@article {L{\"o}nnberg074971, author = {Tapio L{\"o}nnberg and Valentine Svensson and Kylie R James and Daniel Fernandez-Ruiz and Ismail Sebina and Ruddy Montandon and Megan S. F. Soon and Lily G Fogg and Michael J. T. Stubbington and Frederik Otzen Bagger and Max Zwiessele and Neil Lawrence and Fernando Souza-Fonseca-Guimaraes and William R. Heath and Oliver Billker and Oliver Stegle and Ashraful Haque and Sarah A. Teichmann}, title = {Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation}, elocation-id = {074971}, year = {2016}, doi = {10.1101/074971}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Differentiation of na{\"\i}ve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to multiple levels of heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell RNA transcriptomics and computational modelling of temporal mixtures, we reconstructed the developmental trajectories of Th1 and Tfh cell populations during Plasmodium infection in mice at single-cell resolution. These cell fates emerged from a common, highly proliferative and metabolically active precursor. Moreover, by tracking clonality from T cell receptor sequences, we infer that ancestors derived from the same na{\"\i}ve CD4+ T cell can concurrently populate both Th1 and Tfh subsets. We further found that precursor T cells were coached towards a Th1 but not a Tfh fate by monocytes/macrophages. The integrated genomic and computational approach we describe is applicable for analysis of any cellular system characterized by differentiation towards multiple fates.One Sentence Summary Using single-cell RNA sequencing and a novel unsupervised computational approach, we resolve the developmental trajectories of two CD4+ T cell fates in vivo, and show that uncommitted T cells are externally influenced towards one fate by inflammatory monocytes.}, URL = {https://www.biorxiv.org/content/early/2016/09/13/074971}, eprint = {https://www.biorxiv.org/content/early/2016/09/13/074971.full.pdf}, journal = {bioRxiv} }