Beneficiaries

Helmholtz Centre for Infection Research
Braunschweig, Germany

Website

www.helmholtz-hzi.de/en

Short Name

HZI

Brief description of institution/company

The Helmholtz Centre for Infection Research (HZI) is a publicly funded research centre with more than 800 employees in research and administration. The focus of the centre lies on infectious diseases, with the main goal in understanding infection pathways and immune responses to develop novel drugs for efficient therapies and treatments of infections.

Scientists

Prof. Dr. Jochen Huehn

Department

Experimental Immunology

Phone

+49 531 6181 3310

Email

jochen.huehn@helmholtz-hzi.de

Website of Lab

www.helmholtz-hzi.de/exim

Role in Consortium

Coordinator, WP leader and Supervisor

Brief CV

since 2008Full Professor for Experimental Immunology (Hannover Medical School) and Head of Department Experimental Immunology (HZI)
2006 - 2008Junior Professor for Immune Regulation, Charité University Medicine Berlin, Germany
2000 - 2006Postdoc at Charité University Medicine Berlin, Germany
1996 - 2000PhD thesis at Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
1991 - 1996Undergraduate training in Biochemistry/Molecular Biology, University of Hamburg, Germany

Selected Awards

2007Langener Science Award
2007Wolfgang Schulze Award for Rheumatism Research
2002Avrion Mitchison-Award for Rheumatism Research

Keywords Research Activities

  • Epigenetic control of immune cell development
  • Thymic T cell development
  • Peripheral T cell differentiation
  • Foxp3+ regulatory T cells
  • Impact of infection and inflammation on plasticity of T cell subsets

Key publications or research/innovation products

  1. Yang BH, Floess S, Hagemann S, Deyneko IV, Groebe L, Pezoldt J, Sparwasser T, Lochner M, Huehn J (2015). Development of a unique epigenetic signature during in vivo Th17 differentiation. Nucleic Acids Res. 43:1537-1548.
  2. Miyao T, Floess S, Setoguchi R, Luche H, Fehling HJ, Waldmann H, Huehn J, Hori S (2012) Plasticity of Foxp3+ T cells reflects promiscuous Foxp3 expression in conventional T cells but not reprogramming of regulatory T cells. Immunity 36:262-275.
  3. Huehn J, Polansky JK, Hamann A (2009) Epigenetic control of FOXP3 expression: the key to a stable regulatory T-cell lineage? Nat Rev Immunol 9:83-89.
  4. Lahl K, Loddenkemper C, Drouin C, Freyer J, Arnason J, Eberl G, Hamann A, Wagner H, Huehn J*, Sparwasser T* (2007) Selective depletion of Foxp3+ regulatory T cells induces a scurfy-like disease. J Exp Med 204:57-63. *equal contribution
  5. Floess S, Freyer J, Siewert C, Baron U, Olek S, Polansky J, Schlawe K, Chang HD, Bopp T, Schmitt E, Klein-Hessling S, Serfling E, Hamann A, Huehn J (2007) Epigenetic control of the foxp3 locus in regulatory T cells. PLoS Biol 5:e38.

Prof. Dr. Michael Meyer-Hermann

Department

Systems Immunology

Email

michael.meyer-hermann@helmholtz-hzi.de

Website of Lab

www.systems-immunology.de

Role in Consortium

Training and Secondments

Brief CV

since 2010Full Professor at the Faculty of Life Sciences (University of Technology, Braunschweig) and Head of the Department of Systems Immunology (HZI)
2005 - 2010Fellow at the Frankfurt Institute for Advanced Studies (FIAS), Goethe-University, Frankfurt/Main, Germany
2003 - 2005Research fellow at the Centre for Mathematical Biology, Mathematical Institute, Oxford University, UK
1998 - 2003Head and initiator of the Research Group "Theoretical Biophysics" and "Assistent" at the Institute for Theoretical Physics of the Dresden University of Technology, Germany
1994 - 1998PhD in Quantum Field Theory at the Institute for Theoretical Physics of the Goethe-University Frankfurt/Main
1988 - 1994Undergraduate training in Theoretical Phyics, Mathematics, and Philosophy at the Goethe-University Frankfurt/Main, Germany, and at the University Pierre et Marie Curie Paris, France.

Selected Awards

2009Offer (Ruf): W3-position at the Helmholtz Centre for Infection Research and the Braunschweig University of Technology
2009Offer (Ruf): W2-position at Hans-Knöll-Institute and Jena University
2006ALTANA-Award (500k€) for fundamental research in Theoretical Immunology
2003EU Marie-Curie Fellowship
1994Award of the WE-Heraeus-Foundation

Keywords Research Activities

  • Mathematical modelling of biological systems
  • Adaptive immune responses (B and T cells)
  • Viral and bacterial infections
  • Metabolic and neurodegenerative dysfunction
  • Interactions of the Neuro-Endocrine-Immune-System

Key publications or research/innovation products

  1. Hernandez-Vargas EA, Wilk E, Canini L, Toapanta FR, Binder S, Uvarovskii A, Ross TM, Guzman C, Perelson* AS, Meyer-Hermann* M (2014). The effects of aging on influenza virus infection dynamics. J Virol 88: 4123-4131 [*shared corresponding author].
  2. Zhang* Y, Meyer-Hermann* M, George L, Khan M, Figge MT, Falciani F, Kosco-Vilbois M, Toellner K-M (2013). Germinal centre B cells govern their own fate via antibody feedback. J Exp Med 210: 457-464. [*shared first author]
  3. Meyer-Hermann M, Mohr E, Pelletier N, Zhang Y, Victora GD, Toellner K-M (2012). A theory of germinal center B cell selection, division and exit. Cell Reports 2: 162-174.
  4. Victora GD, Schwickert TA, Fooksman DR, Meyer-Hermann M, Dustin ML, Nussenzweig MC (2010). Germinal center selection mechanism revealed by multiphoton microscopy using a photoactivatable fluorescent reporter. Cell 143: 592-605.
  5. Garin* A, Meyer-Hermann* M, Contie M, Figge MT, Buatois V, Gunzer M, Toellner K-M, Elson G, Kosco-Vilbois MH (2010). Toll-Like Receptor 4 signaling by Follicular Dendritic Cells is pivotal for germinal center onset and affinity maturation. Immunity 33: 84-95. [*shared first author]

Prof. Dr. Tim Sparwasser

Department

Institute of Infection Immunology, Twincore, a joint venture of MHH/ HZI, Centre for Experimental and Clinical Infection Research

Phone

+49 511 220027 201

Email

sparwasser.office@mh-hannover.de

Website of Lab

http://www.twincore.de/institute/infektionsimmunologie/

Role in Consortium

Supervisor

Brief CV

2008 to dateW3-Professor of Infection Immunology; Director, Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research / Hannover Medical School (MHH)
2008Habilitation, Institute f. Med. Microbiology, Immunology & Hygiene, TU Munich (Supervisor: Prof. Dr. H. Wagner)
2002 - 2008Group leader and specialization in Medical Microbiology (Residency), Institute f. Medical Microbiology
1999 - 2002Howard Hughes Medical Institute (HHMI) Postdoctoral Fellow, Skirball Institute of Biomolecular Medicine, NY University Medical Center, New York
1996 - 1999Internship ("AiP") and Postdoctoral Fellow, Institute f. Med. Microbiology, Immunology & Hygiene, TU Munich
1994 - 1995Human Medicine, Stony Brook University NY; Basel Universitätsmedizin; Ludwig-Maximilian-University Munich
1989 - 1994Human Medicine, Johannes Gutenberg University Mainz

Selected Awards

1999 - 2002HHMI Postdoctoral Fellowship Award for Physicians
1999DGHM Young Investigator Award (German Society of Microbiology & Hygiene)
1989 - 1995German National Academic Foundation (Studienstiftung des dt. Volkes)

Keywords Research Activities

  • TLRs, pattern recognition receptors
  • Dendritic Cells
  • Vaccination
  • Regulatory T Cells

Key publications or research/innovation products

  1. Lochner, M., L. Berod, and T. Sparwasser. 2015. Fatty acid metabolism in the regulation of T cell function. Trends Immunol 36:81-91.
  2. Berod, L., C. Friedrich, A. Nandan, J. Freitag, S. Hagemann, K. Harmrolfs, A. Sandouk, C. Hesse, C.N. Castro, H. Bahre, S.K. Tschirner, N. Gorinski, M. Gohmert, C.T. Mayer, J. Huehn, E. Ponimaskin, W.R. Abraham, R. Muller, M. Lochner, and T. Sparwasser. 2014. De novo fatty acid synthesis controls the fate between regulatory T and T helper 17 cells. Nat Med 20:1327-1333.
  3. Arnold-Schrauf, C., M. Dudek, A. Dielmann, L. Pace, M. Swallow, F. Kruse, A.A. Kuhl, B. Holzmann, L. Berod, and T. Sparwasser. 2014. Dendritic cells coordinate innate immunity via MyD88 signaling to control Listeria monocytogenes infection. Cell Rep 6:698-708.
  4. Pace, L., A. Tempez, C. Arnold-Schrauf, F. Lemaitre, P. Bousso, L. Fetler, T. Sparwasser, and S. Amigorena. 2012. Regulatory T cells increase the avidity of primary CD8+ T cell responses and promote memory. Science 338:532-536.
  5. Lahl, K., C. Loddenkemper, C. Drouin, J. Freyer, J. Arnason, G. Eberl, A. Hamann, H. Wagner, J. Huehn, and T. Sparwasser. 2007. Selective depletion of Foxp3+ regulatory T cells induces a scurfy-like disease. J Exp Med 204:57-63.

University College London
UK

Website

www.ucl.ac.uk

Short Name

UCL

Brief description of institution/company

University College London is ranked fourth in the QS World University Rankings 2013/14 and is the top-rated University in the UK for research strength. The project will be hosted within the newly founded UCL Institute of Immunity & Transplantation, which has major strengths in immune tolerance and immunotherapy and provides an outstanding research and training environment. The mission of the Institute is to foster cutting-edge immunology research with the aim of providing improved diagnosis and treatment of diseases.

Scientists

Prof. Lucy S.K. Walker

Department

Institute of Immunity & Transplantation

Phone

+44 (0)20 7794 0500

Email

lucy.walker@ucl.ac.uk

Website of Lab

www.lucywalkerlab.com/

Role in Consortium

Deputy coordinator, WP leader and Supervisor

Brief CV

since 2013Professor of Immune Regulation, University College London, UK
2009 - 2012MRC Senior Fellow and Reader in Treg Biology, University of Birmingham, UK
2004 - 2008MRC Career Development Fellow & Senior Lecturer, University of Birmingham, UK
2000 - 2003Wellcome Trust International Prize Travelling Fellowship, UCSF, USA
1998PhD in Immunology, University of Bath, UK
1994Undergraduate Degree in Biology, University of Nottingham, UK

Selected Awards

2012Selected for the Innovators in Diabetes (iDia) programme
2011JDRF National Science Photography Prize
1994Elizabeth and J D Marsden Prize for high distinction

Keywords Research Activities

  • Control of Peripheral T cell activation
  • Costimulation of T cell responses (CD28, CTLA-4)
  • Foxp3+ regulatory T cells
  • T cell cytokine production
  • T cells in autoimmune diabetes

Key publications or research/innovation products

  1. Wang, C., Heuts, F., Ovcinnikovs, V., Wardzinski, L., Bowers, C., Schmidt, E. M., Kogimtzis, A., Kenefeck, R., Sansom, D. M., and Walker, L. S. CTLA-4 controls follicular helper T cell differentiation by regulating the strength of CD28 engagement.
    Proc Natl Acad Sci U S A (2015) 112(2):524-9
  2. Schubert, D., Bode, C., Kenefeck, R., Hou, T., Wing, J., Kennedy A., Bulashevska, A. ..et al, Sakaguchi, S., Walker, L. S*., Sansom, D. M.*, and Grimbacher, B*. Autosomal dominant immune dysregulation syndrome in humans with CTLA-4 mutations. *Joint Senior Authors
    Nature Medicine (2014) 20:1410-1416
  3. Attridge, K., Wang, C. J., Wardzinski, L., Kenefeck, R., Chamberlain, J. L., Manzotti, C., Kopf, M., and Walker, L. S. IL-21 inhibits T cell IL-2 production and impairs Treg homeostasis.
    Blood (2012) 119, 4656-4664
  4. Qureshi, O. S., Zheng, Y., Nakamura, K., Attridge, K., Manzotti, C., Schmidt, E. M., Baker, J., Jeffery, L. E., Kaur, S., Briggs, Z., Hou, T. Z., Futter, C. E., Anderson, G., Walker, L. S., and Sansom, D. M. Trans-endocytosis of CD80 and CD86: a molecular basis for the cell-extrinsic function of CTLA-4.
    Science (2011) 332, 600-603
  5. Walker L.S., Anna Chodos, Mark Eggena, Hans Dooms and Abul K. Abbas. Antigen-specific proliferation of CD4+CD25+ regulatory T cells in vivo.
    Journal of Experimental Medicine (2003) 198(2):249-258

Medical University of Vienna
Austria

Website

www.meduniwien.ac.at

Short Name

MUW

Brief description of institution/company

The Medical University of Vienna (MUW) is the largest medical organisation in Austria and provides Europe's largest hospital, the AKH in Vienna, with all of its medical staff. It employs a staff of 5,000, of which 1,800 are researchers and 1,600 are medical doctors. As one of the largest research centres in Europe, MUW concentrates on a total of five research clusters (including Immunology) and five clinical research fields.

Scientists

Wilfried Ellmeier, PhD, Professor of Immunobiology

Department

Division of Immunobiology, Institute of Immunology

Phone

+43 1 40160 33293

Email

wilfried.ellmeier@meduniwien.ac.at

Website of Lab

www.meduniwien.ac.at/immunologie/ellmeier

Role in Consortium

Training coordinator and Supervisor

Brief CV

since 07/2008Full Professor of Immunobiology
2005 - 2007Associate Professor (a.o.Univ.Prof), Medical University of Vienna
since 2000Group Leader, Institute of Immunology, University of Vienna
1995 - 1999Postdoctoral Fellow (Laboratory of Dan Littman), Skirball Institute, Howard Hughes Medical Institute, New York University Medical Center, New York, NY, USA
1990 - 1994Doctoral studies, University of Vienna, with distinction; PhD Thesis performed at the Institute for Molecular Pathology (IMP) in Vienna
1985 - 1990Studies in Biochemistry, University of Vienna, with distinction

Selected Awards

2012Elected corresponding member of the Austrian Academy of Sciences
2005Novartis prize 2004 in Biology
2001START Prize of the Austrian Science Fund (most prestigious prize in Austria for young scientist; similar to ERC Starting Grant)

Keywords Research Activities

  • Transcriptional control of CD4/CD8 cell fate choice.
  • Transcription factor networks regulating peripheral T cell function
  • Maintenance of T cell lineage identity and integrity
  • Characterization of signaling pathways modulating Th differentiation
  • The role of histone deacetylases in the regulation of T cell-mediated immunity

Key publications or research/innovation products

  1. Boucheron, N, Tschismarov, R, Goeschl, L, Moser, Mirjam, Lagger, S, Sakaguchi, S, Winter, Lenz, F, Vitko, D., Breitwieser, FP, Haust, L, Hassan, H, Bennett, KL, Colinge, J, Schreiner, W, Matthias, P, Egawa, T, Taniuchi, I, Matthias, P, Seiser, C* and Ellmeier, W.* (2014). CD4 T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2. Nature Immunology, 15(5):439-48. (*shared senior-authorship).
  2. Hassan, H., Sakaguchi, S., Tenno, M., Kopf, A., Boucheron, N. Carpenter, A., Egawa, T., Taniuchi, I. Ellmeier, W. (2011) Cd8 enhancer E8I and Runx factors regulate CD8α expression in activated CD8+ T cells. PNAS, 108(45):18330-5
  3. Sakaguchi S, Hombauer M, Bilic I, Naoe Y, Schebesta A, Taniuchi I, Ellmeier, W. (2010). The zinc-finger protein MAZR is part of the transcription factor network that controls the CD4 versus CD8 lineage fate of double-positive thymocytes. Nature Immunology, 11:442-8.
  4. Bilic, I., Kösters, K., Unger, B., Sekimata, M. Hertweck, A., Maschek, R., Wilson, C.B. and Ellmeier, W. (2006). Negative regulation of CD8 expression via CD8 enhancer-mediated recruitment of the zinc finger protein MAZR. Nature Immunology, 7, 392-400.

QIAGEN Aarhus A/S
Aarhus, Denmark

Website

www.clcbio.com/

Short Name

QIAAR

Brief description of institution/company

QIAAR is the worlds leading software provider within software for Next Generation Sequencing data analysis. We employ more than 90 people and our products are used by over 2,000 academic and industrial organizations, including all Top10 Big Pharma and agricultural companies. QIAAR is part of QIAGEN, a Netherlands-based multinational company employing more than 4500 people. QIAGEN is the leading provider of Sample to Insight solutions that transform biological materials into valuable molecular insights including secondary NGS analysis tools developed by QIAAR. All QIAAR product development is carried out in Aarhus, Denmark by a team of more than 60 bioinformaticians, computer scientists and usability experts.

Scientists

Dr. Leif Schauser

Department

Engineering

Phone

+45 36946344

Email

Leif.Schauser@qiagen.com

Website of Lab

www.clcbio.com/

Role in Consortium

Supervisor

Brief CV

since 2013Senior Bioinformatics Scientist, QIAGEN Aarhus A/S, Denmark
2007 - 2013Scientific coordinator, Interdisciplinary Nanoscience Center, Aarhus University, Denmark
2001 - 2007Associate Professor, Bioinformatics Research Center, Aarhus University, Denmark
1998 - 1999Assistant Professor, Institute of Molecular and Structural biology, Aarhus University, Denmark

Keywords Research Activities

  • Metagenomics
  • Bacterial typing
  • Bioinformatics
  • Statistics

Key publications or research/innovation products

  1. Sanggaard KW ... Schauser, L ... Wang J. Spider genomes provide insight into composition function and evolution of venom and silk. Nature Communications 5, 3765
  2. Fredslund J, Madsen LH, Hougaard BK, Sandal N, Stougaard J, Bertioli D, Schauser L. (2006) GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses Nucleic Acids Res. 34:W670-5.
  3. Mailund T, Schierup MH, Pedersen CN, Madsen JN, Hein J, Schauser L. (2006) GeneRecon--a coalescent based tool for fine-scale association mapping. Bioinformatics 22:2317-8.
  4. Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L. (2005) CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 6:252+
  5. Schauser, L., Roussis, A., Stiller, J., and Stougaard, J. (1999) A plant regulator controlling the development of symbiotic root nodules. Nature 401: 191- 195.

Bayer Pharma AG
Wuppertal/Berlin, Germany

Website

www.bayerpharma.de

Short Name

BHC

Brief description of institution/company

Bayer HealthCare Pharmaceuticals is the pharmaceutical division of Bayer HealthCare AG. We market our products in more than 100 countries, and in 2014 generated sales of more than 12 billion. More than 39.000 members of staff currently work for Bayer HealthCare Pharmaceuticals worldwide.

We aim to improve people's quality of life with our products. To achieve this, we concentrate on the research and development of innovative drugs and novel therapeutic approaches. At the same time, we are constantly improving established products. In this context, Bayer HealthCare Pharmaceuticals uses the experience it has gained from over a century in the business.

Bayer drives the strategic development of its research and development capabilities, one of them being Computational Life Sciences (CLS). As a member of the CLS network at Bayer, Clinical Pharmacometrics is responsible for all Modeling & Simulation based activities at Bayer HealthCare Pharmaceuticals from preclinical development through clinical development until life cycle management of marketed pharma products. Our vision is to contribute to quantitatively informed, knowledge-driven, fact-based decision making throughout the whole R&D process. We provide strategic options & solutions for all development projects by application of the specific scientific transfer capabilities of pharmacometrics strategists and the use of all available quantitative computational approaches including among others Systems Biology & Pharmacology and Population Approach Modeling & Simulation.

Scientists

Dr. Jörg Lippert

Department

Clinical Pharmacometrics

Phone

+49 202 36 5036

Email

joerg.lippert@bayer.com

Role in Consortium

Supervisor

Keywords Research Activities

  • Pharmacometrics
  • Systems Biology
  • Systems Pharmacology
  • Preclinical Safety
  • Immunotoxicology

Key publications or research/innovation products

  1. Bayer has a rich research and product development pipeline (http://pharma.bayer.com/en/research-and-development/development-pipeline/pop_up_development_pipeline.php) including T cell targeting agents such as PSMA-BiTe.
  2. Kuepfer, L., Lippert, J., Eissing, T. (2012). Multiscale mechanistic modeling in pharmaceutical research and development. Adv Exp Med Biol 736, 543-561
  3. Lippert, J., Brosch, M., von Kampen, O., Meyer, M., Siegmund, H.U., Schafmayer, C., Becker, T., Laffert, B., Görlitz, L., Schreiber, S., Neuvonen, P.J., Niemi, M., Hampe, J., Kuepfer, L. (2012). A mechanistic, model-based approach to safety assessment in clinical development. CPT Pharmacometrics Syst Pharmacol 1:e13
  4. Eissing, T., Kuepfer, L., Becker, C., Block, M., Coboeken, K., Gaub, T., Goerlitz, L., Jaeger, J., Loosen, R., Ludewig, B., Meyer, M., Niederalt, C., Sevestre, M., Siegmund, H.U., Solodenko, J., Thelen, K., Telle, U., Weiss, W., Wendl, T., Willmann, S., Lippert, J. (2011). A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks. Front Physiol 2:4

Dr. Thomas Steger-Hartmann

Department

Investigational Toxicology

Phone

+49 30 4681 4256

Email

thomas.steger-hartmann@bayer.com

Role in Consortium

Training

Wellcome Trust Sanger Institute
Hinxton, UK

Website

www.sanger.ac.uk

Short Name

Sanger

Brief description of institution/company

The Wellcome Trust Sanger Institute is a charitably funded genomic research centre located in Hinxton, nine miles south of Cambridge in the UK.

A leader in the Human Genome Project, we are now focused on understanding the role of genetics in health and disease. Our passion for discovery drives our quest to uncover the basis of genetic and infectious disease. We aim to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens.

Scientists

Dr. Sarah Teichmann

Department

Teichmann Group

Phone

+44 1223 492520

Email

sarah.teichmann@ebi.ac.uk

Website of Lab

www.teichlab.org

Role in Consortium

WP leader and Supervisor

Brief CV

Since Feb 2013:Research Group Leader, EMBL-European Bioinformatics Institute & Senior Group Leader, Welcome Trust Sanger Institute & Director of Research, Dept Physics/Cavendish Laboratory, Univ. of Cambridge
2006 - 2012:MRC Programme Leader at the MRC Laboratory of Molecular Biology, Cambridge, UK
2001 - 2005:MRC Career Track Programme Leader at the MRC Laboratory of Molecular Biology, Cambridge, UK and Research Fellow of Trinity College, Cambridge
2000 - 2001:Beit Memorial Fellow for Medical Research in the laboratory of Dame Janet Thornton FRS in the Dept of Biochemistry & Molecular Biology, University College London
1996 - 2000:PhD at MRC Laboratory of Molecular Biology and Trinity College, Cambridge, in laboratory of Dr. C. Chothia FRS
1993 - 1996:BA Biochemistry, Trinity College, Cambridge University

Selected Awards

  • Lister Research Prize (2010),
  • Colworth Medal of the Biochemical Society (2011),
  • Crick Lecture of the Royal Society (2012),
  • EMBO Member (2012)
  • Bernhard-Rensch-Lecture, Univ. Munster/Germany (2013)
  • Baranyi Award, Biophysical Society, USA (2015)
  • Fellowship, Academy of Medical Sciences, UK (2015)
  • EMBO Gold Medal (2015)
  • Keywords Research Activities

    • genomics
    • bioinformatics
    • biophysics
    • immunology

    Key publications or research/innovation products

    1. Stubbington, M.J.T., Mahata, B., Svensson, V., Deonarine, A., Nissen, J.K., Betz, A.G., Teichmann, S.A. (2015) An Atlas of mouse CD4+ T cell transcriptomes. Biology Direct, 6:6394.
    2. Xie, X., Stubbington,, M.J.T., Nissen, J.K., Andersen, K.G., Hebenstreit,, D., Teichmann, S.A. & Betz, A.G. (2015) The regulatory T cell lineage factor Foxp3 regulates gene expression through several distinct mechanisms mostly independent of direct DNA binding. PLoS Genetics, in press.
    3. Buettner, F., Natarajan, K. Casale, P., Proserpio, V., Theis, F.J., Teichmann, S.A., Marioni, J.C., Stegle, O. (2015). Accounting for cell-to-cell heterogeneity in single-cell RNA-Seq data reveals novel structure between cells. Nature Biotech, 33, 55-160.
    4. Mahata B., Zhang X., Kolodziejczyk A.A, Proserpio, V., Haim-Vilmovsky, L., Taylor, A.E., Hebenstreit, D., Dingler, F.A., Moignard, V., Gottgens, B., Arlt, W., McKenzie, A.N.J. & Teichmann, S.A. (2014) Single Cell RNA-Sequencing Reveals T helper Cells Synthesizing Steroids de novo to Contribute to Immune Homeostasis. Cell Reports, 7, 1130-42
    5. Brennecke P., Anders S., Kim J.K. Baying B., Zhang X., Proserpio V., Kolodziejczyk A., Benes V., Teichmann S.A., Marioni J., C., Heisler M.G. (2013) Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods, 10, 1093-5.

    Instituto de Medicina Molecular
    Lisboa, Portugal

    Website

    https://imm.medicina.ulisboa.pt/en

    Short Name

    iMM Lisboa

    Brief description of institution/company

    The Instituto de Medicina Molecular de Lisboa (iMM Lisboa) is a non-profit private research institute affiliated with the University of Lisbon Medical School and located in the campus of the University Hospital of Santa Maria. iMM Lisboa hosts more than 480 researchers working in a broad range of fields that encompass multidisciplinary approaches ranging from basic to clinical and translational research. iMM Lisboa expertise is focused on Cell and Developmental Biology, Immunology, Infection, Neurosciences and Oncobiology.

    Scientists

    Luis Graca, MD DPhil

    Department

    Lymphocyte Regulation

    Phone

    +351 217 999 411

    Email

    lgraca@medicina.ulisboa.pt

    Website of Lab

    https://imm.medicina.ulisboa.pt/en/investigacao/labs/graca-lab/

    Role in Consortium

    Supervisor

    Brief CV

    Since 2013Associate Professor of Immunology, Faculty of Medicine, University of Lisbon
    Since 2005Head of Cellular Immunology Unit, Instituto de Medicina Molecular of Lisboa – iMM Lisboa
    2004 - 2005Postdoc at Telethon Institute for Cjild Health Research, University of Western Australia, Perth
    2002 - 2004Postdoc at Sir William Dunn School of Pathology, University of Oxford, UK
    1998 - 2002DPhil in Immunology at Sir William Dunn School of Pathology, University of Oxford, UK
    1996 - 1997 Medical Internship at Hospital Santa Maria, Lisbon, Portugal

    Selected Awards

    2011NEDAI Prize in Autoimmunity Reseach.
    2010BES National Innovation Award for Heath Technologies.
    2009Prof. Heimburger Award in Coagulation Diseases

    Keywords Research Activities

    • Specialized regulatory T cell subsets
    • Regulation of humoral responses
    • Induction and maintenance of immune tolerance
    • Allergy and autoimmune diseases
    • Transplantation tolerance

    Key publications or research/innovation products

    1. Oliveira VG, Agua-Doce A, Curotto de Lafaille M, Lafaille JJ, Graca L. (2013) Adjuvant facilitates anti-CD4 mediated immune tolerance to recombinant factor VIII in hemophilia through a Foxp3-independent mechanism that relies on IL-10. Blood. 121:3938-3945.
    2. Monteiro M, Almeida CF, Agua-Doce A, Graca L. (2013) Induced IL-17-producing invariant Natural Killer T cells require activation in presence of TGF-β. J Immunol. 190:805-811.
    3. Duarte J, Carrié N, Oliveira VG, Almeida C, Agua-Doce A, Rodrigues L, Simas P, Mars LT, Graca L. (2012) T cell apoptosis and induction of Foxp3+ regulatory T cells underlie the therapeutic efficacy of CD4-blockade in experimental autoimmune encephalomyelitis. J Immunol. 189:1680-1688.
    4. Wollenberg I, Agua-Doce A, Hernández A, Almeida C, Oliveira V, Faro J, Graca L. (2011) Regulation of germinal centre reaction by Foxp3+ follicular regulatory T cells. J Immunol. 187: 4553-4560.
    5. Monteiro M, Almeida CF, Caridade M, Ribot JC, Duarte J, Agua-Doce A, Wollenberg I, Silva-Santos B, Graca L. (2010) Identification of Regulatory Foxp3+ Invariant NKT Cells Induced by TGF-β. J Immunol. 185: 2157-2163.

    Prof. Dr. Ana E. Sousa

    Department

    Human Immunodeficiency & Immune Reconstitution

    Phone

    +351 217999521

    Email

    asousa@medicina.ulisboa.pt

    Website of Lab

    https://imm.medicina.ulisboa.pt/en/investigacao/labs/sousa/

    Role in Consortium

    Supervisor

    Brief CV

    Since 2003Group Leader - Instituto de Medicina Molecular (iMM), Lisbon
    Since 2013Associate Professor "Agregado"/Principal Investigator, Faculdade de Medicina, Universidade de Lisboa (FMUL)
    Since 2014Director of the Clinical Immunology Laboratory, FMUL
    Since 2014Member of the Plenary Council of the Portuguese National Ethical Committee for Clinical Research
    2009 - 2012President of the Portuguese Society for Immunology
    2000 - 2001Internal Medicine Specialist, University Hospital de Santa Maria, Lisbon
    1996 - 2000PhD thesis - Clinical Immunology - FMUL
    1989 - 1994Internal Medicine Training, University Hospital de Santa Maria, Lisbon

    Selected Awards

    2015NEDAI Award in Research in Autoimmunity, NEDAI/Portuguese Society of Internal Medicine
    2008Pfizer Award in Clinical Research, Lisbon Society of Medical Sciences
    2005Bristol-Myers Squibb Research Award in Infection by virus of Human Immunodeficiency, Portuguese Association for AIDS Clinical Research

    Keywords Research Activities

    • Human T cell biology
    • Human T cell development
    • HIV/AIDS immunopathogenesis – HIV-2 infection
    • Primary Immunodeficiencies
    • Immune Reconstitution

    Key publications or research/innovation products

    1. Caramalho I, V Nunes-Silva, AR Pires, C Mota, AI Pinto, H Nunes-Cabaço, RB Foxall, AE Sousa. (2015) Human regulatory T-cell development is dictated by Interleukin-2 and -15 expressed in a non-overlapping pattern in the thymus. J Autoimmun 56:98-110.
    2. Markert ML, JG Marques, B Neven, BH Devlin, EA McCarthy, IK Chinn, AS Albuquerque, SL Silva, C Pignata, G de Saint Basile, RM Victorino, C Picard, M Debre, N Mahlaoui, A Fischer, and AE Sousa. (2011) First use of thymus transplantation therapy for FOXN1 deficiency (nude/scid): a report of two cases. Blood 117:688-96.
    3. Nunes-Cabaço H, Caramalho I, Sepúlveda N and Sousa AE. (2011) Differentiation of human thymic regulatory T cells at the double positive stage. Eur J Immunol; 41, 3604-3614
    4. Azevedo R.I., M.V. Soares, J.T. Barata, R. Tendeiro, A. Serra-Caetano, R.M.M. Victorino, A.E. Sousa. (2009) "IL-7 sustains CD31 expression in human naive CD4+ T cells and preferentially expands the CD31+ subset in a PI3K-dependent manner". Blood 113:2999-3007.
    5. Sousa, AE, J Carneiro, M Meier-Schellersheim, Z Grossman, RM Victorino (2002) CD4 T cell depletion is linked directly to immune activation in the pathogenesis of HIV-1 and HIV-2 but only indirectly to the viral load. J Immunol 169:3400-06.

    Babraham Institute
    Cambridge, UK

    Website

    www.babraham.ac.uk

    Short Name

    BI

    Brief description of institution/company

    The Babraham Institute is a publicly funded world-class research institution, situated at the heart of the Babraham Research Campus, near Cambridge. Our mission is to be an international leader in research focusing on basic cell and molecular biology. Our research addresses fundamental biological questions of how cells and organisms develop and respond to the environment. The Institute's research is supported by strategic funding from the Biotechnology and Biological Sciences Research Council who fund our four core areas of research: epigenetics, lymphocyte signalling, nuclear dynamics and signalling.

    Scientists

    Dr. Michelle Linterman

    Department

    Lymphocyte Signalling and Development

    Phone

    +44 1223 496515

    Email

    michelle.linterman@babraham.ac.uk

    Website of Lab

    www.babraham.ac.uk/our-research/lymphocyte/michelle-linterman

    Role in Consortium

    WP leader and Supervisor

    Brief CV

    since 2013Group leader Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
    since 2013College Lecturer in Biology, Churchill College, University of Cambridge, UK
    2009 - 2013Post-doctoral Research Fellow, University of Cambridge, Cambridge, UK
    2006 - 2009PhD. The Australian National University, Canberra, Australia
    2005Honours Degree (First class). The Australian National University, Canberra Australia
    2001 - 2004BBMedSc. Victoria University, Wellington, New Zealand

    Selected Awards

    2010Raymond & Beverly Sackler Junior Research Fellowship
    2010NH&MRC Overseas Biomedical Post-Doctoral Fellowship
    2009EMBO Long-Term Post-Doctoral Fellowship
    2009The Frank Fenner Medal, The John Curtin School of Medical Research
    2009The Dewar Milne Prize in Immunology, The John Curtin School of Medical Research

    Keywords Research Activities

    • The germinal centre response
    • T follicular helper and T follicular regulatory cells
    • Ageing of the immune system

    Key publications or research/innovation products

    1. Linterman MA, Denton AE, Divekar DP, Zvetkova I, Kane L, Clare S, Dougan G, Espéli M, Smith KGC. CD28 expression is required after T cell priming for helper T cell responses and protective immunity to infection. eLife. 2015
    2. Wallin EF, Jolly E, Suchánek O, Bradley JA, Espéli M, Jayne DRW, Linterman MA*, Smith KGC*. Human T-follicular helper and T-follicular regulatory cell maintenance is independent of germinal centers. 2014 (*equal contribution)
    3. Linterman MA, Pierson W, Lee SK, Kallies A, Kawamoto S, Rayner TF, Srivastava M, Divekar DP, Beaton L, Hogan JJ, Fagarasan S, Liston A, Smith KGC*, Vinuesa CG*. Foxp3+ follicular regulatory T cells control the germinal center response. Nature Medicine. 2011 (*equal contribution)
    4. Linterman MA, Beaton L, Yu D, Ramiscal RR, Srivastava M, Hogan JJ, Verma NK, Smyth MJ, Rigby RJ, Vinuesa CG. IL-21 acts directly on B cells to regulate Bcl-6 expression and germinal center responses. Journal of Experimental Medicine. 2010.
    5. Linterman MA, Rigby RJ, Wong RK, Yu D, Brink R, Cannons JL, Schwartzberg PL, Cook MC, Walters GD, Vinuesa CG. Follicular helper T cells are required for systemic autoimmunity. Journal of Experimental Medicine. 2009.

    Dr. Marc Veldhoen

    Department

    Lymphocyte Signalling and Development

    Phone

    +44 1223 496349

    Email

    marc.veldhoen@babraham.ac.uk

    Website of Lab

    www.babraham.ac.uk/our-research/lymphocyte/marc-veldhoen

    Role in Consortium

    WP leader and Supervisor

    Brief CV

    since 2010Group leader (Tenured) Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
    2006 - 2010Senior Investigator Scientist
    National Institute for Medical Research, London, UK
    2003 - 2006Career Development fellow
    National Institute for Medical Research, London, UK
    2000 - 2003PhD thesis at National Institute for Medical Research, London, UK
    1995 - 1999BSc Medical Biology, Faculty of Medicine, Utrecht University, NL

    Selected Awards

    2010EMBO Young investigator award

    Keywords Research Activities

    • Peripheral T cell differentiation
    • Role of AhR in immunity
    • Impact of infection and inflammation on plasticity of T cell subsets
    • Impact of metabolism on T cell differentiation and function
    • Impact of environmental factors on T cell differentiation and function

    Key publications or research/innovation products

    1. Li, Y., Innocentin, S., Withers, D.R., Roberts, N.A., Gallagher, A.R., Grigorieva, E.F., Wilhelm, C., and Veldhoen, M. (2011). Exogenous Stimuli Maintain Intraepithelial Lymphocytes via Aryl Hydrocarbon Receptor Activation. Cell 147, 629-640.
    2. Martin, B., Hirota, K., Cua, D.J., Stockinger, B., and Veldhoen, M. (2009). Interleukin-17-producing gammadelta T cells selectively expand in response to pathogen products and environmental signals. Immunity 31, 321-330.
    3. Veldhoen, M., Uyttenhove, C., van Snick, J., Helmby, H., Westendorf, A., Buer, J., Martin, B., Wilhelm, C., and Stockinger, B. (2008). Transforming growth factor-beta 'reprograms' the differentiation of T helper 2 cells and promotes an interleukin 9-producing subset. Nature immunology 9, 1341-1346.
    4. Veldhoen, M., Hirota, K., Westendorf, A.M., Buer, J., Dumoutier, L., Renauld, J.C., and Stockinger, B. (2008). The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins. Nature 453, 106-109.
    5. Veldhoen, M., Hocking, R.J., Atkins, C.J., Locksley, R.M., and Stockinger, B. (2006). TGFbeta in the context of an inflammatory cytokine milieu supports de novo differentiation of IL-17-producing T cells. Immunity 24, 179-189.

    University of Turku
    Finland

    Website

    www.utu.fi/en

    Short Name

    UTU

    Brief description of institution/company

    The University of Turku (UTU) is a leading Finnish university with internationally acknowledged research and expertise. It promotes interdisciplinary research and provides students with high-quality research-based education. Turku Centre for Biotechnology is a joint department of the University of Turku and Åbo Akademi University, providing high-end technologies and expertise to academic and industrial researchers with focus on discovering molecular events underlying biological function and identifying how this information can be used to improve life quality.

    Scientists

    Prof. Dr. Laura Elo, Research Director

    Department

    Turku Centre for Biotechnology

    Phone

    +358 2 333 8009

    Email

    laura.elo@utu.fi

    Website of Lab

    www.btk.fi/research/research-groups/elo/

    Role in Consortium

    WP leader and Supervisor

    Brief CV

    2014 –Research Director in Bioinformatics, Turku Centre for Biotechnology, University of Turku, Finland
    2013 –Group Leader, Computational Biomedicine Group, University of Turku, Finland (currently 15 members)
    2011 –Adjunct Professor in Biomathematics, University of Turku, Finland
    2009 - 2013 Academy of Finland Postdoctoral fellow
    Postdoctoral work done with Molecular Immunology Group, Prof. Riitta Lahesmaa, Turku Centre for Biotechnology, Finland, and Prof. Benno Schwikowski, Systems Biology Unit, Institut Pasteur, Paris, France
    2008Postdoctoral fellow, Department of Mathematics and Statistics, University of Turku, Finland
    2004 - 2007 PhD Research fellow, Department of Mathematics, University of Turku, and Graduate School in Computational Biology, Bioinformatics, and Biometry, Finland

    Selected Awards

    2013 - 2018 JDRF Career Development Award
    2011Elias Tillandz prize for the best scientific publication in Biocity Turku
    2007Award for the best PhD thesis in Bioinformatics in Finland

    Keywords Research Activities

    • Bioinformatics
    • Computational systems biology of human disease
    • Network-based modeling of human disease development
    • Optimization of statistical modeling of -omics data
    • Data analysis tools for clinical applications towards personalized medicine

    Key publications or research/innovation products

    1. Seyednasrollah F, Laiho A, Elo LL (2015) Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform 16(1):59-70.
    2. Kallionpää H*, Elo LL*, Laajala E*, Mykkänen J, Ricaño-Ponce I, Vaarma M, Laajala TD, Hyöty H, Ilonen J, Veijola R, Simell T, Wijmenga C, Knip M, Lähdesmäki H, Simell O, Lahesmaa R (2014) Innate immune activity is detected prior to seroconversion in children with HLA-conferred type 1 diabetes susceptibility. Diabetes 63(7):2402-14. *equal contribution
    3. Elo LL, Schwikowski B (2013) Analysis of time-resolved gene expression measurements across individuals. PLoS One 8(12):e82340.
    4. Elo LL*, Järvenpää H*, Tuomela S*, Raghav S*, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R (2010) Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity 32(6):852-62. *equal contribution
    5. Laajala E, Aittokallio T, Lahesmaa R, Elo LL (2009) Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol 10(7):R77.

    INSERM (Institut National de la Santé et de la Recherche Médicale)

    Website

    www.cimi-paris.upmc.fr/index.php/en/

    Short Name

    CIMI-Paris, part of INSERM and UPMC

    Brief description of institution/company

    Center of Immunology and Microbial Infections of Paris (CIMI-Paris) is an academic research center with more than 200 researchers and administrative staff. Its goal is to improve our understanding of the immune system in normal and pathological situations, mainly in the field of infectious diseases, inflammation and autoimmunity and to propose innovative vaccines and treatments of these diseases.

    Scientists

    Dr. Benoit Salomon

    Department

    Immunology

    Phone

    +33 1 42 17 74 74 and 01 40 77 97 36

    Email

    benoit.salomon@upmc.fr

    Website of Lab

    www.cimi-paris.upmc.fr/index.php/en/

    Role in Consortium

    Supervisor

    Brief CV

    since 2007Research Director (DR2 Inserm) and team leader of the research group on Treg Biology and Therapy, Inserm and University Pierre et Marie Curie (Paris 6), Paris, France.
    2000 - 2006Research associate (CR1 Inserm) and principal investigator, Inserm and University Pierre et Marie Curie (Paris 6), Paris, France.
    1997 - 2000Postdoc in the lab of Jeffrey Bluestone, University of Chicago, USA.
    1992 - 1996PhD thesis at University Pierre et Marie Curie (Paris 6), Paris, France.
    1989 - 1991Undergraduate student at University Pierre et Marie Curie, Paris, France.
    1985 - 1989Veterinary Medical school, Toulouse, France.

    Selected Awards

    2015Equipe FRM: award from the Fondation de la Recherche Médicale
    2014"Coups d'élan pour la Recherche Française": award from the Bettencourt Schueller Foundation Insitute.

    Keywords Research Activities

    • Foxp3+ regulatory T cells (Treg)
    • Autoimmunity
    • TNF
    • Impact of inflammation on Treg biology
    • Cellular metabolism in Treg

    Key publications or research/innovation products

    1. Zaragoza B, Chen X, Oppenheim JJ, Baeyens A, Gregoire S, Chader D, Miyara M and Salomon BL. Suppressive activity of human Treg cells is maintained in the presence of TNF. Nat Med 2015. In press.
    2. Baeyens A, Saadoun D, Billiard F, Rouers A, Gregoire S, Zaragoza B, Grinberg-Bleyer Y, Marodon G, Piaggio E and Salomon BL. Effector T cells boost regulatory T cell expansion by IL-2, TNF, OX40 and plasmacytoid dendritic cells depending on the immune context. J Immunol. 2015. 194:999-1010.
    3. Fourcade G, BM Colombo, S Grégoire, A Baeyens, L Rachdi, F Guez, V Goffin, R Scharfmann, and BL Salomon. Fetal pancreas transplants are dependent on prolactin for their development and prevent type 1 diabetes in syngeneic but not allogeneic mice. Diabetes. 2013. 62:1646-1655.
    4. Grinberg-Bleyer Y, D Saadoun, A Baeyens, F Billiard, J Goldstein, S Grégoire, G Martin, R Elhage, N Derian, W Carpentier, G Marodon, D Klatzmann, E Piaggio* and B L. Salomon*. Pathogenic T cells have a paradoxical protective effect in murine autoimmune diabetes by boosting Tregs. J Clin Invest. 2010. 120:4558-4568.
    5. Grinberg-Bleyer Y, A Baeyens, S You, R Elhage, G Fourcade, S Gregoire, N Cagnard, W Carpentier, Q Tang, J Bluestone, L Chatenoud, D Klatzmann, BL Salomon* and E Piaggio*. IL-2 reverses established type one diabetes by a local effect on pancreatic regulatory T cells. J Exp Med. 2010. 207:1871-1878.