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A microRNA upregulated in asthma airway T cells promotes TH2 cytokine production

Nature Immunology volume 15, pages 1162–1170 (2014)Cite this article

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Abstract

MicroRNAs (miRNAs) exert powerful effects on immunological function by tuning networks of target genes that orchestrate cell activity. We sought to identify miRNAs and miRNA-regulated pathways that control the type 2 helper T cell (TH2 cell) responses that drive pathogenic inflammation in asthma. Profiling miRNA expression in human airway-infiltrating T cells revealed elevated expression of the miRNA miR-19a in asthma. Modulating miR-19 activity altered TH2 cytokine production in both human and mouse T cells, and TH2 cell responses were markedly impaired in cells lacking the entire miR-17∼92 cluster. miR-19 promoted TH2 cytokine production and amplified inflammatory signaling by direct targeting of the inositol phosphatase PTEN, the signaling inhibitor SOCS1 and the deubiquitinase A20. Thus, upregulation of miR-19a in asthma may be an indicator and a cause of increased TH2 cytokine production in the airways.

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Figure 1: miR-19a expression is elevated in CD4+ T cells from asthmatic lungs.
Figure 2: The miR-17∼92 cluster promotes TH2 cytokine production.
Figure 3: The miR-17∼92 cluster promotes TH2 cytokine production in a cell-intrinsic and proliferation-independent manner.
Figure 4: miR-19a and miR-19b 'rescue' the TH2 cytokine defect in 17∼92Δ cells.
Figure 5: miR-19a promotes IL-13 production in human CD4+ T cells.
Figure 6: Several miR-19 targets negatively regulate TH2 cytokine production.
Figure 7: The miR-17∼92 cluster promotes TH2-driven inflammation in vivo.

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Acknowledgements

We thank M. McCune, Y. Bronevetsky and E. Krow-Lucal for help with human biospecimens, and R. Kageyama for discussion of the manuscript. Supported by the US National Institutes of Health (HL107202, HL109102), the Sandler Asthma Basic Research Center, a Scholar Award from The Leukemia & Lymphoma Society, a US National Science Foundation predoctoral fellowship (2010101500 to L.J.S.), the Swiss Foundation for Grants in Biology and Medicine (PASMP3-142725), the National Multiple Sclerosis Society and the UCSF Program for Breakthrough Biomedical Research, which is funded in part by the Sandler Foundation.

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  1. Dirk Baumjohann

    Present address: Present address: Institute for Immunology, Ludwig-Maximilians-Universität, Munich, Germany.,

Authors and Affiliations

  1. Department of Microbiology and Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California, USA

    Laura J Simpson, Sana Patel, Dirk Baumjohann, Misty M Montoya, Marisella Panduro, Kelly A Remedios & K Mark Ansel

  2. Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA

    Nirav R Bhakta, John V Fahy & Prescott G Woodruff

  3. Immunology, Tissue Growth, and Repair Biomarker Discovery, Genentech, South San Francisco, California, USA

    David F Choy & Joseph R Arron

  4. Department of Immunology, Genentech, South San Francisco, California, USA

    Hans D Brightbill

  5. Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California, USA

    Xin Ren, Yanli Wang & Xiaozhu Huang

  6. Department of Pathology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California, USA

    Heather H Pua

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Contributions

L.J.S. designed, performed and analyzed most experiments. S.P., D.F.C., H.D.B., X.R., Y.W., H.H.P., D.B., M.M.M., M.P. and K.A.R. helped design and perform some experiments. X.H. helped design animal airway allergy experiments. N.R.B. analyzed human miRNA expression data. P.G.W., J.V.F. and J.R.A. designed and helped perform the clinical study for human miRNA expression analysis. K.M.A. helped design, analyze and interpret all experiments. L.J.S. and K.M.A. wrote the manuscript. All authors reviewed and approved the manuscript.

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Correspondence to K Mark Ansel.

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Competing interests

D.F.C., H.D.B. and J.R.A. are employees of Genentech and are shareholders of the Roche Group. This work was supported in part by a grant to P.G.W. and J.V.F. from Genentech.

Integrated supplementary information

Supplementary Figure 1 Heatmap of all subjects and miRNAs analyzed by multiplex qPCR.

(a) Method shown for isolation of RNA from CD3+ CD4+ T cells from BAL fluid from healthy and asthmatic subjects. RNA was reverse transcribed and preamplified, and miRNA expression was analyzed using the Fluidigm Biomark qPCR system. (b) Unsupervised hierarchical clustering using the 23 most variable miRNAs (between healthy and steroid-naïve asthma) was determined in R (version 2.14.1) using the hclust function with “complete” method. The heatmap (R version 2.14.1; heatmap function) was generated using the hierarchical clustering above, including expression of all miRNAs determined by multiplex qPCR using the Biomark system (Fluidigm). In the heatmap, red indicates expression level higher than the mean across all subjects, blue denotes expression level lower than the mean, and grey indicates expression not determined (N.D). In the first row, green indicates asthmatic subjects, and yellow indicates healthy subjects. In the second row, purple indicates inhaled corticosteroid (ICS) treatment, and white indicates no ICS. miRNAs are arranged by average expression across all subjects (lowest to highest). Significance was determined by Welch t-test comparing the healthy and SN asthma groups. (Full table of p-values is provided in Supplementary Table 2.)

Supplementary Figure 2 miR-17∼92 expression in 17∼92Δ and 17∼92+ naive CD4 T cells.

(a) Schematic of the genomic loci of the miR-17∼92, miR-106a∼363, and miR-106b∼25 clusters. Colors indicate miRNAs belonging to the same family; yellow = miR-17 family, blue = miR-18 family, teal = miR-19 family, pink = miR-92 family. (b) miRNA expression was determined by SYBR qPCR in 17∼92+/+ (black bars) and 17∼92Δ/Δ (white bars) naïve CD4 T cells. Expression was normalized to 5.8S rRNA in each sample. Data are representative of 2 experiments.

Supplementary Figure 3 miR-19 activity in 17∼92Δ and 17∼92+ cells and effects of mimics and inhibitors.

(a) DGCR8+/+ and DGCR8Δ/Δ CD4 T cells transduced with retroviral sensors expressing GFP with 4 perfectly complementary binding sites for miR-1 (psens1), miR-19a (psens19a), or miR-19b (psens19b) in the 3’UTR. (b) DGCR8Δ/Δ CD4 T cells transduced with miR-19a (psens19a) or miR-19b (psens19b) sensors and transfected with control mimic (CM), miR-19a mimic (19a), or miR-19b mimic (19b). (c) DGCR8+/+ CD4 T cells transduced with psens19a or psens19b, and transfected with control inhibitor (CI) or anti-miR-19a and anti-miR-19b inhibitors (anti-19ab). (d) Analysis of cytokine expression by flow cytometry in DGCR8+/+ CD4 T cells cultured for 5 days in nonpolarizing conditions and transfected with control inhibitor (CI), and anti-miR-19b inhibitors (anti-19). Data represent mean +/- SEM. * p = 0.03. (e) DGCR8+/+ CD4 T cells cultured for 5 days in nonpolarizing conditions and transfected with control mimic (CM), miR-19a mimic (19a), or miR-19b mimic (19b). Data represent mean +/- SEM.

Supplementary Figure 4 Effects of miR-17∼92 members on proliferation.

Analysis (day 5) of cell proliferation by flow cytometry of Th2-polarized cells labeled with CellTrace Violet (CTV). Grey filled histogram represents 17∼92+/+ cells transfected with control mimic (CM), black histogram represents 17∼92Δ/Δ cells transfected with control mimic (CM), and red histogram represents cells transfected with the corresponding miRNA mimic. Data are representative of 3 independent experiments, with 3 technical replicates in each experiment.

Supplementary Figure 5 Identification of myeloid cells in BAL fluid in an in vivo allergic airway inflammation model.

(a) Method for TH2 OT-II cell adoptive transfer model of allergic airway inflammation. See Materials and Methods for details. (b) Gating strategy used to identify eosinophils (CD45+ CD11b+ Siglec F+), neutrophils (CD45+ CD11b+ Ly6G+), and alveolar macrophages (CD45+ CD11c+ Siglec F+) in bronchoalveolar lavage (BAL) fluid from mice that received 17∼92+/+ or 17∼92 Δ/Δ OT-II Th2 cells and were challenged with ovalbumin for 3 consecutive days. Cells are first gated as CD45+, Live (eF780 viability dye-/CD4-/CD8-/CD19-), singlet, NK1.1-, and then divided into the above mentioned cell types. Numbers of each cell type are determined by the product of the frequency of that cell type (as a percentage of live cells) and the total BAL cell count determined by Coulter Counter.

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Simpson, L., Patel, S., Bhakta, N. et al. A microRNA upregulated in asthma airway T cells promotes TH2 cytokine production. Nat Immunol 15, 1162–1170 (2014). https://doi.org/10.1038/ni.3026

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