Objective The immune system consists of a complex continuum of cell types that communicate with each other and non-immune tissues in homeostasis, and during infections, autoimmunity and cancer. Conventional transcriptional and functional profiling enabled by cell surface marker sorting has revealed a great deal about how specific cell types operate en masse, yet important transcriptional heterogeneity that exists within cell populations remains unexplored. High-throughput single cell RNA-seq can overcome this limitation by profiling entire transcriptomes of thousands of individual cells, revealing cell-to-cell variation by decoding patterns within populations masked in bulk transcriptomes. We will exploit this to dissect the mouse CD4+ T cell compartment, a heterogeneous white blood cell population that initiates adaptive immune responses.In AIM 1, we will chart the dynamics of in vivo CD4+ cell states in mouse before, during and after immune response challenges. By sequencing thousands of single cell transcriptomes, we will map the landscape of CD4+ T cell states in an unbiased, quantitative and comprehensive way. In AIM 2, we will predict key transcription factors, cell surface markers, and signalling molecules, including cytokines/chemokines in each cell state through novel computational approaches. Furthermore, our analyses will establish regulatory modules and networks of gene-gene interactions active in immune responses. In AIM 3, we will (a) confirm the in vivo impact of new cell states by performing adoptive cell transfer assays; and (b) validate our predictions of regulatory molecules and interactions using a massively parallel CRISPR/Cas knockout screen in vitro. This powerful integrated approach combines single cell RNA-sequencing, bioinformatics and genetic engineering to dissect CD4+ T cell states, a central compartment of mammalian adaptive immunity, and reveal basic principles of gene regulation. Fields of science medical and health sciencesbasic medicinepharmacology and pharmacydrug discoverymedical and health scienceshealth sciencesinfectious diseasesmalariamedical and health sciencesmedical biotechnologygenetic engineeringmedical and health sciencesbasic medicineimmunologymedical and health sciencesbasic medicinephysiologyhomeostasis Keywords Single cell genomics bioinformatics T helper cells Programme(s) H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC) Main Programme Topic(s) ERC-CoG-2014 - ERC Consolidator Grant Call for proposal ERC-2014-CoG See other projects for this call Funding Scheme ERC-COG - Consolidator Grant Host institution GENOME RESEARCH LIMITED Net EU contribution € 1 778 456,25 Address WELLCOME SANGER INSTITUTE WELLCOME GENOME CAMPUS HINXTON CB10 1SA SAFFRON WALDEN United Kingdom See on map Region East of England East Anglia Cambridgeshire CC Activity type Research Organisations Links Contact the organisation Opens in new window Website Opens in new window Participation in EU R&I programmes Opens in new window HORIZON collaboration network Opens in new window Total cost € 1 778 456,25 Beneficiaries (2) Sort alphabetically Sort by Net EU contribution Expand all Collapse all GENOME RESEARCH LIMITED United Kingdom Net EU contribution € 1 778 456,25 Address WELLCOME SANGER INSTITUTE WELLCOME GENOME CAMPUS HINXTON CB10 1SA SAFFRON WALDEN See on map Region East of England East Anglia Cambridgeshire CC Activity type Research Organisations Links Contact the organisation Opens in new window Website Opens in new window Participation in EU R&I programmes Opens in new window HORIZON collaboration network Opens in new window Total cost € 1 778 456,25 EUROPEAN MOLECULAR BIOLOGY LABORATORY Germany Net EU contribution € 202 228,75 Address Meyerhofstrasse 1 69117 Heidelberg See on map Region Baden-Württemberg Karlsruhe Heidelberg, Stadtkreis Activity type Research Organisations Links Contact the organisation Opens in new window Website Opens in new window Participation in EU R&I programmes Opens in new window HORIZON collaboration network Opens in new window Total cost € 202 228,75