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Genome Biol. 2016 May 12;17:103. doi: 10.1186/s13059-016-0957-5.

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.

Author information

1
EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.
2
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
3
Department of Physics, University of Naples Federico II, CNR-Spin, Istituto Nazionale di Fisica Nucleare (INFN), Napoli, Italy.
4
Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge, CB3 0HE, UK.
5
Centre for Stem Cells and Regenerative Medicine, Kings College London, London, SE1 9RT, UK.
6
MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
7
Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
8
Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
9
Department of Physics, University of Naples Federico II, CNR-Spin, Istituto Nazionale di Fisica Nucleare (INFN), Napoli, Italy. mario.nicodemi@na.infn.it.
10
EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK. st9@sanger.ac.uk.
11
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. st9@sanger.ac.uk.

Abstract

BACKGROUND:

Differentiation of lymphocytes is frequently accompanied by cell cycle changes, interplay that is of central importance for immunity but is still incompletely understood. Here, we interrogate and quantitatively model how proliferation is linked to differentiation in CD4+ T cells.

RESULTS:

We perform ex vivo single-cell RNA-sequencing of CD4+ T cells during a mouse model of infection that elicits a type 2 immune response and infer that the differentiated, cytokine-producing cells cycle faster than early activated precursor cells. To dissect this phenomenon quantitatively, we determine expression profiles across consecutive generations of differentiated and undifferentiated cells during Th2 polarization in vitro. We predict three discrete cell states, which we verify by single-cell quantitative PCR. Based on these three states, we extract rates of death, division and differentiation with a branching state Markov model to describe the cell population dynamics. From this multi-scale modelling, we infer a significant acceleration in proliferation from the intermediate activated cell state to the mature cytokine-secreting effector state. We confirm this acceleration both by live imaging of single Th2 cells and in an ex vivo Th1 malaria model by single-cell RNA-sequencing.

CONCLUSION:

The link between cytokine secretion and proliferation rate holds both in Th1 and Th2 cells in vivo and in vitro, indicating that this is likely a general phenomenon in adaptive immunity.

KEYWORDS:

Adaptive immunity; CD4+ T cells; Cell cycle; Differentiation; Live imaging; Single-cell RNA-seq

PMID:
27176874
PMCID:
PMC4866375
DOI:
10.1186/s13059-016-0957-5
[Indexed for MEDLINE]
Free PMC Article

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