Identification of the Molecular Mechanisms of non-response to Treatments, Relapses and Remission in Autoimmune, Inflammatory, and Allergic Conditions

Project Information

3TR

Grant agreement ID: 831434

DOI 10.3030/831434

EC signature date 22 August 2019

Start date 1 September 2019

End date 31 August 2026

Funded under

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Total cost € 87 721 177,75

EU contribution € 40 273 191,50

Coordinated by

FUNDACION PUBLICA ANDALUZA PROGRESO Y SALUD M.P.
Spain

Deliverables

Documents, reports (2)

Report on the monitoring strategy adopted
Report on SOPs and templates

Websites, patent fillings, videos etc. (2)

Project Website
Project clip

Publications

Peer reviewed articles (34)

Plasma proteins elevated in severe asthma despite oral steroiduse and unrelated to Type-2 inflammation

Author(s): Maria Sparreman Mikus, Johan Kolmert, Lars I. Andersson, Jörgen Östling, Richard G. Knowles, Cristina Gómez, Magnus Ericsson, John-Olof Thörngren, Payam Emami Khoonsari, Barbro Dahlén, Maciej Kupczyk, Bertrand De Meulder, Charles Auffray, Per S. Bakke, Bianca Beghe, Elisabeth H. Bel, Massimo Caruso, Pascal Chanez, Bo Chawes, Stephen J. Fowler, Mina Gaga, Thomas Geiser, Mark Gjomarkaj, Ildikó
Published in: European Respiratory journal, Issue 13993003, 2022, ISSN 1399-3003
Publisher: European Respiratory Society
DOI: 10.1183/13993003.00142-2021

Development of Core Outcome Measures sets for paediatric and adult Severe Asthma (COMSA)

Author(s): Khaleva, Ekaterina; Rattu, Anna; Brightling, Chris; Bush, Andrew; Bossios, Apostolos; Bourdin, Arnaud; Chung, Kian Fan; Chaudhuri, Rekha; Coleman, Courtney; Dahlén, Sven Erik; Djukanovic, Ratko; Deschildre, Antoine; Fleming, Louise; Fowler, Stephen J.; Gupta, Atul; Hamelmann, Eckard; Hashimoto, Simone; Hedlin, Gunilla; Koppelman, Gerard H.; Melén, Erik; Murray, Clare S.; Pilette, Charles; Porsbj
Published in: EUROPEAN RESPIRATORY JOURNAL, Issue 5, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.00606-2022

Distinct gene dysregulation patterns herald precision medicine potentiality in systemic lupus erythematosus

Author(s): Julius Lindblom, Daniel Toro-Domínguez, Elena Carnero-Montoro, Lorenzo Beretta, Maria Orietta Borghi, Jessica Castillo, Yvonne Enman, PRECISESADS Clinical Consortium, Chandra Mohan, Marta E. Alarcón-Riquelme, Guillermo Barturen, Ioannis Parodis
Published in: Journal of Autoimmunity Volume 136, April 2023, 103025, 2023, ISSN 1095-9157
Publisher: Elsevier
DOI: 10.1016/j.jaut.2023.103025

Core outcome sets, developed collaboratively with patients, can improve the relevance and comparability of clinical trials

Author(s): Alexander G. Mathioudakis, Ekaterina Khaleva, Markus Fally, Paula R. Williamson, Jens-Ulrik Jensen, Tim W. Felton, Chris Brightling, Andrew Bush, Tonya Winders, John Linnell, Valeria Ramiconi, Courtney Coleman, Tobias Welte, Graham Roberts, Jørgen Vestbo
Published in: ERS Journal, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.02107-2022

Transcription Factor Activity Inference in Systemic Lupus Erythematosus

Author(s): Raúl López-Domínguez, Daniel Toro-Domínguez, Jordi Martorell-Marugan, Adrian García-Moreno, Christian H. Holland, Julio Saez-Rodriguez, Daniel Goldman, Michelle Petri, Marta E. Alarcón-Riquelme and Pedro Carmona-Sáez
Published in: Life, Issue 20751729, 2021, ISSN 2075-1729
Publisher: MDPI
DOI: 10.3390/life11040299

Urinary Leukotriene E 4 and Prostaglandin D 2 Metabolites Increase in Adult and Childhood Severe Asthma Characterized by Type 2 Inflammation. A Clinical Observational Study

Author(s): Johan Kolmert, Cristina Gómez, David Balgoma, Marcus Sjödin, Johan Bood, Jon R. Konradsen, Magnus Ericsson, John-Olof Thörngren, Anna James, Maria Mikus, Ana R. Sousa, John H. Riley, Stewart Bates, Per S. Bakke, Ioannis Pandis, Massimo Caruso, Pascal Chanez, Stephen J. Fowler, Thomas Geiser, Peter Howarth, Ildikó Horváth, Norbert Krug, Paolo Montuschi, Marek Sanak, Annelie Behndig, Dominick E
Published in: American Journal of Respiratory and Critical Care Medicine, Issue 203/1, 2021, Page(s) 37-53, ISSN 1073-449X
Publisher: American Thoracic Society
DOI: 10.1164/rccm.201909-1869oc

Molecular characterisation of lupus low disease activity state (LLDAS) and DORIS remission by whole-blood transcriptome-based pathways in a pan-European systemic lupus erythematosus cohort

Author(s): Ioannis Parodis, Julius Lindblom, Guillermo Barturen, Rafaela Ortega-Castro, Ricard Cervera, Jacques-Olivier Pers, Fernanda Genre, Falk Hiepe, Maria Gerosa, László Kovács, Ellen De Langhe, Silvia Piantoni , Georg Stummvoll, Carlos Vasconcelos, Barbara Vigone, Torsten Witte; PRECISESADS Clinical Consortium; Marta E Alarcón-Riquelme, Lorenzo Beretta
Published in: Annals of the Rheumatic Diseases, 2024, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1136/ard-2023-224795

Definitions of non-response and response to biological therapy for severe asthma: a systematic review

Author(s): Ekaterina Khaleva; Anna Rattu; Chris Brightling; Andrew Bush; Arnaud Bourdin; Apostolos Bossios; Kian Fan Chung; Rekha Chaudhuri; Courtney Coleman; Ratko Djukanovic; Sven-Erik Dahlén; Andrew Exley; Louise Fleming; Stephen J. Fowler; Atul Gupta; Eckard Hamelmann; Gerard H. Koppelman; Erik Melén; Vera Mahler; Paul Seddon; Florian Singer; Celeste Porsbjerg; Valeria Ramiconi; Franca Rusconi; Valenty
Published in: "ERJ Open Research, 2023, 9 (3), pp.00444-2022. ⟨10.1183/23120541.00444-2022⟩", Issue 3, 2023, ISSN 2312-0541
Publisher: European Respiratory Society
DOI: 10.1183/23120541.00444-2022

Serum profiling identifies CCL8, CXCL13, and IL-1RA as markers of active disease in patients with systemic lupus erythematosus

Author(s): Julius Lindblom, Lorenzo Beretta, Maria Orietta Borghi, and PRECISESADS Clinical Consortium, Marta E. Alarcón-Riquelme, Ioannis Parodis
Published in: Front Immunol, 2023, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2023.1257085

Risankizumab in severe asthma: A Phase IIa, placebo-controlled study

Author(s): Christopher E. Brightling, Parameswaran Nair, Renaud Louis, Dave Singh
Published in: The New England Journal of Medicine, 2021, ISSN 1533-4406
Publisher: Massachusetts Medical Society
DOI: 10.1056/nejmoa2030880

Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data

Author(s): Manuel Rueda, Ivo C Leist, Ivo G Gut
Published in: J Biomed Inform, 2024, ISSN 1532-0480
Publisher: Elsevier
DOI: 10.1016/j.jbi.2023.104558

Activating Transcription Factor 6 Mediates Inflammatory Signals in Intestinal Epithelial Cells Upon Endoplasmic Reticulum Stress

Author(s): Stephanie T. Stengel, Antonella Fazio, Simone Lipinski, Martin T. Jahn, Konrad Aden, Go Ito, Felix Wottawa, Jan W.P. Kuiper, Olivia I. Coleman, Florian Tran, Dora Bordoni, Joana P. Bernardes, Marlene Jentzsch, Anne Luzius, Sandra Bierwirth, Berith Messner, Anna Henning, Lina Welz, Nassim Kakavand, Maren Falk-Paulsen, Simon Imm, Finn Hinrichsen, Matthias Zilbauer, Stefan Schreiber, Arthur Kaser, Ri
Published in: Gastroenterology, Issue 159/4, 2020, Page(s) 1357-1374.e10, ISSN 0016-5085
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2020.06.088

Current Insights on Biomarkers in Lupus Nephritis: A Systematic Review of the Literature

Author(s): Leonardo Palazzo, Julius Lindblom, Chandra Mohan, Ioannis Parodis
Published in: J. Clin. Med., 2022, ISSN 2077-0383
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/jcm11195759

DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon

Author(s): Antonella Fazio, Dora Bordoni, Jan W. P. Kuiper, Saskia Weber-Stiehl, Stephanie T. Stengel, Philipp Arnold, David Ellinghaus, Go Ito, Florian Tran, Berith Messner, Anna Henning, Joana P. Bernardes, Robert Häsler, Anne Luzius, Simon Imm, Finn Hinrichsen, Andre Franke, Samuel Huber, Susanna Nikolaus, Konrad Aden, Stefan Schreiber, Felix Sommer, Gioacchino Natoli, Neha Mishra & Philip Rosenstiel
Published in: Nature communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33844-2

Tezepelumab and Mucus Plugs in Patients with Moderate-to-Severe Asthma

Author(s): Lars H. Nordenmark, Ph.D., Åsa Hellqvist, M.Sc., Claire Emson, Ph.D., Sarah Diver, M.D., Celeste Porsbjerg, M.D., Ph.D., Janet M. Griffiths, Ph.D., John D. Newell, Jr, M.D., +5, and Christopher E. Brightling, F.Med.Sci.
Published in: NEJM Evidence, 2023, ISSN 2766-5526
Publisher: NEJM group
DOI: 10.1056/evidoa2300135

Glycosylation Alterations in Multiple Sclerosis Show Increased Proinflammatory Potential

Author(s): Ana Cvetko, Domagoj Kifer, Olga Gornik, Lucija Klarić, Elizabeth Visser, Gordan Lauc, James F. Wilson, Tamara Štambuk
Published in: Biomedicines, Issue 8/10, 2020, Page(s) 410, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines8100410

Immune-Related Urine Biomarkers for the Diagnosis of Lupus Nephritis

Author(s): Morell M., Pérez-Cózar F, Marañón C.
Published in: International Journal of Molecular Science, Issue 14220067, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22137143

Stabilization of Human Whole Blood Samples for Multicenter and Retrospective Immunophenotyping Studies

Author(s): Paulina Rybakowska, Catalina Burbano, Sofie Van Gassen, Nieves Varela, Rocío Aguilar‐Quesada, Yvan Saeys, Marta E. Alarcón‐Riquelme, Concepción Marañón
Published in: Cytometry Part A, 2020, ISSN 1552-4922
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.24241

PeacoQC: Peak-based selection of high quality cytometry data

Author(s): Annelies Emmaneel, Katrien Quintelier, Dorine Sichien, Paulina Rybakowska, Concepción Marañón, Marta E. Alarcón-Riquelme, Gert Van Isterdael, Sofie Van Gassen, Yvan Saeys
Published in: Cytometry Part A, Issue 15524930, 2021, Page(s) 325-338, ISSN 1552-4930
Publisher: International Society for Advancement of Cytometry
DOI: 10.1002/cyto.a.24501

Molecular subtypes explain lupus epigenomic heterogeneity unveiling new regulatory genetic risk variants

Author(s): Olivia Castellini-Pérez, Elena Povedano, Guillermo Barturen, Manuel Martínez-Bueno, Andrii Iakovliev, Martin Kerick, Raúl López-Domínguez, Concepción Marañón, Javier Martín, Esteban Ballestar, PRECISEADS Clinical Consortium, PRECISEADS Flow Cytometry Study Group, María Orietta Borghi, Weiliang Qiu, Cheng Zhu, Srinivas Shankara, Athina Spiliopoulou, Emanuele de Rinaldis, Elena Carnero-Mon
Published in: npj Genomic Medicine, Issue 9, 38, 2024, ISSN 2056-7944
Publisher: Springer Nature
DOI: 10.1038/s41525-024-00420-0

HLA-DRB1 and HLA-DQA1 associated with immunogenicity to adalimumab therapy in patients with rheumatoid arthritis

Author(s): Chuan Fu Yap, Nisha Nair, Annick de Vries, Floris C Loeff, Ann W Morgan, John D Isaacs, Anthony G Wilson, Kimme L Hyrich, Anne Barton, Darren Plant
Published in: Ann Rheum Dis., 2024, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1136/ard-2023-223955

Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Author(s): Neha Mishra, Konrad Aden, Johanna I. Blase, Nathan Baran, Dora Bordoni, Florian Tran, Claudio Conrad, Diana Avalos, Charlot Jaeckel, Michael Scherer, Signe B. Sørensen, Silja H. Overgaard, Berenice Schulte, Susanna Nikolaus, Guillaume Rey, Gilles Gasparoni, Paul A. Lyons, Joachim L. Schultze, Jörn Walter, Vibeke Andersen, SYSCID Consortium, Emmanouil T. Dermitzakis, Stefan Schreiber & Philip Ros
Published in: Genome Medicine, 2022, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-022-01112-z

Rare Variants in Systemic Lupus Erythematosus: From Monogenic to Polygenic Disease

Author(s): Ruth D. Rodríguez, Marta E. Alarcón-Riquelme
Published in: Medical Research Archives, 2023, ISSN 2375-1916
Publisher: European Society of Medicine
DOI: 10.18103/mra.v11i10.4363

Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression

Author(s): Daniel Toro-Domínguez, Jordi Martorell-Marugán, Manuel Martinez-Bueno, Raúl López-Domínguez, Elena Carnero-Montoro, Guillermo Barturen, Daniel Goldman, Michelle Petri, Pedro Carmona-Sáez, Marta E Alarcón-Riquelme
Published in: Briefings in Bioinformatics, Issue 14774054, 2022, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbac332

Narrative review to capture patients’ perceptions and opinions about non-response and response to biological therapy for severe asthma

Author(s): Courtney Coleman; Ekaterina Khaleva; Anna Rattu; Betty Frankemölle; Hanna Nielsen; Graham Roberts; Clare Williams
Published in: Crossref, Issue 6, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.00837-2022

Data processing workflow for large-scale immune monitoring studies by mass cytometry

Author(s): Paulina Rybakowska, Sofie Van Gassen, Katrien Quintelier, Yvan Saeys, Marta E. Alarcón-Riquelme, Concepción Marañón
Published in: Computational and Structural Biotechnology Journal, Issue 19, 2021, Page(s) 3160-3175, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2021.05.032

The Potential of Computational Modeling to Predict Disease Course and Treatment Response in Patients with Relapsing Multiple Sclerosis

Author(s): Francesco Pappalardo, Giulia Russo, Marzio Pennisi, Giuseppe Alessandro Parasiliti Palumbo, Giuseppe Sgroi, Santo Motta, Davide Maimone
Published in: Cells, Issue 9/3, 2020, Page(s) 586, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells9030586

Real-world efficacy of treatment with benralizumab, dupilumab, mepolizumab and reslizumab for severe asthma: A systematic review and meta-analysis

Author(s): David Charles, Jemma Shanley, Sasha-Nicole Temple, Anna Rattu, Ekaterina Khaleva, Graham Roberts
Published in: Clinical & Experimental Allergy, Issue 13652222, 2022, Page(s) 616-627, ISSN 1365-2222
Publisher: Britisch Society for Allergy & Clinical Immunology
DOI: 10.1111/cea.14112

Identifying and appraising outcome measures for severe asthma: a systematic review

Author(s): Anna Rattu, Ekaterina Khaleva, Chris Brightling, Sven-Erik Dahlén, Apostolos Bossios, Louise Fleming, Kian Fan Chung, Erik Melén, Ratko Djukanovic, Rekha Chaudhuri, Andrew Exley, Gerard H. Koppelman, Arnaud Bourdin, Franca Rusconi, Celeste Porsbjerg, Courtney Coleman, Clare Williams, Hanna Nielsen, Elizabeth Davin, Phil Taverner, Sofia Romagosa Vilarnau, Graham Roberts on behalf of the 3TR Conso
Published in: ERS Journal, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.01231-2022

Patient Reported Outcomes in Chronic Inflammatory Diseases: Current State, Limitations and Perspectives

Author(s): Florian Tran, Jan Henrik Schirmer, Ilka Ratjen, Wolfgang Lieb, Philip Helliwell, Johan Burisch, Juliane Schulz, Florian Schrinner, Charlot Jaeckel, Ulf Müller-Ladner, Stefan Schreiber, Bimba F. Hoyer
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2021.614653

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Author(s): Joana P Bernardes 1, Neha Mishra 1, Florian Tran 2, Thomas Bahmer 3, Lena Best 4, Johanna I Blase 1, Dora Bordoni 1, Jeanette Franzenburg 5, Ulf Geisen 6, Jonathan Josephs-Spaulding 4, Philipp Köhler 7, Axel Künstner 8, Elisa Rosati 1, Anna C Aschenbrenner 9, Petra Bacher 10, Nathan Baran 1, Teide Boysen 1, Burkhard Brandt 11, Niklas Bruse 12, Jonathan Dörr 6, Andreas Dräger 13, Gunnar Elke 14
Published in: Immunity, Issue 10747613, 2020, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2020.11.017

Stem Cells and Organoid Technology in Precision Medicine in Inflammation: Are We There Yet?

Author(s): Florian Tran, Christine Klein, Alexander Arlt, Simon Imm, Evelyn Knappe, Alison Simmons, Philip Rosenstiel, Philip Seibler
Published in: Frontiers in Immunology, Issue 16643224, 2020, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2020.573562

Tryptophan degradation as a systems phenomenon in inflammation - an analysis across 13 chronic inflammatory diseases

Author(s): Danielle M M Harris, Silke Szymczak, Sven Schuchardt, Johannes Labrenz, Florian Tran, Lina Welz, Hanna Graßhoff, Henner Zirpel, Melike Sümbül, Mhmd Oumari, Nils Engelbogen, Ralf Junker, Claudio Conrad, Diamant Thaçi, Norbert Frey, Andre Franke, Stephan Weidinger, Bimba Hoyer, Philip Rosenstiel, Silvio Waschina, Stefan Schreiber, Konrad Aden
Published in: EBio Medicine, 2024, ISSN 2352-3964
Publisher: Elsevier BV
DOI: 10.1016/j.ebiom.2024.105056

3TR: a pan-European cross-disease research consortium aimed at improving personalised biological treatment of asthma and COPD.

Author(s): Celeste Porsbjerg; Anke H. Maitland-van der Zee; Guy Brusselle; Giorgio Walter Canonica; Alvar Agusti; Rosa Faner; Claus Vogelmeier; Martijn C. Nawijn; Maarten van den Berge; Franca Rusconi; Charles Pilette; Valeria Ramiconi; Courtney Coleman; Rekha Chaudhuri; Kian Fan Chung; Jadwiga A. Wedzicha; Sejla Saglani; Marc P. van der Schee; Liam G Heaney; Arnaud Bourdin; Graham Roberts; Graham Roberts; G
Published in: European Respiratory Journal, 58(4):2102168. EUROPEAN RESPIRATORY SOC JOURNALS LTD, Issue 7, 2021, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.02168-2021

Conference proceedings (2)

Risankizumab in severe asthma: A Phase IIa, placebo-controlled study

Author(s): Brightling, Christopher E.; Nair, Parameswaran; Louis, Renaud; Singh, Dave
Published in: Airway pharmacology and treatment, Issue 1, 2020
Publisher: European Respiratory Society
DOI: 10.1183/13993003.congress-2020.3699

Adapting asthma clinical trials in response to the COVID-19 pandemic - the BenRex study design

Author(s): Smith SJ, Gillespie L, Heaney LG, Brightling CE , McConnachie A¬, Siddiqui S, Mistry V4, Brown V , Jackson DJ, Lee NW, Fowler SJ, Mansur AH, Burhan H, Saralaya D, Kurukulaaratchy R, Nasser S, Pfeffer P, Brown T, Lordan J, Pavord ID, Chaudhuri R.
Published in: European Respiratory Journal, 2021, ISSN 1399-3003
Publisher: European Respiratory Society
DOI: 10.1183/13993003.congress-2021.pa1108