Genome-wide Profiling of Interleukin-4 and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming

Biomathematics Research Group, Department of Mathematics, University of Turku, FI-20014 Turku, Finland.
Immunity (Impact Factor: 19.75). 06/2010; 32(6):852-62. DOI: 10.1016/j.immuni.2010.06.011
Source: PubMed

ABSTRACT Dissecting the molecular mechanisms by which T helper (Th) cells differentiate to effector Th2 cells is important for understanding the pathogenesis of immune-mediated diseases, such as asthma and allergy. Because the STAT6 transcription factor is an upstream mediator required for interleukin-4 (IL-4)-induced Th2 cell differentiation, its targets include genes important for this process. Using primary human CD4(+) T cells, and by blocking STAT6 with RNAi, we identified a number of direct and indirect targets of STAT6 with ChIP sequencing. The integration of these data sets with detailed kinetics of IL-4-driven transcriptional changes showed that STAT6 was predominantly needed for the activation of transcription leading to the Th2 cell phenotype. This integrated genome-wide data on IL-4- and STAT6-mediated transcription provide a unique resource for studies on Th cell differentiation and, in particular, for designing interventions of human Th2 cell responses.

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Available from: Sunil kumar Raghav, Aug 20, 2015
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    • "STAT5A, STAT5B IL2 ChIP-seq [125] STAT5A, STAT5B IL4 ChIP-seq [127] STAT6 IL4 ChIP-seq + Exp. array [41] STAT6; H3K4me3, H3K27me3, H3K36me3 (WT and Stat6−/−) IL4 ChIP-seq + Exp. array [60] GATA3, TBX21 IL4 ChIP-chip + Exp. "
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    ABSTRACT: Molecular mechanisms guiding naïve T helper cell differentiation into functionally specified effector cells are intensively studied. The rapidly growing knowledge is mainly achieved by using mouse cells or disease models. Comparatively exiguous data is gathered from human primary cells although they provide the "ultimate model" for immunology in man, have been exploited in many original studies paving the way for the field, and can be analyzed more easily than ever with the help of modern technology and methods. As usage of mouse models is unavoidable in translational research, parallel human and mouse studies should be performed to assure the relevancy of the hypothesis created during the basic research. In this review, we give an overview on the status of the studies conducted with human primary cells aiming at elucidating the mechanisms instructing the priming of T helper cell subtypes. The special emphasis is given to the recent high-throughput studies. In addition, by comparing the human and mouse studies we intend to point out the regulatory mechanisms and questions which are lacking examination with human primary cells.
    Seminars in Immunology 11/2013; 25(4). DOI:10.1016/j.smim.2013.10.013 · 6.12 Impact Factor
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    • "After isolation the CD4+ cells were pooled to prepare cell cultures consisting cells from several neonates. The same pooled cells as utilized for Th0 (activated) and Th2 (activated and IL-4 stimulated) culture conditions by Elo et al. (2010) were used parallel for Th1 polarizing cultures. For activation, the cells were treated with plate-bound anti- CD3 (500 ng/24-well culture plate well, #IM1304, Immunotech) and soluble anti-CD28 (500 ng/ml, #IM1376, Immunotech) in density of 2-4 × 10 6 cells/ml of Yssel's medium (Iscove modified Dulbecco medium, #31980-048, Invitrogen) supplemented with Yssel medium concentrate [117], 1% human AB serum (#C11-011, PAA) and 100 U/ ml Penicillin and 100 μg/ml Streptomycin (#P0781, Sigma) at 37°C in 5% CO2. "
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    ABSTRACT: Background A proper balance between different T helper (Th) cell subsets is necessary for normal functioning of the adaptive immune system. Revealing key genes and pathways driving the differentiation to distinct Th cell lineages provides important insight into underlying molecular mechanisms and new opportunities for modulating the immune response. Previous computational methods to quantify and visualize kinetic differential expression data of three or more lineages to identify reciprocally regulated genes have relied on clustering approaches and regression methods which have time as a factor, but have lacked methods which explicitly model temporal behavior. Results We studied transcriptional dynamics of human umbilical cord blood T helper cells cultured in absence and presence of cytokines promoting Th1 or Th2 differentiation. To identify genes that exhibit distinct lineage commitment dynamics and are specific for initiating differentiation to different Th cell subsets, we developed a novel computational methodology (LIGAP) allowing integrative analysis and visualization of multiple lineages over whole time-course profiles. Applying LIGAP to time-course data from multiple Th cell lineages, we identified and experimentally validated several differentially regulated Th cell subset specific genes as well as reciprocally regulated genes. Combining differentially regulated transcriptional profiles with transcription factor binding site and pathway information, we identified previously known and new putative transcriptional mechanisms involved in Th cell subset differentiation. All differentially regulated genes among the lineages together with an implementation of LIGAP are provided as an open-source resource. Conclusions The LIGAP method is widely applicable to quantify differential time-course dynamics of many types of datasets and generalizes to any number of conditions. It summarizes all the time-course measurements together with the associated uncertainty for visualization and manual assessment purposes. Here we identified novel human Th subset specific transcripts as well as regulatory mechanisms important for the initiation of the Th cell subset differentiation.
    BMC Genomics 10/2012; 13(1):572. DOI:10.1186/1471-2164-13-572 · 4.04 Impact Factor
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    • "Another study also demonstrated that STAT-6 knockdown resulted in downregulation of SATB1 expression at both RNA and protein level (Ahlfors et al., 2010). Microarray-based gene expression profiling data from different groups using mouse and human models depicted similar results showing downregulation of SATB1 (Wei et al., 2010; Elo et al., 2010). Bsed on these finding, we hypothesize that STAT-6 may directly bind to the SATB1 promoter and mediate activating epigenetic histone modifications leading to the upregulation of SATB1 during T H 2 differentiation. "
    Hematology - Science and Practice, 03/2012; , ISBN: 978-953-51-0174-1
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