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TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells

Tsagaratou, Ageliki and González-Avalos, Edahí and Rautio, Sini and Scott-Browne, James P. and Togher, Susan and Pastor, William A. and Rothenberg, Ellen V. and Chavez, Lukas and Lähdesmäki, Harri and Rao, Anjana (2017) TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells. Nature Immunology, 18 (1). pp. 45-53. ISSN 1529-2908. PMCID PMC5376256.

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[img] Image (JPEG) (Supplementary Figure 1: Characterization of Tet2-3 DKO mice) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 2: Analysis of CD4 and CD8 T cell development in wild type and Tet2-3 DKO mice) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 3: Profound loss of TET proteins is required for dysregulated expansion and function of iNKT cells) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 4: Cytokine production in Tet2-3 DKO iNKT cells) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 5: Increase of NKT17 subset and reduction of NKT1 precursors in the NK1.1- Tet2-3 DKO iNKT cells) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 6: Correlation of DNA modifications (5mC and 5hmC) with gene expression) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 7: Differentially modified regions (DMRs) and differentially accessible regions (DARs) in genes related to the iNKT cell specification program) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 8: Portraits of DNA modification and gene expression of selected downregulated cytokines and transcription factors in Tet2-3 DKO iNKT cells) - Supplemental Material
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[img] PDF (Supplementary Figures 1–8 and Supplementary Methods) - Supplemental Material
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TET proteins oxidize 5-methylcytosine in DNA to 5-hydroxymethylcytosine and other oxidation products. We found that simultaneous deletion of Tet2 and Tet3 in mouse CD4+CD8+ double-positive thymocytes resulted in dysregulated development and proliferation of invariant natural killer T cells (iNKT cells). Tet2-Tet3 double-knockout (DKO) iNKT cells displayed pronounced skewing toward the NKT17 lineage, with increased DNA methylation and impaired expression of genes encoding the key lineage-specifying factors T-bet and ThPOK. Transfer of purified Tet2-Tet3 DKO iNKT cells into immunocompetent recipient mice resulted in an uncontrolled expansion that was dependent on the nonclassical major histocompatibility complex (MHC) protein CD1d, which presents lipid antigens to iNKT cells. Our data indicate that TET proteins regulate iNKT cell fate by ensuring their proper development and maturation and by suppressing aberrant proliferation mediated by the T cell antigen receptor (TCR).

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Rothenberg, Ellen V.0000-0002-3901-347X
Additional Information:© 2016 Macmillan Publishers Limited. Received 24 April; accepted 25 October; published online 21 November 2016. We thank C. Kim, K. van Gunst, L. Nosworthy, D. Hinz and R. Simmons at the LJI Flow Cytometry Core for help with fluorescence-activated cell sorting; G. Seumois and J. Day at the LJI Functional Genomics Center for assistance with next-generation sequencing (Illumina HiSeq 2500); M. Kronenberg, I. Engel and C.-W. Lio (LJI) for discussions, the LJI Bioinformatics Core for routine analysis; Z. Mikulski and B. Kiosses at the LJI microscopy core, M. Chadwell at the LJI Histology core, and the Histology Core at the University of California at San Diego Moores Cancer Center; and R. Bosselut (National Cancer Institute) for pMX-ThPOK-IRES-GFP. Supported by US National Institutes of Health (R01 AI44432, CA151535 and R35CA210043), the Leukemia and Lymphoma Society (Translation Research Project grant 6187-12 to A.R.), the Academy of Finland Centre of Excellence in Molecular Systems Immunology and Physiology Research (H.L. and. S.R.), an Albert Billings Ruddock Professorship at Caltech (E.V.R.), the Cancer Research Institute (Irvington Institute postdoctoral fellowship to A.T.), the Fraternal Order of Eagles Fellow of the Damon Runyon Cancer Research Foundation (DRG-2069-11 to J.P.S.-B.) and the National Science Foundation (W.A.P.). Data availability: Data that support the findings of this study have been deposited in GEO with the accession code GSE66834. Source data for Figures 3,5,6 are provided with the paper. Accession codes. GEO accession: GSE66834. Author Contributions: A.R. and A.T. designed the study; A.T. performed all of the experiments, and A.R. and A.T. wrote the manuscript. E.G.-A. analyzed WGBS and ATAC-seq data sets under the supervision of L.C. and J.P.S.-B., respectively. S.R. analyzed RNA-seq and CMS-IP data sets under the supervision of H.L. S.T. helped with in vivo adoptive transfer experiments. W.A.P. generated the Tet3^(fl/fl) mice. E.V.R. provided critical input and suggestions during the course of this study and helped write the manuscript. The authors declare no competing financial interests.
Funding AgencyGrant Number
NIHR01 AI44432
Leukemia and Lymphoma Society6187-12
Academy of FinlandUNSPECIFIED
Albert Billings Ruddock ProfessorshipUNSPECIFIED
Cancer Research InstituteUNSPECIFIED
Damon Runyon Cancer Research FoundationDRG-2069-11
Issue or Number:1
PubMed Central ID:PMC5376256
Record Number:CaltechAUTHORS:20161128-134111050
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Official Citation:TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells Ageliki Tsagaratou, Edahí González-Avalos, Sini Rautio, James P Scott-Browne, Susan Togher, William A Pastor, Ellen V Rothenberg, Lukas Chavez, Harri Lähdesmäki & Anjana Rao Nature Immunology (2017) doi:10.1038/ni.3630
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:72324
Deposited By: George Porter
Deposited On:28 Nov 2016 22:25
Last Modified:14 Apr 2020 22:03

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