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STRUGGLE SIGNED

Statistical physics of immune-viral co-evolution

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

STRUGGLE project word cloud

Explore the words cloud of the STRUGGLE project. It provides you a very rough idea of what is the project "STRUGGLE" about.

generation evolutionary individual vaccines statistical population occurring details destroys datasets implications mutational agriculture rhabdoviruses sequencing models outcomes dependence threatening power interactions molecular cross functional binding throughput quantitative antigen emerges virus stochastic infections receptors covers immunity global life body vaccination libraries stimulation experiments phenotypes dynamical predict repertoire infers data viral strains stimulated scales struggle history validate modeling combines strategies immunotherapies viruses receptor co model physics flu characterization immune repertoires escape human constrained fish analyzing screens trout cell informed aids host predictive obtain populations antibodies vaccine evolution

Project "STRUGGLE" data sheet

The following table provides information about the project.

Coordinator	CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS Organization address address: RUE MICHEL ANGE 3 city: PARIS postcode: 75794 website: www.cnrs.fr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	France [FR]
Project website	https://www.phys.ens.fr/
Total cost	1˙909˙750 €
EC max contribution	1˙909˙750 € (100%)
Programme	1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
Code Call	ERC-2016-COG
Funding Scheme	ERC-COG
Starting year	2017
Duration (year-month-day)	from 2017-11-01 to 2022-10-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS Organization address address: RUE MICHEL ANGE 3 city: PARIS postcode: 75794 website: www.cnrs.fr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FR (PARIS)	coordinator	1˙909˙750.00

Map

Project objective

The immune system within each individual host destroys viruses, which manage to escape immunity on the global scale. Recent experiments show population-level responses of both immune repertoires and viruses, and a history dependence of their functional phenotypes. This constrained long-term co-evolution of immune receptor and viral populations is a stochastic many-body problem occurring at many scales, in which the response emerges based on the past states of both the repertoire and viral populations. STRUGGLE infers the details of viral-immune receptor interactions from functional datasets to obtain a predictive statistical model of co-evolution between immune repertoires and viruses.

STRUGGLE covers the many scales of immune-virus interactions: from the molecular level, analyzing high-throughput mutational screens of libraries of antibodies binding a given antigen, through the population-level response of immune repertoires, analyzing next-generation sequencing of vaccine-stimulated whole repertoires, to the population level, modeling the long term co-evolution of both repertoires and viruses.

STRUGGLE combines a statistical data analysis approach with cross-scale many-body physics to: - build a molecular model for antigen-receptor binding; - learn statistical models for repertoire-level response to viral antigen stimulation; - validate dynamical models of interactions between antigen and immune receptors; - theoretically evaluate the predictive power of the immune system and viruses; - and predict virus strains and immune responses based on past infections.

The outcomes of STRUGGLE include the quantitative characterization of the human T-cell response to flu vaccines, with implications for vaccination strategies, and the trout B-cell response to life-threatening rhabdoviruses, which aids vaccine design for fish, with wide use in agriculture. The statistical properties of the co-evolutionary process are needed for informed development of immunotherapies.

Publications

List of publications.
year	authors and title	journal	last update
2019	Serena Bradde, Thierry Mora, Aleksandra M. Walczak Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition published pages: 20180095, ISSN: 0962-8436, DOI: 10.1098/rstb.2018.0095	Philosophical Transactions of the Royal Society B: Biological Sciences 374/1772	2019-05-27
2018	Yuval Elhanati, Zachary Sethna, Curtis G. Callan, Thierry Mora, Aleksandra M. Walczak Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination published pages: 167-179, ISSN: 0105-2896, DOI: 10.1111/imr.12665	Immunological Reviews 284/1	2019-05-27
2018	Pogorelyy, Mikhail V; Minervina, Anastasia A; Chudakov, Dmitriy M; Mamedov, Ilgar Z; Lebedev, Yuri B; Mora, Thierry; Walczak, Aleksandra M Method for identification of condition-associated public antigen receptor sequences published pages: , ISSN: 2050-084X, DOI: 10.1101/195057	eLife 3	2019-04-12
2018	Yuval Elhanati, Zachary Sethna, Curtis G. Callan, Thierry Mora, Aleksandra M. Walczak Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination published pages: 167-179, ISSN: 0105-2896, DOI: 10.1111/imr.12665	Immunological Reviews 284/1	2019-04-13
2018	Pogorelyy, Mikhail V; Minervina, Anastasia A; Shugay, Mikhail; Chudakov, Dmitriy M; Lebedev, Yuri B; Mora, Thierry; Walczak, Aleksandra M Detecting T-cell receptors involved in immune responses from single repertoire snapshots published pages: , ISSN: , DOI:	1	2019-04-13
2018	Armita Nourmohammad, Jakub Otwinowski, Marta Luksza, Thierry Mora, Aleksandra M Walczak Clonal competition in B-cell repertoires during chronic HIV-1 infection published pages: , ISSN: , DOI: 10.1101/271130		2019-04-13
2019	Andreas Mayer,Vijay Balasubramanian, Aleksandra M. Walczak, Thierry Mora How a well-adapting immune system remembers published pages: , ISSN: 1091-6490, DOI: 10.1101/347856	PNAS	2019-04-13
2019	Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora Genesis of the Î±Î² T-cell receptor published pages: e1006874, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1006874	PLOS Computational Biology 15/3	2019-04-13
2018	Mikhail V. Pogorelyy, Anastasia A. Minervina, Maximilian Puelma Touzel, Anastasiia L. Sycheva, Ekaterina A. Komech, Elena I. Kovalenko, Galina G. Karganova, Evgeniy S. Egorov, Alexander Yu. Komkov, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Thierry Mora, Aleksandra M. Walczak, Yuri B. Lebedev Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins published pages: 12704-12709, ISSN: 0027-8424, DOI: 10.1073/pnas.1809642115	Proceedings of the National Academy of Sciences 115/50	2019-04-12
2019	Serena Bradde, Thierry Mora, Aleksandra M. Walczak Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition published pages: 20180095, ISSN: 0962-8436, DOI: 10.1098/rstb.2018.0095	Philosophical Transactions of the Royal Society B: Biological Sciences 374/1772	2019-04-12

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