Horizon 2020 projects



ZENCODE (Marie Sklodowska Curie Actions - ITN, 2015-2018)

Computational and functional annotation of genomic elements during development of the model vertebrate zebrafish


The recent explosion of next generation sequencing (NGS) data has caught Europe unprepared and led to a critical shortage of computational biology expertise. As NGS methods are expected to become pervasive from basic science to personalised medicine there is an urgent need for highly skilled young scientists trained in both computational biology and experimental wet lab biology. Our network addresses this important problem of the postgenomic era. We aim to provide multi-disciplinary skills for a solid foundation in computational biology and developmental genomics. Developmental genomics is central to understanding of ontogeny and many genetic and congenital anomalies, but was outside the scope of the landmark ENCODE and FANTOM projects. ENCODE highlighted the need for an in vivo vertebrate model that enables high throughput in vivo functional testing of hypotheses generated from genome scale annotation. Zebrafish is an ideal model for extending the scope of genomics to vertebrate development. We aim to comprehensively annotate functional elements, decipher genomic codes of transcription, as well as coding and non-coding gene function during development and enhance zebrafish as an attractive developmental, comparative and disease model. The participants include 7 non-academic members (2 of which are beneficiaries), major zebrafish genomics laboratories, eminent computational biologists and world class genomics technology experts active in FANTOM and ENCODE. The training program involves 15 ESRs, more than 40 intersectoral and interdisciplinary secondments totalling 19 months, 7 training courses and 2 workshops/conferences. The main outcome of this programme is a cohort of researchers with computational, experimental laboratory and transferable skills ready to further their career in academia, public health and the private sector.



University of Birmingham, Birmingham, UNITED KINGDOM (Coordination)

Dr. B. Peers, GIGA-Development, University of Liège, BELGIUM

Imperial College, London, UNITED KINGDOM

Karlsruher Institut für Technologie, Karlsruher, GERMANY

Karolinska Institute Stockholm, Stockholm, SWEDEN

Max Planck Gesellschaft zur Foerderung der Wissenchaften e.v., München, GERMANY

Genome Research Council, London, UNITED KINGDOM

King's College London, London, UNITED KINGDOM

The Institue of Physical and Chemical Research (RIKEN), Saitama, JAPAN

Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, SPAIN




TREGeneration (Health, Demographic Change and Wellbeing, 2015-2019)

Repair of tissue and organ damage in refractory chronic graft versus host disease after hematopoietic stem cell transplantation by the infusion of purified allogeneic donor regulatory T lymphocytes


Our proposal encompasses parallel clinical trials addressing the feasibility and the effectiveness of donor-derived regulatory T cells (Treg) as a therapeutic agent in the treatment and prevention of tissue and organ damage resulting from graft versus host disease (GVHD) after hematopoietic stem cell transplantation (HSCT).
We propose a collaborative clinical study in which Treg therapy for GHVD is the common dominator. However, by bringing together several clinical centers with expertise in this area, we are also having the opportunity to simultaneously address other issues that would not otherwise be addressable by each clinical center on its own. Firstly, by using different Treg preparation strategies, we will be able to determine whether ex vivo isolated Treg are sufficient or whether in vitro expansion and subsequently higher dosages are required. Secondly, we will investigate if sole Treg infusion is effective or if rather co-administration of therapeutic agents that are likely to induce Treg survival and expansion in vivo (rapamycin; IL-2) is required for a successful response to Treg therapy.
The studies on GVHD treatment outcome will be pursued together with a detailed analysis of immune monitoring, comprising T cell receptor clonotype tracking and tissue regeneration markers, in order to further understand the mechanisms underlying the therapeutic and regenerative potential of Treg cells.
Our consortium has developed a concerted approach to the topic of Treg therapy in GVHD. This is a unique opportunity to determine the validity of this cellular immunotherapy approach in GVHD prevention and treatment, with potential for a significant impact on patient quality of life, survival rate and ultimately on the quality of health care provided.



Instituto de Medicina Molecular (IMM), Lisboa, PORTUGAL (Coordination)

F. Baron, GIGA-Infection, Inflammation and Immunity, University of Liège, BELGIUM

Y. Beguin, GIGA-Infection, Inflammation and Immunity, University of Liège, BELGIUM

Max Planck Gesellschaft zur Foerderung der Wissenchaften e.v., München, GERMANY

University of Liverpool, Liverpool, UNITED KINGDOM

GABO:milliarium mbH & Co KG, München, GERMANY

Azienda Ospedaliero Universitaria Policlinico S. Orsola Malpighi, Bologna, ITALY

Alacris Theranostics GmbH, Berlin, GERMANY



BIOCYCLE (Health, Demographic Change and Wellbeing, 2015-2021)

BIOlogical therapy CYCLEs towards tailored, needsdriven, safer and cost-effective management of Crohn's disease


"The BIOCYCLE Project proposes to test and critically assess the benefits and risks of an innovative regimen for improving the treatment of Crohn’s disease (CD), a chronic immune-mediated inflammatory disease affecting the gastro-intestinal tract of an increasing number of patients. Currently, the combination of anti-TNFα monoclonal antibodies and immunosuppressants used without interruption is the gold standard for treating CD. However, long treatments are needed which raise safety concerns and costs. For maintaining the same level of efficacy while reducing risks and costs, the idea of BIOCYCLE is to use a regimen based on ""Treatment Cycles"" characterized by alternating periods where both drugs are administrated and periods where only either anti-TNFα or immunosuppressant is used. The central part of the Project will be a large-scale controlled multi-centric clinical study including 300 patients in EU and USA to test the feasibility of shifting from drugs combination used without interruption (control) to Treatment Cycles (experimental arms). Primary and secondary objectives of the clinical study have already been validated for generating the best qualitative and quantitative data on clinical outcomes, predictors of disease evolution and costs. In parallel, the Project will calculate costs-of-illness associated with the different regimens and will perform surveys among patients, caregivers and healthcare systems representatives to assess their readiness to include/support Treatment Cycles in the clinical practice. This will be the basis of a critical appraisal of Treatment Cycles and guidelines for helping caregivers to decide which treatment regimen best fits the specific needs of their patient. If proven, the benefits of Treatment Cycles for treating CD will be discussed with key-opinion leaders involved in the treatment of other immune-mediated inflammatory chronic diseases to support the evolution of disease-driven treatments towards needs-driven treatments."



Prof. E. louis, Centre Hospitalier Universitaire de Liège (CHU), GIGA, University of Liège, BELGIUM

Université Catholique de Louvain, Louvain La Neuve, BELGIUM

Charity University Medicine Berlin, Berlin, GERMANY

Göteborg University, Göteborg, SWEDEN

University of Edinburgh, Edinburgh, UNITED KINGDOM


Groupe d'Etudes Therapeutiques des Affections Inflammatoires Digestives Association (GETAID), Paris, FRANCE

Skane Lans Landsting (Regionskane), Kristianstad, SWEDEN

Medical research Infr. Development and Health Service fund by the Sheba Medical Center, Ramat Gan, ISRAEL

IBD in Motion GmbH (IBDIM), Vienna, AUSTRIA

Crohn's colitis foundation of America, Inc., New York, USA

Association François Aupetit (AFA), Paris, FRANCE