofi. C. Brightling reports support for the present study from the ATLANTIS study (Chiesi grant) and Leicester NIHR BRC, grants from 4D Pharma, Areteia, AstraZeneca, Chiesi, Genentech, GSK, Mologic, Novartis, Regeneron Pharmaceuticals, Roche and Sanofi, and consultancy fees from 4D Pharma, Areteia, AstraZeneca, Chiesi, Genentech, GSK, Mologic, Novartis, Regeneron Pharmaceuticals, Roche and Sanofi. P. Chanez reports grants from ALK, AstraZeneca, Boehringer Ingelheim, Chiesi, GSK, Menarini, Novartis and Sanofi Aventis, consultancy fees from ALK, AstraZeneca, Boehringer Ingelheim, Chiesi, GSK, Menarini, Novartis and Sanofi Aventis, payment or honoraria for lectures, presentations, manuscript writing or educational events from ALK, AstraZeneca, Boehringer Ingelheim, Chiesi, GSK, Menarini, Novartis and Sanofi Aventis, and support for attending meetings from ALK, AstraZeneca, Boehringer Ingelheim, Chiesi, GSK, Menarini, Novartis and Sanofi Aventis. B. De Meulder reports support for the present study from the Innovative Medicines Initiative. R. Djukanovic reports consultancy fees from Synairgen plc, GSK, ZenasBio and Celltrion, leadership role as Chair of the European Respiratory Society's clinical research collaboration on severe asthma (SHARP), and stock (or stock options) with Synairgen plc. L. Fabbri reports consultancy fees from Chiesi Farmaceutici and AstraZeneca, payment or honoraria for lectures, presentations, manuscript writing or educational events from Chiesi Farmaceutici, AstraZeneca, GSK, Alfasigma and Novartis, support for attending meetings from Chiesi Farmaceutici, GSK and Novartis, and participation on a data safety monitoring board or advisory board with Novartis and Chiesi. S.J. Fowler reports grants from the NIHR, and payment or honoraria for lectures, presentations, manuscript writing or educational events from Boehringer Ingelheim. P. Howarth reports employment with GSK. J. Kolmert reports consultancy fees from Gesynta Pharma AB and Lipum AB. M. Kraft reports grants from the NIH, American Lung Association, Synairgen, Janssen, AstraZeneca and Sanofi, consultancy fees from AstraZeneca, Sanofi, Chiesi, GSK, Kinaset and Genentech, payment or honoraria for lectures, presentations, manuscript writing or educational events from Chiesi, support for attending meetings from the European Respiratory Society, one patent issued and tiled filed to development of therapeutics for inflammatory lung disease as CoFounder and Chief Medical Officer, RaeSedo, Inc., participation on a data safety monitoring board or advisory board with ALung, leadership role with the National Heart, Lung and Blood Advisory Council, stock (or stock options) with RaeSedo, Inc. (equity ownership), and the following financial (or non-financial) interests: Section Editor of UpToDate. A.H. Maitland-van der Zee reports grants from Health Holland, GSK, Boehringer Ingelheim and Vertex, consultancy fees from Boehringer Ingelheim and AstraZeneca, payment or honoraria for lectures, presentations, manuscript writing or educational events from GSK, and participation on a data safety monitoring board or advisory board for a study on BPD in neonates. A. Papi reports grants from Chiesi, AstraZeneca, GSK and Sanofi, consultancy fees from Chiesi, AstraZeneca, GSK, Novartis, Sanofi, Iqvia, Avillion, Elpen Pharmaceuticals, Moderna and Roche, payment or honoraria for lectures, presentations, manuscript writing or educational events from Chiesi, AstraZeneca, GSK, Menarini, Zambon, Mundipharma, Sanofi, Edmond Pharma, Iqvia, Avillion, Sanofi and Regeneron, participation on a data safety monitoring board or advisory board with Chiesi, AstraZeneca, GSK, Novartis, Sanofi, Iqvia, Avillion, Elpen Pharmaceuticals and Moderna, receipt of equipment, materials, drugs, medical writing, gifts or other services from Consorzio Futuro in Ricerca. K. Rabe reports payment or honoraria for lectures, presentations, manuscript writing or educational events from AstraZeneca, Boehringer Ingelheim, Chiesi Pharmaceuticals, Novartis, Sanofi/Regeneron, GSK, Berlin Chemie and Roche Pharma, participation on a data safety monitoring board or advisory board with AstraZeneca, Boehringer Ingelheim, Sanofi/Regeneron and CSL Behring, and leadership roles with the German Center for Lung Research (DZL), German Chest Society (DGP) and American Thoracic Society. D.E. Shaw reports consultancy fees from GSK, AstraZeneca and Novartis, payment or honoraria for lectures, presentations, manuscript writing or educational events from GSK and AstraZeneca, and support for attending meetings from GSK. D. Singh reports consultancy fees from Aerogen, AstraZeneca, Boehringer Ingelheim, Chiesi, Cipla, CSL Behring, EpiEndo, Genentech, GSK, Glenmark, Gossamer Bio, Kinaset Therapeutics, Menarini, Novartis, Orion, Pulmatrix, Sanofi, Synairgen, Teva, Theravance, Biopharma and Verona Pharma. M. van Den Berge reports grants from GSK, Roche, Genentech and Novartis. Y. Guo reports support for the present study from the Innovative Medicines Initiative. S. Wagers reports consultancy fees from King's College Hospital NHS Foundation Trust, Academic Medical Research, AMC Medical Research BV, Asthma UK, Athens Medical School, Boehringer Ingelheim International GmbH, CHU de Toulouse, CIRO, DS Biologicals Ltd, École Polytechnique Fédérale De Lausanne, European Respiratory Society, FISEVI, Fluidic Analytics Ltd, Fraunhofer IGB, Fraunhofer ITEM, GSK Research & Development Ltd, Holland & Knight, Karolinska Institutet Fakturor, KU Leuven, Longfonds, National Heart and Lung Institute, Novartis Pharma AG, Owlstone Medical Limited, PExA AB, UCB Biopharma SPRL, Umeå University, University Hospital Southampton NHS Foundation Trust, Università Campus Bio-Medico di Roma, Universita Cattolica Del Sacro Cuore, Universität Ulm, University of Bern, University of Edinburgh, University of Hull, University of Leicester, University of Loughborough, University of Luxembourg, University of Manchester, University of Nottingham, Vlaams Brabant, Dienst Europa, Imperial College London, Boehringer Ingelheim, Breathomix, Gossamer Bio, AstraZeneca, CIBER, OncoRadiomics, University of Leiden, University of Wurzburg, Chiesi Pharmaceutical, University of Liege, Teva Pharmaceuticals, Sanofi, Pulmonary Fibrosis Foundation and Three Lakes Foundation. P.J. Sterk reports consultancy fees from SME Breathomix, and stock (or stock options) with SME Breathomix. S-E. Dahlen reports grants from AstraZeneca, GSK and Sanofi, consultancy fees from AstraZeneca, Cayman Chemicals, GSK and Regeneron, and payment or honoraria for lectures, presentations, manuscript writing or educational events from AstraZeneca, GSK and Sanofi. I.M. Adcock reports support for the present study from the Innovative Medicines Initiative, grants from GSK, MRC, EPSRC and Sanofi, consultancy fees from GSK, Sanofi, Chiesi and Kinaset, payment or honoraria for lectures, presentations, manuscript writing or educational events from AstraZeneca, Sanofi, Eurodrug and Sunovion, and support for attending meetings from AstraZeneca. S. Siddiqui consultancy fees from AstraZeneca, GSK, CSL Behring, Areteia Therapeutics, ERT Medical, Chiesi and Roche, and payment or honoraria for lectures, presentations, manuscript writing or educational events from GSK, Chiesi and AstraZeneca. P. Montuschi reports support for the present study from the Innovative Medicines Initiative. The remaining authors have no potential conflicts of interest to disclose.

Figures

None
Overview of the study. (q)CT: (quantitative) computed tomography; RAC: radiomultiomic-associated cluster; BMI: body mass index; IGF: insulin-like growth factor; FEF25–75%: forced expiratory flow at 25–75% of forced vital capacity; ECM: extracellular matrix; RV: residual volume; TLC: total lung capacity. See the supplementary material for a full list of definitions of abbreviations of genes, proteins and pathways.
FIGURE 1
FIGURE 1
Scatter dot plots of selected quantitative computed tomography (qCT) parameters and pulmonary function tests across radiomultiomic-associated clusters (RACs) and healthy control subjects (HS). a) Inspiratory wall area average of mean values of right and left lung segmental bronchi standardised by body surface area (WA mean BSA). b) Expiratory lumen area average of median values of right and left lung segmental bronchi (LA median). c) Inspiratory percentage of low attenuation area with CT numbers < −950 HU (LAA −950 HU). d) Inspiratory 15th percentile of the cumulative frequency distribution of CT numbers (percentile 15). e) Expiratory percentage of low attenuation area with CT numbers < −856 HU (LAA −856 HU). f) Expiratory CT lung volume adjusted for the phantom density rods (adjusted CT lung volume). g) Residual volume/total lung capacity (RV/TLC) ratio. h) Pre-bronchodilator forced expiratory volume in 1 s (FEV1) percentage predicted. i) Pre-bronchodilator FEV1/forced vital capacity (FVC) ratio (percentage). Mean±sd or median with interquartile range values are shown depending on data distribution (see tables 1 and 2 and supplementary tables S6 and S7).
FIGURE 2
FIGURE 2
Comparative analysis of U-BIOPRED and ATLANTIS datasets across three analytical techniques. a) Clustering dendrograms of the consensus matrices for U-BIOPRED (left) and ATLANTIS (right) with the number of clusters k=3, illustrating the hierarchical clustering results and relationships between subjects based on their similarity. b) Principal component analysis (PCA) plots for U-BIOPRED (left) and ATLANTIS (right), where the first principal component (PC1) is plotted against the second principal component (PC2). Each dot represents a subject, coloured according to their membership in different quantitative computed tomography (qCT) clusters, highlighting the distribution and separation of subjects within the principal component space. c) Loadings of the used qCT features on PC1 and PC2 for U-BIOPRED (left) and ATLANTIS (right), showing the contribution and correlation of various qCT features to the principal components, aiding in understanding the underlying factors driving the clustering and separation observed in the subject-level PCA plots.
FIGURE 3
FIGURE 3
Enrichment maps for integrated pathway enrichment analysis in radiomultiomic-associated clusters (RACs). ActivePathways results are represented as enrichment maps, with nodes representing pathways and pathways with many shared genes connected into networks representing broader biological themes. Cytoscape software and the EnrichmentMap app were used to visualise integrated pathway enrichments as networks. Node colours correspond to the enriched pathways according to the supporting omics datasets, based on the scores matrix initially analysed in ActivePathways. See the supplementary material for a full list of definitions of abbreviations of genes, proteins and pathways.
FIGURE 4
FIGURE 4
Modulation of serum proteomic pathways in severe asthma radiomultiomic-associated clusters (RACs). Enrichment scores (ESs) of 25 pathways (rows) are illustrated for subjects (columns) segmented by RACs. For each column, pathway names are shown on the right. Signatures and a list of proteins that represent a subset of pathways are shown in supplementary table S17. Serum proteins are measured by the somaSCAN proteomics and are differentially expressed across RACs (shown at the end of the pathway names for each comparison, e.g. 1vs2). See the supplementary material for a full list of definitions of abbreviations of genes, proteins and pathways.
FIGURE 5
FIGURE 5
Heatmap showing the correlations between serum proteomics pathways and lung function (LF) tests and quantitative computed tomography (qCT) parameters in the three radiomultiomic-associated clusters (RACs). Positive correlations are shown in red; negative correlations are shown in green. See the supplementary material for a full list of definitions of abbreviations of genes, proteins and pathways. See the main text and supplementary table S2 for the definitions and details of the qCT parameters.

Comment in

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