- Chtanova T.
- Newton R.
- Liu S.M.
- Weininger L.
- Young T.R.
- Silva D.G.
- Bertoni F.
- Rinaldi A.
- Chappaz S.
- Sallusto F.
- Rolph M.S.
- Mackay C.R.
- MacMurray A.J.
- Moralejo D.H.
- Kwitek A.E.
- Rutledge E.A.
- Van Yserloo B.
- Gohlke P.
- Speros S.J.
- Snyder B.
- Schaefer J.
- Bieg S.
- Jiang J.
- Ettinger R.A.
- Fuller J.
- Daniels T.L.
- Pettersson A.
- Orlebeke K.
- Birren B.
- Jacob H.J.
- Lander E.S.
- Lernmark A.
- Hellquist A.
- Zucchelli M.
- Kivinen K.
- Saarialho-Kere U.
- Koskenmies S.
- Widen E.
- Julkunen H.
- Wong A.
- Karjalainen-Lindsberg M.L.
- Skoog T.
- Vendelin J.
- Cunninghame-Graham D.S.
- Vyse T.J.
- Kere J.
- Lindgren C.M.
Preparation of Microsomal Fraction—
Fractionation of the Peptides—
ProICAT and ProID—
SEQUEST, XPRESS, and the Transproteomic Pipeline—
Reversed Database Searches to Determine the False Positive Rates for ProICAT and ProID and to Determine the SEQUEST Xcorr Values—
Statistical Methods and Data Management—
Western Blot Analysis—
Quantitative Real Time RT-PCR—
Knockdown of STAT6 with siRNA Oligonucleotide/shRNAs—
Characterization of the Microsomal Fraction Proteome of Human Th Lymphocytes Stimulated with IL-4—
|A. Protein identifications|
|False positive rate||<0.1||8.8||1.4|
|B. Protein identifications with quantitative information|
|1.4-fold up-regulated proteins||3 (21)|
|1.4-fold down-regulated proteins||5 (25)|
Relative Quantitation of the Protein Abundances in the Microsomal Fraction of Naiüve Th Lymphocytes—
IL-4-induced Differences in the Protein Expression of the Microsomal Fraction of the CB CD4+ Cells—
Expression of GIMAP Family Members 1 and 4 in Th1 and Th2 Cells—
IL-4-induced STAT6 Signaling Negatively Regulates GIMAP4 Expression—
- Fournie G.J.
- Cautain B.
- Xystrakis E.
- Damoiseaux J.
- Mas M.
- Lagrange D.
- Bernard I.
- Subra J.F.
- Pelletier L.
- Druet P.
- Saoudi A.
- Cytokines and transcription factors that regulate T helper cell differentiation: new players and new insights.J. Clin. Immunol. 2003; 23: 147-161
- Induction of Th1 and Th2 CD4+ T cell responses: the alternative approaches.Annu. Rev. Immunol. 1997; 15: 297-322
- T helper cell differentiation: regulation by cis elements and epigenetics.Immunity. 2006; 24: 369-379
- Two types of murine helper T cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins.J. Immunol. 1986; 136: 2348-2357
- Heterogeneity of cytokine secretion patterns and functions of helper T cells.Adv. Immunol. 1989; 46: 111-147
- T helper cell effector fates—who, how and where?.Curr. Opin. Immunol. 2006; 18: 271-277
- IL-4 directs the development of Th2-like helper effectors.J. Immunol. 1990; 145: 3796-3806
- Differential regulation of T helper phenotype development by interleukins 4 and 10 in an αβ T-cell-receptor transgenic system.Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 6065-6069
- The presence of interleukin 4 during in vitro priming determines the lymphokine-producing potential of CD4+ T cells from T cell receptor transgenic mice.J. Exp. Med. 1992; 176: 1091-1098
- The IL-4 receptor: signaling mechanisms and biologic functions.Annu. Rev. Immunol. 1999; 17: 701-738
- Signaling pathways in Th2 development.Immunol. Rev. 2004; 202: 203-222
- Molecular cloning of a cDNA encoding the human interleukin 4 receptor.Int. Immunol. 1990; 2: 669-675
- Interleukin-2 receptor gamma chain: a functional component of the interleukin-4 receptor.Science. 1993; 262: 1880-1883
- Involvement of the jak-3 janus kinase in signalling by interleukins 2 and 4 in lymphoid and myeloid cells.Nature. 1994; 370: 153-157
- Interaction of IL-2R beta and gamma c chains with Jak1 and Jak3: Implications for XSCID and XCID.Science. 1994; 266: 1042-1045
- The IL-4 receptor alpha-chain cytoplasmic domain is sufficient for activation of JAK-1 and STAT6 and the induction of IL-4-specific gene expression.J. Immunol. 1997; 158: 5860-5867
- Jaks and STATs: biological implications.Annu. Rev. Immunol. 1998; 16: 293-322
- Analysis of the life cycle of Stat6. Continuous cycling of Stat6 is required for IL-4 signaling.J. Biol. Chem. 2002; 277: 36563-36569
- Signaling mechanisms, interaction partners, and target genes of STAT6.Cytokine Growth Factor Rev. 2006; 17: 173-188
- Th1 and Th2 in human diseases.Clin. Immunol. Immunopathol. 1996; 80: 225-235
- Lymphokine production by human T cells in disease states.Annu. Rev. Immunol. 1994; 12: 227-257
- Transcript imaging of the development of human T helper cells using oligonucleotide arrays.Nat. Genet. 2000; 25: 96-101
- Gene microarrays reveal extensive differential gene expression in both CD4+ and CD8+ type 1 and type 2 T cells.J. Immunol. 2001; 167: 3057-3063
- Identification of novel genes regulated by IL-12, IL-4, or TGF-β during the early polarization of CD4+ lymphocytes.J. Immunol. 2003; 171: 5328-5336
- Identification of novel IL-4/Stat6-regulated genes in T lymphocytes.J. Immunol. 2003; 171: 3627-3635
- T follicular helper cells express a distinctive transcriptional profile, reflecting their role as non-Th1/Th2 effector cells that provide help for B cells.J. Immunol. 2004; 173: 68-78
- Kinetic analysis of genomewide gene expression reveals molecule circuitries that control T cell activation and Th1/2 differentiation.Proc. Natl. Acad. Sci. U. S. A. 2004; 101: 3023-3028
- Early target genes of IL-12 and STAT4 signaling in Th cells.J. Immunol. 2004; 172: 6775-6782
- Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets.J. Immunol. 2005; 175: 7837-7847
- Identification of genes involved in the initiation of human Th1 or Th2 cell commitment.Eur. J. Immunol. 2005; 35: 3307-3319
- Identification of novel Th2-associated genes in T memory responses to allergens.J. Immunol. 2006; 176: 4766-4777
- Genome-wide identification of novel genes involved in early Th1 and Th2 cell differentiation.J. Immunol. 2007; 178: 3648-3660
- Proteome analysis reveals ubiquitin-conjugating enzymes to be a new family of interferon-α-regulated genes.Eur. J. Biochem. 2000; 267: 4011-4019
- Proteome characterization of human T helper 1 and 2 cells.Proteomics. 2004; 4: 84-92
- Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12.Proteomics. 2005; 5: 4719-4732
- Proteomic profiling of surface proteins on Th1 and Th2 cells.J. Proteome Res. 2005; 4: 400-409
- Proteomic and transcriptomic characterization of interferon-alpha-induced human primary T helper cells.Proteomics. 2005; 5: 371-379
- Proteome profiling of interleukin-12 treated human T helper cells.Proteomics. 2005; 5: 3137-3141
- Interleukin-4 inhibits caspase-3 by regulating several proteins in the Fas pathway during initial stages of human T helper 2 cell differentiation.Mol. Cell. Proteomics. 2007; 6: 238-251
- Mass spectrometry-based proteomics turns quantitative.Nat. Chem. Biol. 2005; 1: 252-262
- Quantitation in proteomics.in: Wilkins M.R. Appel R.D. Williams K.L. Hochstrasser D.F. Proteome Research: Concepts, Technology and Application. Springer-Verlag, Berlin, Germany2007: 69-93
- Mass spectrometry-based proteomics.Nature. 2003; 422: 198-207
- Mass spectrometry and protein analysis.Science. 2006; 312: 212-217
- Qscore: an algorithm for evaluating SEQUEST database search results.J. Am. Soc. Mass Spectrom. 2002; 13: 378-386
- Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome.J. Proteome Res. 2003; 2: 43-50
- Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.Nat. Methods. 2007; 4: 207-214
- Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.Nat. Biotechnol. 1999; 17: 994-999
- Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography.Mol. Cell. Proteomics. 2003; 2: 299-314
- Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response.Mol. Cell. Proteomics. 2003; 2: 1198-1204
- Comparative analysis of the human gimap gene cluster encoding a novel GTPase family.Gene (Amst.). 2004; 341: 291-304
- IAN family critically regulates survival and development of T lymphocytes.PLoS Biol. 2006; 4: e103
- Gimap4 accelerates T-cell death.Blood. 2006; 108: 591-599
- A natural hypomorphic variant of the apoptosis regulator Gimap4/IAN1.J. Immunol. 2007; 179: 1784-1795
- Malaria-suppressible expression of the anti-apoptotic triple GTPase mGIMAP8.J. Cell. Biochem. 2005; 96: 339-348
- The lymphopenia mutation of the BB rat causes inappropriate apoptosis of mature thymocytes.Eur. J. Immunol. 1999; 29: 1832-1841
- Ian4 is required for mitochondrial integrity and T cell survival.Proc. Natl. Acad. Sci. U. S. A. 2003; 100: 10382-10387
- Lymphopenia in the BB rat model of type 1 diabetes is due to a mutation in a novel immune-associated nucleotide (ian)-related gene.Genome Res. 2002; 12: 1029-1039
- The human GIMAP5 gene has a common polyadenylation polymorphism increasing risk to systemic lupus erythematosus.J. Med. Genet. 2007; 44: 314-321
- hIan5: the human ortholog to the rat Ian4/Iddm1/lyp is a new member of the ian family that is overexpressed in B-cell lymphoid malignancies.Genes Immun. 2004; 5: 109-116
- Serum-free medium for generation and propagation of functional human cytotoxic and helper T cell clones.J. Immunol. Methods. 1984; 72: 219-227
- Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry.Nat. Biotechnol. 2001; 19: 946-951
- A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments.Proteomics. 2005; 5: 2748-2760
- A statistical model for identifying proteins by tandem mass spectrometry.Anal. Chem. 2003; 75: 4646-4658
- Human immune associated nucleotide 1: a member of a new guanosine triphosphatase family expressed in resting T and B cells.Blood. 2002; 99: 3293-3301
- Signaling lymphocytic activation molecule (SLAM) is differentially expressed in human Th1 and Th2 cells.J. Immunol. Methods. 2000; 242: 9-19
- Enrichment of nucleofected primary human CD4+ T cells: a novel and efficient method for studying gene function and role in human primary T helper cell differentiation.J. Immunol. Methods. 2006; 310: 30-39
- Proteome informatics I: bioinformatics tools for processing experimental data.Proteomics. 2006; 6: 5435-5444
- Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data.Proteomics. 2004; 4: 619-628
- An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.Proteomics. 2005; 5: 3475-3490
- Human ortholog to mouse gene imap38 encoding an ER-localizable G-protein belongs to a gene family clustered on chromosome 7q32–36.Gene (Amst.). 2002; 282: 159-167
- Expression of the ian family of putative GTPases during T cell development and description of an ian with three sets of GTP/GDP-binding motifs.Int. Immunol. 2005; 17: 1257-1268
- Single expression of CD45RC and RT6 in correlation with T-helper 1 and T-helper 2 cytokine patterns in the rat.Cell. Immunol. 2000; 199: 89-96
- Induction of IgE synthesis and potentiation of anti-ovalbumin IgE antibody response by HgCl2 in the rat.J. Immunol. 1981; 126: 699-792
- Cellular and genetic factors involved in the difference between brown Norway and lewis rats to develop respectively type-2 and type-1 immune-mediated diseases.Immunol. Rev. 2001; 184: 145-160
- Eosinophilic bowel disease controlled by the BB rat-derived lymphopenia/Gimap5 gene.Gastroenterology. 2006; 131: 1475-1485
Published, MCP Papers in Press, August 12, 2008, DOI 10.1074/mcp.M800139-MCP200
This work was supported by grants from the National Technology Agency of Finland (TEKES), Academy of Finland, Sigrid Juselius Foundation, Turku University Hospital Fund, Finnish Cultural Foundation, Vaüinoü and Laina Kivi Foundation, Tampere Tuberculosis Foundation, and Ida Montin Foundation. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
The on-line version of this article (available at http://www.mcponline.org) contains supplemental material.
User LicenseCreative Commons Attribution (CC BY 4.0) |
- Read, print & download
- Redistribute or republish the final article
- Text & data mine
- Translate the article
- Reuse portions or extracts from the article in other works
- Sell or re-use for commercial purposes
Elsevier's open access license policy