Open Access Highly Accessed Research article

Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling

Ruben L Smeets169*, Wilco WM Fleuren23, Xuehui He7, Paul M Vink1, Frank Wijnands1, Monika Gorecka1, Henri Klop1, Sussane Bauerschmidt4, Anja Garritsen1, Hans JPM Koenen7, Irma Joosten7, Annemieke MH Boots18 and Wynand Alkema2345

Author Affiliations

1 Department of Immune Therapeutics, Merck Research Laboratories (MRL), MSD, Oss, the Netherlands

2 Computational Drug Discovery (CDD), CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

3 Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands

4 Department of Molecular Design and Informatics, Merck Research Laboratories (MRL), MSD, Oss, the Netherlands

5 NIZO Food Research, Ede, The Netherlands

6 Department of Laboratory Medicine, laboratory for Clinical Chemistry, Radboud University Medical Centre, Nijmegen, The Netherlands

7 Department of Laboratory Medicine, laboratory for Medical Immunology, Radboud University Medical Centre, Nijmegen, The Netherlands

8 Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands

9 Department of Laboratory Medicine, laboratory for Clinical Chemistry, Radboud University Medical Centre, Nijmegen, Geert Grooteplein 10, Postbus 9101, 6500 HB Nijmegen, The Netherlands

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BMC Immunology 2012, 13:12  doi:10.1186/1471-2172-13-12

Published: 14 March 2012

Additional files

Additional file 1:

Figure S1. PCA using the ratio data vs. the respective controls. Cells were treated for 8 hours with the single stimuli CD28, CD3 and PMA (black squares) and with the stimulatory combinations PMA/CD28 (blue circles) CD3/CD28 (green triangles) and CD3_PMA (red diamonds). The corresponding treatments with the stimulus + inhibitor combination are represented by the same symbols. Eg. the red diamond with the AEB071 label represents the samplein treated with CD3 + PMA and AEB071. This graph shows that PMA/CD28 stimulation was mainly affected by AEB071, whereas PMA/CD3 stimulation was mainly modulated by CsA, A420983 and AEB071. The symbols around the origin represent the treatments with the MAPK inhibitors, which only had a marginal effect on the stimuli used (the labels have been omitted for clarity). The numbers denote the number of significantly regulated probe sets for these conditions compared to the respective controls. These numbers were very low for the conditions including MAPK inhibitors and CD28 stimulation alone and for A420983 and CsA after PMA/CD28 stimulation (centered around the origin of the graph) and have therefore been omitted for clarity. For details of regulated probe sets for all conditions and the overlap between these sets, see Additional file 2: Table S1. Repeating this analysis with different values for the fold change and p-value cut off yielded essentially the same results for the multivariate analysis.

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Additional file 2:

Table S1. For each treatment, regulated probe sets were selected by comparison with the corresponding control. Probe sets were identified as being significantly regulated if adjusted p-value was < 10-10 and fold change > 4. The numbers in each cell show the number of overlapping genes between two treatments. The cells highlighted in grey indicate the most informative numbers because in these comparisons, only one of the parameters is changed between two conditions. The other numbers are shown for the sake of completeness, but are less informative because the comparisons are between treatments in which two parameters at the same time have been changed.

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Additional file 3:

Files S1. Each of these files contain 4 columns. The first is the Affymetrix probe set id, the second columns gives the Euclidean distance to the gene expression profile of interest (file 1: CCL1, file 2: IL-2, file 3: EGR1). The third and fourth columns show the corresponding gene symbol and description respectively.

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Additional file 4:

Files S2. Each of these files contain 4 columns. The first is the Affymetrix probe set id, the second columns gives the Euclidean distance to the gene expression profile of interest (file 1: CCL1, file 2: IL-2, file 3: EGR1). The third and fourth columns show the corresponding gene symbol and description respectively.

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Additional file 5:

Files S3. Each of these files contain 4 columns. The first is the Affymetrix probe set id, the second columns gives the Euclidean distance to the gene expression profile of interest (file 1: CCL1, file 2: IL-2, file 3: EGR1). The third and fourth columns show the corresponding gene symbol and description respectively.

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Additional file 6:

Figure S2. A schematic presentation of signaling pathways and induced gene profiles via differential stimulation of T cells. This figure highlights the findings of this study indicating that TCR/CD3-induced Calcium signaling is necessary for efficient T helper 1 development, whereas absence of calcium signaling and sufficient activation of NFκB/AP1 lead to T helper 2 development (as indicated by green-red intensity plots). A selected list of genes is listed derived from the IL-2 and CCL1 gene profiles shown in Figure 7.

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