November 2019 | Samhain 2019

SBI Participation in Major European Research Network

Fri, 1 November 19 18:39

We are delighted to report that UCD researchers are among the largest-ever Innovative Medicine Initiative 2 (IMI2) immunology project which aims to improve disease management of non-responders to therapy across seven immune-mediated diseases.  Prof Walter Kolch and Dr David Gomez led the UCD Systems Biology Ireland participation in the 3TR initiative which kicked off their activities with a first meeting in Granada, Spain from 30th – 31st October 2019.

Autoimmune, inflammatory and allergic diseases are common chronic diseases that significantly affect the wellbeing of millions of people around the globe and pose a substantial burden to healthcare systems. While different treatments are available, response and disease progression in individual patients remain unpredictable. Currently, still too little is known about the molecular basis underpinning these diseases. In order to be able to better predict treatment response and potentially identify novel biomarkers leading to improved patient management and personalised therapy, a deeper understanding of the cellular mechanisms driving disease development is urgently needed.

In a never-before-seen effort to bring together experts from different medical fields, profiling technologies, systems biology and bioinformatics with specialists from innovative SMEs and leading pharmaceutical companies, 3TR – a public-private partnership project under the IMI umbrella – sets out to fundamentally increase our knowledge of the molecular pathways and mechanisms linked to response and non-response to therapy in seven different immune-mediated, allergic and inflammatory diseases: systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease (incl. ulcerative colitis and Crohn’s disease), asthma, and chronic obstructive pulmonary disease. Despite their heterogeneity, recent studies have shown that on the molecular level certain patterns are shared by patients across these diseases, thus suggesting they may also share pathways of response to treatment and disease progression.

A groundbreaking approach: integrated, cross-disease analysis

“For the first time, the 3TR team will align and integrate the analysis of autoimmune, allergic, and inflammatory conditions to identify the relationship between longitudinal molecular and microbiome profiles in blood cells and tissues, and disease paths. In a unique approach we will study the seven diseases both in parallel and jointly”,

explains Marta Alarcón-Riquelme, scientific coordinator of 3TR and Head of Medical Genomics at the GENYO centre at the Fundación Pública Andaluza Progreso y Salud.

“We believe that this high-resolution multi-omics profiling analysis of individualised response to treatment and disease progression will facilitate stratification and identification of molecular patterns that better predict response or non-response to therapy. This comprehensive approach will help identify biomarkers to improve patient management within these diseases.”

Data management and translation into clinics

All data generated within the project will be gathered on a centralised data management platform. The latter will enable detailed and comprehensive, state-of-the-art bioinformatics and biostatistics analyses based on machine learning and dynamic, mechanistic methods.

By involving medical associations in close relationship with patient groups 3TR will also contribute to swiftly translating relevant knowledge and project outcomes into clinics. “3TR has great potential to transform and significantly enhance the management of patients with chronic inflammatory diseases by introducing a scientific evidence-based rationale for treatment selection, rather than following the traditional trial and error approach. This will increase therapeutic success, reduce risks of avoidable side effects in patients unlikely to benefit from the drug they are prescribed, reduce health care costs, but above all: improve the patient’s quality of life”, underlines Dr Pierre Meulien, Executive Director of the Innovative Medicines Initiative (IMI).

Dr David Gomez, principal investigator at UCD Systems Biology Ireland (SBI) described the UCD contribution to this research initative.

“We are involved in the analysis and integration of data available in the consortium, including data from more than 50 clinical trials (existing and new trials that will be performed during the life of the project), and the experiments that are performed in the consortium. The data is generated by clinical and industry partners. In collaboration with other partners, SBI will develop new approaches to use this data to generate computational models that can be used to understand the molecular basis of the 7 diseases that we are studying and identify the commonalities among these diseases. We will use artificial intelligence/machine learning approaches to integrate the data and build in our existing method MiNETi for the integration of OMICs data.  The final aim is to use the predicting power of the computational models to get a better understanding of the molecular mechanisms of these diseases and ultimately new treatment for patients that do not respond to existing therapies."

About 3TR

Taxonomy, Treatment, Targets and Remission. Identification of the Molecular Mechanisms of non-response to Treatments, Relapses and Remission in Autoimmune, Inflammatory, and Allergic Conditions.  An €80.6M 48-month research project coordinated by Fundación Pública Andaluza Progreso y Salud.

3TR brings together 69 partner organisations from 15 European member states including academic and research institutions, small and medium-sized enterprises (SME) and pharmaceutical companies. For a full partner list, please visit:

The project is supported with a funding of over € 80 million from the Innovative Medicines Initiative 2 (IMI2), a joint undertaking of the European Commission and the European Federation of Pharmaceutical Industries and Associations (EFPIA).

Visit the 3TR website:

Follow 3TR on Twitter: @3TR_IMI

About the Innovative Medicines Initiative

The Innovative Medicines Initiative (IMI) is Europe’s largest public-private initiative aiming to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. IMI facilitates collaboration between the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organisations, and medicines regulators. It is a partnership between the European Union (represented by the European Commission) and the European pharmaceutical industry (represented by EFPIA, the European Federation of Pharmaceutical Industries and Associations).

For further information: