Funded by the European Union
Quantitative T cell ImmunologyITN (2013-2017)
Grant Lythe (coordinator)
Carmen Molina-Parıs (deputy coordinator)
Jessica Brennan (administrator)
Alex Braithwaite (financial officer)
Mid-term review meetingBioquant, DKFZ Heidelberg, 13 January 2015
Funded by the European Union
QuanTI in a nutshell
Beneficiary Beneficiary name Private sector SME Country Month begin Month end
1 (coordinator) Leeds N N UK 1 48
2 Imperial N N UK 1 48
3 Utrecht N N Netherlands 1 48
4 UMCU N N Netherlands 1 48
5 NKI N N Netherlands 1 48
6 DKFZ N N Germany 1 48
7 Charite N N Germany 1 48
8 Pasteur N N France 1 48
9 INSERM N N France 1 48
10 NUIM N N Ireland 1 48
11 NUIG N N Ireland 1 48
12 BTS Y N Germany 1 48
Number Associated partner name Short name Country Type SME Role in the project
1 Microsoft Research Cambridge Microsoft UK Private N Training, Research, Secondments
2 WEHI WEHI Australia Public N Training, Research, Secondments
3 AstraZeneca AZ UK Private N Training, Research, Secondments
4 Unilever Unilever UK Private N Training, Research, Secondments
5 TalaveraScience Talavera UK Private Y Training
6 Universidad de Vigo Vigo Spain Public N Training, Research
Funded by the European Union
Tour de table
• Becca Asquith, Imperial College London• Jose Borghans, UMC Utrecht• Antonio Freitas, Institut Pasteur• Carmen Molina-Paris, University of Leeds• Benedita Rocha, INSERM• Cathal Seoighe, NUI Galway• Rob de Boer, Universiteit Utrecht• Leila Perie, Nederlands Kanker Instituut• Christophe Niederalt, Bayer Technology Services• Ken Duffy, NUI Maynooth• Thomas Hofer, DKFZ Heidelberg• Max Lohning, Charit Berlin• Michael Davies, AstraZeneca• Cameron MacKay, Unilever• Paul Jonsen, TalaveraScience
Funded by the European Union
Outline
QuanTI
Science
Training
Network
Management
Ethics
Funded by the European Union
Outline
QuanTI
Science
Training
Network
Management
Ethics
Funded by the European Union
Outline
QuanTI
Science
Training
Network
Management
Ethics
Funded by the European Union
Why Quantitative Immunology (QuanTI)?
• Quantitative (or Systems) Immunology is a maturing disciplinethat combines experimental and theoretical approaches to helpunderstand the interplay of immune cells in health and disease.
• In particular, theoretical and computational modelling canhelp to:
(i) anchor mathematical and computational modelling as anessential component of Immunology,
(ii) frame and test hypotheses,(iii) suggest novel experiments allowing for more conclusive and
quantitative interpretations of immunological phenomena,(iv) generate new understanding to manipulate responses in health
and disease, and(v) provide an inter-sectorial initiative to model human immune
responses in health and disease.
Funded by the European Union
Socio-economic perspective: Health is wealth!
• Current challenges to grant everybody’s legitimate wish for along, happy and healthy life.
• Chronic and infectious diseases, pandemic threats andantimicrobial resistance are on the rise.
• Ageing population: the number of people in the EU aged over65 will have grown by 70% by 2050.
• During the first two years of Horizon 2020 (2014-2015), theEU will invest some �200 million in this challenge.
Funded by the European Union
Socio-economic objectives: QuanTI
• Objective 1: develop suitable models towards the 3Rsobjectives of reducing, refining and develop replacementstrategies as alternatives to animal testing, and
• Objective 2: generate new knowledge that will be applied inhealth and medicine, to improve quality of life, ensuring thatthe results of biomedical research will ultimately benefit allcitizens.
Funded by the European Union
Research objectives of QuanTI
• A quantitative approach to immunology to integrate a widerange of biological data and also increase our understandingof immunological processes at all levels of organisation.
• Synthesising models and immunological data poses achallenge that cannot be successfully managed byimmunologists, mathematicians, computer scientists orphysicists on their own.
• Systems Immunology: the dynamics of T cells in the periphery.QuanTI aims to provide a coherent multi-scale framework to:(i) the establishment and diversity of the T cell pool in theperiphery, and (ii) the differentiation programme of T cellpopulations during adaptive immune responses.
Funded by the European Union
Research Work Packages
• Quantification of T lymphocyte dynamics (WP 1).• Quorum sensing of CD4+ T cell populations (WP 2).• Evaluation of CD8+ T cell repertoires (WP 3).• Defining the branch-point between short-lived effector and
long-lived memory T cells (WP 4).• Can T cell signal integration be understood through
competing stochastic processes? (WP 5).• Cytokine memory in T cells (WP 6).
WP WP title Lead participant Other participants
1 Quantification of T lymphocyte dynamics UMCU Imperial and Bayer
2 Quorum sensing of CD4+ T cell populations Pasteur Leeds, Vigo and AstraZeneca
3 Evaluation of CD8+ T cell repertoires INSERM NUI Galway, Leeds, Vigo and Bayer
4 Defining the branch-point between short-lived effector and long-lived memory T cells NIK Utrecht and Bayer
5 Can T cell signal integration be understood through competing stochastic processes? NUI Maynooth WEHI and Unilever
6 Cytokine memory in T cells Charite DKFZ, AstraZeneca and Bayer
Funded by the European Union
Scientific highlights I
• NUI Galway has developed a software package LymAnalyzerto provide comprehensive analysis of next generationsequencing (NGS) data.
• Utrecht has developed stochastic differential equation modelsand branching process models to test four proposedhypotheses of T cell fate commitment.
• UMCU has finished deuterium labelling of three patientspost-stem cell transplantation and started labellingexperiments in antigen-specific T cells.
• NKI has initiated three research projects that aim to deliver anovel technology to understand T cell fate and kinship.
• NUI Maynooth has published in Science, joint with QuanTIassociated partner, WEHI. (2014)
Funded by the European Union
Scientific highlights II
• Imperial College London has obtained a Welcome Trustinvestigator award, to Becca Asquith (2015-2020) £1.5M
• DKFZ publication accepted in Nature (2015). ESR10 isco-author.
• Leeds has submitted a joint grant proposal to the BBSRCIndustrial Partnerships call, with Associated PartnerAstraZeneca (2015). AZ contributes 10% of the total budget.
Funded by the European Union
Outline
QuanTI
Science
Training
Network
Management
Ethics
Funded by the European Union
Training objectives: QuanTI
• to provide an inspiring and supportive environment for thetraining of early stage researchers (ESR) and for the furthertraining of experienced researchers (ER) in QuantitativeImmunology, in a multi-disciplinary and inter-sectorialenvironment,
• to establish a broad programme of challenging researchprojects, that are both multi-disciplinary and inter-sectorialand lead to lasting and fruitful collaborations between thenetwork partners, and
• to organise state-of-the-art scientific and complementarytraining events to provide ITN researchers with backgroundand stimulation for research and to prepare them foremployment both in academia and industry.
Funded by the European Union
Training
Training in the ITN is being delivered through:
1. local supervision,
2. local academic courses,
3. summer schools and workshops delivered specifically fornetwork researchers,
4. secondments,
5. a series of complementary skills training workshops, and
6. visiting scientists.
Funded by the European Union
Training programme
Local training
• Supervisory team (supervisor and co-supervisor).
• Personal career development plan (PCDP).
• Host-based courses for ESRs and ERs.
• Monitoring of progress (according to the codes of the hostand progress report).
Funded by the European Union
Network events 2013-2014
• Inaugural meeting, NUI Maynooth, 29-30 August 2013.
• QuanTI fellows’ meeting, University of Leeds, 5 March 2014.
• QuanTI Annual meeting, NUI Galway, 25 June 2014.
• Complementary skills training workshop, University of Leeds,23- 26 September 2014.
Funded by the European Union
Upcoming network events (open to external participants)
• Winter School: Molecular networks in innate and adaptiveimmunologyDKFZ, Heidelberg, 14-15 January 2015.
• Winter School: Lymphocyte kineticsUtrecht and Unilever, February 2016.
• QuanTI closing conference: disseminate ITN achievements,Leeds, February 2017.
Funded by the European Union
Secondments
• Researchers will undertake, as part of their research projects,study visits to other partner institutions. They will enableresearchers to take advantage of expertise within the ITN.Furthermore, in the case of ESRs, these secondments will berecognised by the host institution of the researcher and counttowards the training required for a PhD.
Funded by the European Union
List of secondments
Fellow Host beneficiary Place of secondment Length Purpose WP number
ESR1 Imperial Bayer 1 month Training in PBPK WP1
ESR1 Imperial UMCU 1 month Training in experimental labelling techniques WP1
ESR1 Imperial Unilever 1 month Inter-sectorial WP1
ESR2 UMCU Imperial 1 month Training in mathematical modelling WP1
ESR2 UMCU Microsoft 1 month Inter-sectorial WP1
ESR3 Bayer Imperial 1 month Training in mathematical modelling WP1
ESR3 Bayer UMCU 1 month Training in cell labelling WP1
ER1 Pasteur Leeds 2 months Training in mathematical modelling WP2
ER1 Leeds AstraZeneca 1 month Inter-sectorial WP2
ESR4 Leeds Unilever 1 month Inter-sectorial WP2
ESR4 Leeds Pasteur 1 month Training in flow cytometry WP2
ER2 INSERM Leeds 1 month Training in statistical data analysis WP3
ER2 INSERM NUI Galway 1 month Training in bio-informatics WP3
ESR5 Leeds NUI Galway 1 month Training in bio-informatics WP3
ESR5 Leeds INSERM 1 month Training in TCR repertoire analysis WP3
ESR5 Leeds Bayer 1 month Inter-sectorial WP3
ESR6 NUI Galway INSERM 1 month Training in TCR repertoire analysis WP3
ESR6 NUI Galway Leeds 1 month Training in mathematical modelling WP3
ESR6 NUI Galway Microsoft 1 month Inter-sectorial WP3
ER3 UU NKI 1 month Training in cellular barcoding WP4
ER3 UU Bayer 1 month Inter-sectorial WP4
ER3 UU NUI Maynooth 1 month Training in bio-informatics WP4
ESR7 NKI UU 1 month Training in mathematical modelling WP4
ESR7 NKI Bayer 1 month Inter-sectorial WP4
ESR7 NKI WEHI 1 month Exchange of experimental techniques WP4
ER4 Bayer UU 1 month Inter-sectorial WP4
ER4 Bayer NKI 1 month Training in cellular barcoding WP4
ER4 Bayer Unilever 1 month Exchange of modelling techniques WP4
ESR8 NUI Maynooth WEHI 1 month Analysis of experimental data WP5
ESR8 NUI Maynooth UU 1 month Exchange of mathematical/computational techniques WP5
ESR8 NUI Maynooth Unilever 1 month Inter-sectorial WP5
ESR9 NUI Maynooth WEHI 1 month Analysis of experimental data WP5
ESR9 NUI Maynooth NKI 1 month Training in cellular barcoding WP5
ESR9 NUI Maynooth AstraZeneca 1 month Inter-sectorial WP5
ESR10 DKFZ Charite 1 month Analysis of experimental data WP6
ESR10 DKFZ Microsoft 1 month Inter-sectorial WP6
ESR10 DKFZ AstraZeneca 1 month Inter-sectorial WP6
ESR11 Charite DKFZ 1 month Training in mathematical modelling WP6
ESR11 Charite Bayer 1 month Inter-sectorial WP6
Funded by the European Union
Complementary skills
Complementary training activities
• Complementary skills training workshop (Leeds, 23-26 Sep2014): Six sessions: Immunology, Presentation skills, Python,Matlab sequence analysis (session given by QuanTI ER,Aridaman Pandit), message in a podcast, programming in R.
• Complementary skills training workshop (to be hosted byMicrosoft Research Cambridge, June 2015).
• Complementary skills training workshop (Unilever): two-dayworkshop. SDDU Leeds and hosted by Unilever.
• Transferable skills and industrial context workshops: Bayer(year 2) and AstraZeneca (year 4).
Funded by the European Union
External training events
ESRs and ERs participate in summer schools, workshops andconferences, when this is judged to be beneficial. Their supervisoris primarily responsible for drawing attention to such events, butQuanTI publicises opportunities by email, through email and viathe website. External training events expose ESRs and ERs toresearch activities in many areas of systems immunology andmathematical biology, and enable them to build contactspotentially leading to further collaborations and careeropportunities, and to disseminate their research through talks andposter presentations.
Funded by the European Union
Visiting scientists have contributed to QuanTI Network events
Bernard Mahon, Paul Moynagh, Shalin Naık, Walt Mankowski,Ines Amado, Arup Chakraborty, Rhodri Ceredig, Benny Chain,Oreste Acuto, Mario Delgado, Hans-Reimer Rodewald andFrederick Graw.
Funded by the European Union
Outline
QuanTI
Science
Training
Network
Management
Ethics
Funded by the European Union
Interaction with private sector
Industrial partner Bayer Technology Services GmbH: RecruitedESR3 (WP1) and recruiting ER4 (WP4). Providing secondmentsfor WP1, WP3, WP4 and WP6. Systems biology softwareplatforms and parallel computing resource.
Associated Partners
• Microsoft Research Cambridge: Secondments for WP1,WP3 and WP6. Virtual Immune System project.
• AstraZeneca: Secondments for WP2, WP5 and WP6.
• Unilever (SEAC): Secondments for WP1, WP2, WP4 andWP5. Chair of advisory board.
• Talavera Science: input in training.
Funded by the European Union
Dissemination and outreach
Examples of dissemination: presentations at conferences
• Stochastic, statistical and computational approaches toimmunology, ICMS Edinburgh (Jul 2013).
• Systems approaches in immunology Santa Fe, USA (Jan 2014).• Ecole de Physique, Les Houches (Mar 2014)• British Society for Immunology, Mathematical Modelling Affinity
Group meetings, Microsoft Research Cambridge (2013 and 2014).• Host-pathogen interactions, University of Hyderabad (Jul 2014).
Funded by the European Union
Dissemination and outreach
Examples of outreach activities
• Berlin’s Lange Nacht der Wissenschaften.
• Science Week event in Dublin’s Botanic Gardens, 9 Nov 2014.
• ESR2 (UMCU) and ER3 (Utrecht) will teach at the JuniorCollege Utrecht, a special college for pupils at secondaryschools with extraordinary capacities in the Sciences.
Funded by the European Union
Outline
QuanTI
Science
Training
Network
Management
Ethics
Funded by the European Union
Recruitment report
• 14 fellows now in post (11 ESRs and 3 ERs).
• The last QuanTI position, ER4 at Bayer, is currentlyadvertised.
Funded by the European Union
Management of the network
Supervisory board meetings
• Maynooth, 30 August 2013.
• Galway, 26 June 2014.
• Heidelberg, 12 January 2015.
Advisory board
Training committee
Finance committee
IPR committee
ESRs forum
Funded by the European Union
Financial aspects
Distribution of financing
• Pre-financing distributed in July 2013.
• Total received in coordinator’s account: 60% of total projectbudget.
• After submission of the Period 1 report at M24, a furtherpayment of 25% of the project budget will be received anddistributed.
• Once final reports submitted at M48, the final 15% will bereceived and distributed based on final total costs per partner.
Funded by the European Union
Financial Reporting
• Form C and justification of resources must be submittedwithin 60 days after M24 and M48.
• Submitted to Coordinator via FORCE in the ResearchParticipants Portal:http://ec.europa.eu/research/participants/portal/desktop/en/home.html
• Coordinator will check costs are correct and within budgetand submit to the EU.
Funded by the European Union
Financial Reporting: flat rates and funding categories
Category 1 Monthly Living Allowanceflat rates: ESR �38,000 year−1 and ER �58,500 year−1.
Category 2 Monthly Mobility AllowanceResearcher without family: �700 × months. With family: �1000 × months.
Category 3 Training and Research, Transfer of Knowledge�1800 × number of months
Category 4 Management Activities. Real cost category
Category 5 Contribution to Overheads 10% of the total expenditure in Categories 1-4
All amounts expressed in the project reports must be in Euros. ForUK partners, the exchange rate is determined using “first workingday of month following end of reporting period” M25, M49. Pay the
Fellows using a conservative exchange rate and then make a top-up payment after the end of the period to ensure
they receive their full allowance.
Funded by the European Union
CFS
Certificate on the Financial StatementsA CFS must be submitted, by each individual beneficiary whereapplicable, if EC contribution in any period is greater than �375k.Only Leeds, NUIM and Bayer will require an audit certificate.
• If �375K level is reached in P1 and remaining budget will notreach �375K again then a CFS is only needed for P1.
• If �375K level is only reached in P2 then a CFS is needed forP1 and P2.
Funded by the European Union
Outline
QuanTI
Science
Training
Network
Management
Ethics
Funded by the European Union
Ethics
All necessary ethical approvals and animal licenses have beenobtained.
