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Mapping Differentiation under Mixed Culture Conditions Reveals a Tunable Continuum of T Cell Fates

Antebi, Yaron E. and Reich-Zeliger, Shlomit and Hart, Yuval and Mayo, Avi and Eizenberg, Inbal and Rimer, Jacob and Putheti, Prabhakar and Pe'er, Dana and Friedman, Nir (2013) Mapping Differentiation under Mixed Culture Conditions Reveals a Tunable Continuum of T Cell Fates. PLoS Biology, 11 (7). Art. No. e1001616. ISSN 1544-9173. https://resolver.caltech.edu/CaltechAUTHORS:20130911-162947914

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PDF (Figure S1. Co-expression of TF and cytokine mRNA under mixed conditions. doi:10.1371/journal.pbio.1001616.s001) - Supplemental Material
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PDF (Figure S2. Correlations between variables that define Th1 and Th2 response at the single cell level. doi:10.1371/journal.pbio.1001616.s002) - Supplemental Material
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PDF (Figure S3. Measured input functions describing the lineage-specific TFs and cytokines show separation of variables. doi:10.1371/journal.pbio.1001616.s003) - Supplemental Material
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PDF (Figure S4. Constant noise level of TFs for different input signals supports gradual response functions. doi:10.1371/journal.pbio.1001616.s004) - Supplemental Material
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PDF (Figure S5. Cytokine secretion pattern follows the intracellular staining. doi:10.1371/journal.pbio.1001616.s005) - Supplemental Material
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PDF (Figure S6 Cytokine secretion pattern continuously changes as a function of input signals. doi:10.1371/journal.pbio.1001616.s006) - Supplemental Material
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PDF (Figure S7. INF-γ and IL-4 secretion after restimulation are two independent random processes. doi:10.1371/journal.pbio.1001616.s007) - Supplemental Material
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PDF (Figure S8. The distribution of one cytokine expression level is independent of the other cytokine expression state. doi:10.1371/journal.pbio.1001616.s008) - Supplemental Material
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PDF (Figure S9. GATA3/T-bet ratio in subpopulations is insensitive to threshold level. doi:10.1371/journal.pbio.1001616.s009) - Supplemental Material
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PDF (Figure S10. Cytokine secretion is independent of external signal during restimulation. doi:10.1371/journal.pbio.1001616.s010) - Supplemental Material
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PDF (Figure S11. Repeatability of experiments. doi:10.1371/journal.pbio.1001616.s011) - Supplemental Material
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PDF (Figure S12. Theoretical model for the GRN controlling binary cell fate decision shows four different regimes if n = 1. doi:10.1371/journal.pbio.1001616.s012) - Supplemental Material
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PDF (Figure S13. A complex network of known interactions controlling Th1/Th2 differentiation can be reduced into a simple toy model for the transcription factors. doi:10.1371/journal.pbio.1001616.s013) - Supplemental Material
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PDF (Figure S14. Bayesian information criteria show that TF distributions are unimodal. doi:10.1371/journal.pbio.1001616.s014) - Supplemental Material
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PDF (Figure S15. The profile of TF levels is established before restimulation. doi:10.1371/journal.pbio.1001616.s015) - Supplemental Material
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PDF (Figure S16. GATA3/T-bet ratio is constant between the subpopulations and stable over 2 wk of culture. doi:10.1371/journal.pbio.1001616.s016) - Supplemental Material
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PDF (Figure S17. A mixed state is observed also for IL-13, similar to IL-4. doi:10.1371/journal.pbio.1001616.s017) - Supplemental Material
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PDF (Figure S18. Continuous tuning of the levels of IFN-γ, IL-4, and IL-13. doi:10.1371/journal.pbio.1001616.s018) - Supplemental Material
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PDF (Table S1. References for the links in the GRN controlling Th1–Th2 differentiation (Figure S13). doi:10.1371/journal.pbio.1001616.s019) - Supplemental Material
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PDF (Text S1. A parsimonious model of the GRN module governing cell differentiation shows a wide range of continuously tunable mono-stable solutions when positive feedback is gradual and dominates cross-inhibition. doi:10.1371/journal.pbio.1001616.s020) - Supplemental Material
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Abstract

Cell differentiation is typically directed by external signals that drive opposing regulatory pathways. Studying differentiation under polarizing conditions, with only one input signal provided, is limited in its ability to resolve the logic of interactions between opposing pathways. Dissection of this logic can be facilitated by mapping the system's response to mixtures of input signals, which are expected to occur in vivo, where cells are simultaneously exposed to various signals with potentially opposing effects. Here, we systematically map the response of naïve T cells to mixtures of signals driving differentiation into the Th1 and Th2 lineages. We characterize cell state at the single cell level by measuring levels of the two lineage-specific transcription factors (T-bet and GATA3) and two lineage characteristic cytokines (IFN-γ and IL-4) that are driven by these transcription regulators. We find a continuum of mixed phenotypes in which individual cells co-express the two lineage-specific master regulators at levels that gradually depend on levels of the two input signals. Using mathematical modeling we show that such tunable mixed phenotype arises if autoregulatory positive feedback loops in the gene network regulating this process are gradual and dominant over cross-pathway inhibition. We also find that expression of the lineage-specific cytokines follows two independent stochastic processes that are biased by expression levels of the master regulators. Thus, cytokine expression is highly heterogeneous under mixed conditions, with subpopulations of cells expressing only IFN-γ, only IL-4, both cytokines, or neither. The fraction of cells in each of these subpopulations changes gradually with input conditions, reproducing the continuous internal state at the cell population level. These results suggest a differentiation scheme in which cells reflect uncertainty through a continuously tuneable mixed phenotype combined with a biased stochastic decision rather than a binary phenotype with a deterministic decision.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pbio.1001616DOIArticle
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001616PublisherArticle
ORCID:
AuthorORCID
Friedman, Nir0000-0002-9678-3550
Additional Information:© 2013 Antebi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: September 25, 2012; Accepted: June 14, 2013; Published: July 30, 2013. This research was supported by grants from the International Human Frontier Science Program Organization, and the Israel Science Foundation (grant no. 812/08 and 1254/11). NF is incumbent of the Pauline Recanati Career Development Chair of Immunology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank Ziv Porat for technical help with ImageStream use and data analysis. We thank Naama Barkai, Benjamin Chain, Pierre Neveu, and Smita Krishnaswamy for comments on the manuscript and members of the Friedman lab for helpful discussions.
Funders:
Funding AgencyGrant Number
International Human Frontier Science Program OrganizationUNSPECIFIED
Israel Science Foundation812/08
Israel Science Foundation1254/11
Issue or Number:7
Record Number:CaltechAUTHORS:20130911-162947914
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20130911-162947914
Official Citation:Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, et al. (2013) Mapping Differentiation under Mixed Culture Conditions Reveals a Tunable Continuum of T Cell Fates. PLoS Biol 11(7): e1001616. doi:10.1371/journal.pbio.1001616
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:41267
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:17 Sep 2013 23:28
Last Modified:03 Oct 2019 05:47

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