| 1 | Yes | KI | | Valentyna Yasinska and Eva Wikström Jonsson | Mass spec measurements by dopinglaboratory at KI + all data from TranSMART | SED, CEW, S. Fowler, Fan, | Ongoing | Draft MS of core data has been circulated in project group; Revision for submission May/June 2022; Data available for more projects |
| 2 | Yes | KI | | Maria Sparreman Mikus (MSM) and Anna James (AJ) | Antibody-based array | SED, CEW, + many + BIOAIR team | Published ERJ 2022 | A wealth of data for more papers |
| 3 | Yes | KI | | Tim Higenbottam, Lars I Andersson (LIA), MSM, AJ | Multiplex screen | IMA, Nazanin Z-K (NZK), | Just started | |
| 4 | Yes | KI | | Toni Checa, CEW | mass spec | | Measurements started | Sample request approved |
| 5 | Yes | KI | | AJ | EIA + Somascan | | Work in progress (WiP) | Ready after the summer |
| 6 | Yes | KI | | AJ | Immunoassays | Kenji Izuhara | WiP | Comparison sputum and blood included |
| 7 | Yes | KI | | Johan Kolmert (JK) | Data TranSMART & Bioair database | SED, CEW + UBIO team | WiP | Ready after the summer |
| 8 | Yes | KI | | JK + Marek Sanak | TranSMART data from the two UPLC-MS-MS | SED, CEW + UBIO team | Not started | Project development Q3/2022; DAP then |
| 9 | Yes | KI | | Johan Kolmert + Dom Shaw (?) | TranSMART | | | Expand to biomarker stability study? Prepared call with key investigators to discuss alternatives |
| 10 | Yes | KI | | Åsa Wheelock et al | TranSMART data | CEW, IMA, SED | 2022 | Several studies? |
| 11 | Yes | KI | | Stacey Reinke, Craig Wheelock | UPLC-MS-MS | | Published ERJ 2022 | |
| 12 | Yes | KI | | Stacey Reinke, Craig Wheelock | UPLC-MS-MS | | | Data acquired but not compiled |
| 13 | Yes | KI | | Johan Kolmert, Lars Andersson, Anna James (Tahmina Ahkter) | TranSMART | | Passive | Add more cohorts? RASP? SoMOSA? PRISM? |
| 14 | Yes | KI | | Anna James, Lars Andersson, Apostolos Bossios | Luminex panel | Fan, SED | Applied for funding | Validation btw cohorts |
| 15 | Yes | KI | | Henric K. Olsson & Adam Platt, AZ | | IMA, SED, LIA, | First bioinformatic screen started Q1/2022 | |
| 16 | Yes | KI | | Maria Sparreman Mikus, Lars I Andersson, Johan Kolmert, Anna James, Nazanin | | | Started Q4/21 | |
| 17 | Yes | ICL | | | Mitochondrial dysfunction |
| Ian Adcock/Fan Chung | Transcriptomic data from 5 compartments, potential to correlate with metabolomic data | Angelica Tioutou, Janice Koranteng, Nazanin ZK | | Link to Metabolites. 1st paper will be sputum (link to TACs) and then epithelial cells. |
| 18 | Yes | ICL | | Ian Adcock | Transcriptomics from all compartments and SomaLogic data in blood and sputum | Piers Dixey, Pank Bhavsar, Nazanin ZK | | DAP complete. Have MSc student to help Piers. |
| 19 | Yes | ICL | | Fan Chung | Sputum Transcriptomics | Angelica/Hisham, Nazanin ZK | Fan currently working on draft | Similar GSVA to recent Allergy paper on macrophages. Need to draft DAP |
| 20 | Yes | ICL | | | Multi-omic microbiome signature |
| Fan Chung | metagenomics data initially but will require other data including metabolomics when screening data is analysed | Ali Versi | Datasets collected, Code written | Based on Wang Z et al., Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease. ISME J. 2020 Nov;14(11):2748-2765. PMID: 32719402 |
| 21 | Yes | ICL | | Fan Chung/ Sanjay Chotimall | Metagenomics data | Ali/Ivan/Nazanin ZK/Sanjay Chotimall | | Need to draft DAP |
| 22 | Yes | ICL | | Paolo Montuschi | HRCT, Blood transcriptomics and proteomics, bronchial biopsy/brushings transcriptomics, sputum transcriptomics and proteomics | Nazanin ZK, Salman Saddiqui, IMA | Blood analysis completed, bronchial sample analysis ongoing focussed on specific remodelling/proliferative pathways | Fast mover project - aim to have draft by June 2022 |
| 23 | Yes | ICL | | Tim Higenbottam, Lars I Andersson (LIA), MSM, AJ | Multiplex screen | IMA, Nazanin Z-K (NZK), | Just started | |
| 24 | Yes | ICL | | Jay Horvat, Lisa Wood, SED, IMA | Women on OCPs have improved asthma. Studies in animals identified GLUT1 and KPM2 as downstream mediators of ER and PR actions. Can this be vaildated in U-BIOPRED and are there sex differences in GLUT1, KPM2, ER and PR expression at the tissue level and are they linked to any SNPs? | Nazanin ZK, Hayley Scott, Olivia Carroll | Just started | Grant submitted in area to Asthma UK and to be submitted to MHMRC |
| 25 | Yes | ICL | | | IL-5 HBEC signature and T2 prediction |
| Ian Adcock | HBEC RNA-seq, clinical data | Ian/Nazanin/Khezia (?) | | DAP is same as used by Stelios for ERJ paper using IL-13 signature |
| 26 | Yes | ICL | | | epithelial cell subtypes in severe asthma |
| Ian Adcock | HBEC RNA-seq, clinical data | Nazanin/Ian | Sumbitted to ICAN | Need to adapt DAP from array analysis |
| 27 | Yes | ICL | | | Dupilumab cross-disease signature |
| Ian Adcock | Transcriptomic data from 5 compartments, sputum and blood SomaLogic data | Yusef Badi, Nazanin ZK | To finalise and send to MB | DAP completed |
| 28 | Yes | ICL | | | IL-33 cross-disease signature |
| Ian Adcock | Transcriptomic data from 5 compartments, sputum and blood SomaLogic data | Yusef Badi, GSK | Under Revision - Allergy | DAP completed |
| 29 | Yes | ICL | | Ian Adcock | DNA and transcriptomic data across 5 compartments (? Also look at pQTLs using SomaLogic data) | Ian Adcock, Sile Hu, Nazanin ZK | IMA to re-work paper | U-BIOPRED dataset not large enough to get significance using standard analysis so will work backwards |
| 30 | Yes | ICL | | | Predictive biomarkers for neutrophilic and eosinophilic asthma |
| Ian Adcock/Fan Chung | Somalogics and Transcriptomics from Sputum & Serum | Keziah/Marc | | DAP completed |
| 31 | Yes | ICL | | Fan Chung | | Nazanin/Fan | | Is the COVID-19 analysis? Need DAP. |
| 32 | Yes | ICL | | Fan Chung | | Nazanin/Martyn | | Has DAP been sent? |
| 33 | Yes | ICL | | | epithelial cell subtypes in severe asthma |
| Ian Adcock | Transcriptomics data from sputum, blood and bronchial brushings/biopsies | Ying Shi, Nazanin ZK | | Need to draft DAP |
| 34 | Yes | ICL | | | Immune cell subtypes in severe asthma |
| Ian Adcock | Transcriptomics data from sputum, blood and bronchial brushings/biopsies | Katie Raby, Ying Shi, Nazanin ZK | | Need to draft DAP |
| 35 | Yes | ICL | | Ian Adcock | Sputum and blood transcriptomics | Ian, Kai Sun, Nazanin ZK | IMA drafting paper | DAP completed. Used ECLIPSE & U-BIOPRED - Validation with Groningen Lifelines cohort |
| 36 | Yes | ICL | | Fan Chung | Transcriptomics data from sputum, blood and bronchial brushings | Woojung, Nazanin ZK | 1st draft being written | DAP completed |
| 37 | Yes | ICL | | Ian/Fan | Transcriptomic, proteomic and clinical data | Nazanin ZK, Jason | Need to re-write paper in light of Allergy Comments | DAP is writen |
| 38 | Yes | ICL | | | Bacterial outgrowths in severe asthma |
| Fan Chung | metagenomics and 16S data | Ali Versi | Ready to submit | BOGs paper |
| 39 | Yes | ICL | | Fan Chung/ Sanjay Chotimall | Metagenomics data | Ali/Ivan/Mahmoud/Sanjay Chotimall | Analysis complete (Sanjay Chotimall at Singapore) | DAP completed |
| 40 | Yes | ICL | | Kasia Hawrylowicz, Paul Lavender, Ian Adcock | sputum, bronchial (biopsies and brushing) and blood transcriptomics and proteomics | Nazanin ZK | RE-write according to AJRCCM comments. Send to JACI | Collaboration with external group to validate work in small clinical study |
| 41 | Yes | ICL | | | Accepted/completed studies |
| | | | | |
| 42 | Yes | ICL | | Fan Chung | Transcriptomic, proteomic and clinical data | Uruj Hoda | Accepted Clinical & Translational Medicine | |
| 43 | Yes | ICL | | | Urinary metabolomic clustering in severe asthma |
| Craig Wheelock/Stacey Reinke | Metabolomic, genetic, transcriptomic, proteomic and clinical data | Ian Adcock, Nazanin ZK | Published ERJ | Extend carnitine clustering analysis to include mitochondrial dysfunction and FFA pathway analysis |
| 44 | Yes | ICL | | | Succinate and KPM2 in asthma |
| Yvonne Jensen-Henniger, Ian Adcock | Sputum, biopsy, brushing and blood transcriptomics. Sputum SomaLogic. | Cheryl van der Wetering, Nazanin ZK | Accepted Redox Biology | Collaboration with external group to validate animal work |
| 45 | Yes | ICL | | Fan Chung | Sputum Transcriptomics | Angelica Tioutou, Yusef Badi, Nazanin ZK | Accepted AJRCCM | Similar GSVA to recent Allergy paper on macrophages |
| 46 | Yes | ICL | | | Agache’s nasal proteomics |
| Mo Shamji, Ioana Agache, Ian Adcock | Sputum, biopsy, brushing and blood transcriptomics. Sputum SomaLogic. Probably only use sputum and blood in final paper | Nazanin ZK, | Under Revision - JACI | Collaboration with external group |
| 47 | Yes | ICL | | Ian Adcock, Emma Gutmann | Transcriptomic data from 5 compartments, sputum and blood SomaLogic data | Yusef Badi, Nazanin ZK | Published JACI | GSVA across diseases and tissues |
| 48 | Yes | ICL | | | U-BIOPRED RNA-seq bronchial data |
| Ian Adcock/Fan Chung | Processing and upload to tranSMART | Nazanin/Ian | Completed | Ready to use |
| 49 | Yes | KI | | Craig Wheelock | mass spectrometry | Johan Kolmet, Antonio Checa | 2022 Q4 | |
| 50 | Yes | KI | | Craig Wheelock | mass spectrometry | Johan Kolmet, Antonio Checa | 2022 Q4 | |
| 51 | Yes | KI | | Craig Wheelock | mass spectrometry | Romanas Chaleckis, Stacey Reinke | 2023 Q1 | |
| 52 | Yes | KI | | Craig Wheelock | mass spectrometry | Romanas Chaleckis, Stacey Reinke | 2023 Q1 | |
| 53 | Yes | KI | | | Urinary eicosanoid clusters |
| Craig Wheelock | mass spectrometry | Johan Kolmet | 2022 Q3 | |
| 54 | Yes | UNICATT | | | Radiomics for severe asthma endotyping |
| Paolo Montuschi, Ian Adcock | HRCT, serum proteomics, bronchial biopsy proteomics and transcriptomics | Nazanin Zounemat Kermanii, Sven-Erik Dahlen, Salman Siddiqui, Giuseppe Macis, Fan Chung, Susan Wilson, whoever wants to join | 31-08-22 | manuscript |
| 55 | Yes | UNICATT | | | Radiomics for severe asthma: relationships with physiological measures |
| Paolo Montuschi, Ian Adcock | HRCT, serum proteomics, urinary metabolomics | Nazanin Zounemat Kermani, Sven-Erik Dahlen, Salman Siddiqui, Giuseppe Macis, Fan Chung, Susan Wilson, whoever wants to join | 31-08-22 | manuscript |
| 56 | Yes | UNICATT | | | Severe asthma: from molecular phenotyping to endotyping |
| Paolo Montuschi, Ian Adcock | all omics platforms | Nazanin Zounemat Kermani, Sven-Erik-Dahlen, Lars Andersson, Giuseppe Santini, Fan Chung, Johan Kolmert, Craig Wheelock, Anna James, Maria Mikus,Steve Fowler, whoever wants to Join | 31-12-22 | data analsyed |
| 57 | Yes | UNICATT | | | Effects of pharmacotherapies on omics profiling in severe asthma |
| Paolo Montuschi, Ian Adcock | all omics platforms | Nazanin Zounemat Kermani, Sven-Erik Dahlen, Fan Chung, Giuseppe Santini, Lars Ansersson, Johan Komert, Craig Wheelock, Anna James, Maria Mikus, Peter Howarth, Sally Worsley, Mohib Uddin, Steve Fowler, whoever wants to join | 31-12-22 | data analysed |
| 58 | Yes | UNICATT | | | Omics profiling in uncontrolled severe asthma |
| Paolo Montuschi, Ian Adcock | all omics platforms | Nazanin Zounemat Kermani, Sven-Erik Dahlen, Fan Chung, Giuseppe Santini, Mario Malerba, Lars Ansersson, Johan Komert, Craig Wheelock, Anna James, Maria Mikus, Peter Howarth, Sally Worsley, Mohib Uddin, Steve Fowler, whoever wants to join | 31-12-22 | data analysed |
| 59 | Yes | KI | | | Clustering of urine eicosanoids |
| Johan Kolmert | Urine eicosanoid profiling | Craig Wheelock, Sven-Erik Dahlén | 2022-10 submission | Manuscript in preparation |
| 60 | Yes | AstraZeneca | | Glenda Lassi, AstraZeneca | Whole geneome sequencing and analysis of genetic association with different U-BIOPRED subject subsets. | AZ: Glenda Lassi, Henric Olsson, Adam Platt; U-BIOPRED: Sven-Erik Dahlén, Ian Adcock, Lars Andersson | Q4 2022 | Analysis ongoing |
| 61 | Yes | ILC + KI+ Tim Higenbottam | | | Importance of the complement pathways in severe asthma of adults - |
| Profs Ian Adcock and Sven-Erick Dahlen plus Tim Higenbottam | Gene set variation analysis (GSVA) was used to determine enrichment scores (ES) of expressed genes involved in the classical, alternative and lectin pathways in blood (n=498), bronchial brushings (n=149) and sputa (n=121) of patients with SA and MMA. Genes overlapping with the alternative pathways were removed. | N. Zounemat-Kermani; Anna James & Maria.Mikus | Abstract submitted to the ERS awainting decision and planning a proteomic paper | |
| 62 | | UU | | | PERCEBEA - PERsonalised data-driven Combination of Exhaled nitric oxide and Blood Eosinophils for Asthma morbidity outcomes |
| Kjell Alving | Exhaled Breath data (FeNO), Lung Function, Anthropometric data, CBC | Tiago Jacinto, Rita Amaral | Project conclusion: 05/2023 | |
| 63 | Yes | AMC | | | A multi-omics approach to delineate asthma inflammatory phenotypes |
| Sputum metagenomics, transcriptomics, proteomics and lipidomics | Mahmoud Ibrahim | Mahmoud Ibrahim, Susanne J. H. Vijverberg, Anne H. Neerincx, Paul Brinkman, Ariane H. Wagener, John H. Riley, Ana R. Sousa, Stewart Bates, Scott S. Wagers, Bertrand De Meulder, Charles Auffray, Åsa M. Wheelock, Aruna T. Bansal, Massimo Caruso, Pascal Chanez, Mohib Uddin, Julie Corfield, Ildiko Horvath, Norbert Krug, Jacek Musial, Kai Sun, Dominick E. Shaw, Thomas Sandström, Paolo Montuschi, Stephen J. Fowler, René Lutter, Ratko Djukanovic, Peter Howarth, Paul Skipp, Marek Sanak, Ian M. Adcock, Kian Fan Chung, Peter J. Sterk, Aletta D. Kraneveld, and Anke H. Maitland-van der Zee | Completed | published in ERJ 2022 |
| 64 | Yes | AMC | | | Association of endopeptidases with microbial aggravation in severe asthma |
| Sputum metagenomics, transcriptomics, and proteomics | Mahmoud Ibrahim/Nazanin Kermani | Mahmoud Ibrahim*, Nazanin Zounemat Kermani*, Anne H. Neerincx, Susanne J. H. Vijverberg, Yike Guo, Peter Howarth, Sven-Erik Dahlen, Ratko Djukanovic, Peter J. Sterk, Aletta D. Kraneveld, Anke H. Maitland-van der Zee, Kian Fan Chung, and Ian M. Adcock | Completed | published in Allergy 2020 |
| 65 | Yes | AMC | | | Association of antibiotic resistance genes with air pollution gene xpression signature |
| sputum metagenomics, and transcriptomics | Mahmoud Ibrahim | Mahmoud Ibrahim, Ali Versi, Fransiskus Xaverius Ivan, Versi Paul Brinkman, Susanne J H Vijverberg, Anne H Neerincx, John H Riley, Stewart Bates, Simone Hashimoto, Nazanin Zounemat Kermani, Kian Ratko Djukanovic, Sven-Erik Dahlén, Peter H Howarth, Peter J Sterk, Aletta D Kraneveld, Ian M Adcock, Sanjay H Chotirmall, Fan Chung, and Anke H Maitland-van der Zee | 2023 | |
| 66 | Yes | AMC | | | Oropharyngeal microbiome-driven clusters in children with asthma/wheezing |
| Oropharyngeal microbiome, and blood transcriptomics | Mahmoud Ibrahim | Mahmoud Ibrahim, Jonathan Thorsen, Simone Hashimoto, Susanne J. H. Vijverberg, Anne H. Neerincx, Paul Brinkman, Wim van Aalderen, Jakob Stokholm, Morten Arendt Rasmussen, Michael Roggenbuck-Wedemeyer, Nadja Hawwa Vissing, Martin Steen Mortensen, Asker Daniel Brejnrod, Louise J. Fleming, Clare S. Murray, Stephen J. Fowler, Urs Frey, Andrew Bush, Florian Singer, Gunilla Hedlin, Björn Nordlund, Dominick E. Shaw, Kian Fan Chung, Ian M. Adcock, Ratko Djukanovic, Charles Auffray, Aruna T. Bansal, Ana R. Sousa, Scott S. Wagers, Bo Lund Chawes, Klaus Bønnelykke,Søren Johannes Sørensen, Aletta D. Kraneveld, Peter J. Sterk, Graham Roberts, Hans Bisgaard, and Anke H. Maitland-van der Zee | 2022 | |
| 67 | Yes | AMC | | | Prediction of asthma exacerbations in adults with severe asthma |
| GWAS | Maria Santana | Maria Santana, Mahmoud Ibrahim, Susanne Vijverberg, Simone Hashimoto, Maria Pino-Yanes, Luciano Gama, Ryan Costa, Camila Figueiredo, Alvaro Cruz, and Anke-Hilse Maitland-van der Zee | 2022 | |
| 68 | Yes | AMC | | | eNose to identiy clusters in U-BIOPRED pediatric cohort |
| eNose platform on breath samples, and blood transcriptomics | Niels Rutjes, Mahmoud Ibrahim, Paul Brinkman | Niels Rutjes*, Mahmoud Ibrahim*, Paul Brinkman, Susanne J. H. Vijverberg, Simone Hashimoto, Louise J. Fleming, Clare S. Murray, Urs Frey, Andrew Bush, Florian Singer, Gunilla Hedlin, Graham Roberts, Stephen J. Fowler, Peter J. Sterk, and Anke H. Maitland-van der Zee | 2023 | |
| 69 | Yes | AMC | | | Validated unbiased clinical clusters of paediatric asthma and wheeze phenotypes |
| Clinical data, lipidomics, transcriptomics | Simone Hashimoto, Paul Brinkman, Graham Roberts | Paediatric U-BIOPRED group | 2023 | submission to ERJ open in June 23 |
| 70 | Yes | AMC | | | Genetic variations associated with exacerbations in children |
| GWAS | Susanne Vijverberg, Paul Brinkman, Simone Hashimoto, Maria Pino-Yanes | Esther Herrera-Luis, Victor E. Ortega, Elizabeth J. Ampleford, Yang Yie Sio, Raquel Granell, Emmely de Roos, Natalie Terzikhan, Ernesto Elorduy Vergara, Natalia Hernandez-Pacheco, Javier Perez-Garcia, Elena Martin-Gonzalez, Fabian Lorenzo-Diaz, Simone Hashimoto, Paul Brinkman, Andrea L. Jorgensen, Qi Yan, Erick Forno, Susanne J. Vijverberg, Ryan Lethem, Antonio Espuela-Ortiz, Mario Gorenjak, Celeste Eng, Ruperto González-Pérez, José M Hernández-Pérez, Paloma Poza-Guedes, Olaia Sardón, Paula Corcuera, Greg A. Hawkins, Annalisa Marsico, Thomas Bahmer, Klaus F. Rabe, Gesine Hansen, Matthias Volkmar Kopp, Raimon Rios, Maria Jesus Cruz, Francisco-Javier González-Barcala, José María Olaguibel, Vicente Plaza, Santiago Quirce, Glorisa Canino, Michelle Cloutier, Victoria del Pozo, Jose R Rodriguez-Santana, Javier Korta-Murua, Jesús Villar, Uroš Potočnik, Camila Figueiredo, Michael Kabesch, Somnath Mukhopadhyay, Munir Pirmohamed, Daniel B. Hawcutt, Erik Melén, Colin N Palmer, Steve Turner, Anke H. Maitland-van der Zee, Erika von Mutius, Juan C. Celedón, Guy Brusselle, Fook Tim Chew, Eugene Bleecker, Deborah Meyers, Esteban G Burchard, Maria Pino-Yanes | Completed | in press PAI 2022 |