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Dynamic regulatory network controlling TH17 cell differentiation

Abstract

Despite their importance, the molecular circuits that control the differentiation of naive T cells remain largely unknown. Recent studies that reconstructed regulatory networks in mammalian cells have focused on short-term responses and relied on perturbation-based approaches that cannot be readily applied to primary T cells. Here we combine transcriptional profiling at high temporal resolution, novel computational algorithms, and innovative nanowire-based perturbation tools to systematically derive and experimentally validate a model of the dynamic regulatory network that controls the differentiation of mouse TH17 cells, a proinflammatory T-cell subset that has been implicated in the pathogenesis of multiple autoimmune diseases. The TH17 transcriptional network consists of two self-reinforcing, but mutually antagonistic, modules, with 12 novel regulators, the coupled action of which may be essential for maintaining the balance between TH17 and other CD4+ T-cell subsets. Our study identifies and validates 39 regulatory factors, embeds them within a comprehensive temporal network and reveals its organizational principles; it also highlights novel drug targets for controlling TH17 cell differentiation.

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Figure 1: Genome-wide temporal expression profiles of T H 17 differentiation.
Figure 2: A model of the dynamic regulatory network of T H 17 differentiation.
Figure 3: Knockdown screen in T H 17 differentiation using silicon nanowires.
Figure 4: Coupled and mutually antagonistic modules in the T H 17 network.
Figure 5: Mina, Fas, Pou2af1 and Tsc22d3 are key novel regulators affecting the T H 17 differentiation programs.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

The microarray, RNA-seq and ChIP-seq data sets have been deposited in the Gene Expression Omnibus database under accession numbers GSE43955, GSE43969, GSE43948 and GSE43949.

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Acknowledgements

We thank L. Gaffney and L. Solomon for artwork, the Broad’s Genomics Platform for sequencing, and D. Kozoriz for cell sorting. Work was supported by NHGRI (1P50HG006193-01 to H.P. and A.R.), NIH Pioneer Awards (5DP1OD003893-03 to H.P., DP1OD003958-01 to A.R.), NIH (NS 30843, NS045937, AI073748 and AI45757 to V.K.K.), National MS Society (RG2571 to V.K.K.), HHMI (A.R.), and the Klarman Cell Observatory (A.R.).

Author information

Authors and Affiliations

Authors

Contributions

N.Y., A.K.S., J.T.G., H.P., V.K.K. and A.R. conceived the study and designed experiments. N.Y. developed computational methods. N.Y., A.K.S. and J.T.G. analysed the data. A.K.S., J.T.G., H.J., Y.L., A.A., C.W., K.K., S.X., M.J., D.G., R.S., D.Y.L. and J.J.T. conducted the experiments. A.S., M.R.P., P.J.R., M.L.C., M.B. and D.T. provided knockout mice. N.Y., A.K.S., J.T.G., V.K.K., H.P. and A.R. wrote the paper with input from all the authors.

Corresponding authors

Correspondence to Hongkun Park, Vijay K. Kuchroo or Aviv Regev.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Notes, Supplementary Methods, Supplementary Figures 1-12, legends for Supplementary Tables 1-8 (see separate excel files) and Supplementary References. (PDF 1823 kb)

Supplementary Table 1

This file contains a list of microarray probesets that were differentially expressed in the TGF-β1+Il6 microarray data - see Supplementary Information file for full legend. (XLS 323 kb)

Supplementary Table 2

This file shows the functional enrichments for expression clusters -see Supplementary Information file for full legend. (XLS 1034 kb)

Supplementary Table 3

This file shows the regulatory interactions in the three canonical temporal networks (Early, Intermediate, and Late) - see Supplementary Information file for full legend. (XLS 2258 kb)

Supplementary Table 4

This file contains a table of ranked regulators of Th17 differentiation - see Supplementary Information file for full legend. (XLS 80 kb)

Supplementary Table 5

This file contains the results of Nanostring nCounter and Fluidigm analysis - see Supplementary Information file for full legend. (XLS 191 kb)

Supplementary Table 6

This file contains the Primers for Nanostring STA and qRT-PCR/Fluidigm and siRNA sequences - see Supplementary Information file for full legend. (XLS 153 kb)

Supplementary Table 7

This file shows the RNA-seq data analysis - see Supplementary Information file for full legend. (XLS 1539 kb)

Supplementary Table 8

This file shows the Tsc22d3 ChIP-seq data analysis - see Supplementary Information file for full legend. (XLS 108 kb)

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Yosef, N., Shalek, A., Gaublomme, J. et al. Dynamic regulatory network controlling TH17 cell differentiation. Nature 496, 461–468 (2013). https://doi.org/10.1038/nature11981

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