Identification of helper T cell master regulator candidates using the polar score method

Journal of Immunological Methods

Volumn 361, Issue 1-2, 2010, Pages 98-109

  van den Ham, H J ^a,b   de Waal, L ^b   Andeweg, A C ^b   de Boer, R J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Helper T cell differentiation; Master regulator; Microarray analysis; Th9 phenotype

Indexed keywords

INTERLEUKIN 12; INTERLEUKIN 4; INTERLEUKIN 9; TRANSFORMING GROWTH FACTOR BETA;

ARTICLE; GENE EXPRESSION; HELPER CELL; MICROARRAY ANALYSIS; PHENOTYPE; POLARIZATION; PRIORITY JOURNAL; REGULATORY T LYMPHOCYTE; T LYMPHOCYTE; TH17 CELL; BIOLOGY; CELL POLARITY; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; HUMAN; IMMUNOLOGY; PROCEDURES;

CELL POLARITY; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; HUMANS; INTERLEUKIN-12; INTERLEUKIN-4; INTERLEUKIN-9; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; T-LYMPHOCYTES, HELPER-INDUCER; TRANSFORMING GROWTH FACTOR BETA;

EID: 77956878307     PISSN: 00221759     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jim.2010.07.009     Document Type: Article

References (31)

1. Mosmann T.R., Cherwinski H., Bond M.W., Giedlin M.A., Coffman R.L. Two types of murine helper T cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins. J. Immunol. 1986, 136(7):2348.
2. Weaver C.T., Harrington L.E., Mangan P.R., Gavrieli M., Murphy K.M. Th17: an effector CD4 T cell lineage with regulatory T cell ties. Immunity 2006, 24(6):677. 10.1016/j.immuni.2006.06.002.
3. Awasthi A., Kuchroo V.K. Th17 cells: from precursors to players in inflammation and infection. Int Immunol. 2009, 0(O):O. URL http://dx.doi.org/10.1093/intimm/dxp021. 10.1093/intimm/dxp021.
4. Veldhoen M., Uyttenhove C., Van Snick J., Helmby H., Westendorf A., Buer J., Martin B., Wilhelm C., Stockinger B. Transforming growth factor-beta 'reprograms' the differentiation of T helper 2 cells and promotes an interleukin 9-producing subset. Nat. Immunol. 2008, 9(12):1341. URL http://dx.doi.org/10.1038/ni.1659. 10.1038/ni.1659.
5. Soroosh P., Doherty T.A. Th9 and allergic disease. Immunology. 2009, 127(4):450. URL http://dx.doi.org/10.1111/j.1365-2567.2009.03114.x. 10.1111/j.1365-2567.2009.03114.x.
6. Nurieva R.I., Chung Y., Hwang D., Yang X.O., Kang H.S., Ma L., Wang Y.H., Watowich S.S., Jetten A.M., Tian Q., Dong C. Generation of T follicular helper cells is mediated by interleukin-21 but independent of T helper 1, 2, or 17 cell lineages. Immunity 2008, 29(1):138. URL http://dx.doi.org/10.1016/j.immuni.2008.05.009. 10.1016/j.immuni.2008.05.009.
7. Cua D.J., Sherlock J., Chen Y., Murphy C.A., Joyce B., Seymour B., Lucian L., To W., Kwan S., Churakova T., Zurawski S., Wiekowski M., Lira S.A., Gorman D., Kastelein R.A., Sedgwick J.D. Interleukin-23 rather than interleukin-12 is the critical cytokine for autoimmune inflammation of the brain. Nature 2003, 421(6924):744. URL http://dx.doi.org/10.1038/nature01355. 10.1038/nature01355.
8. Langrish C.L., Chen Y., Blumenschein W.M., Mattson J., Basham B., Sedgwick J.D., McClanahan T., Kastelein R.A., Cua D.J. IL-23 drives a pathogenic T cell population that induces autoimmune inflammation. J. Exp. Med. 2005, 201(2):233. URL http://dx.doi.org/10.1084/jem.20041257. 10.1084/jem.20041257.
9. Murphy C.A., Langrish C.L., Chen Y., Blumenschein W., McClanahan T., Kastelein R.A., Sedgwick J.D., Cua D.J. Divergent pro- and antiinflammatory roles for IL-23 and IL-12 in joint autoimmune inflammation. J. Exp. Med. 2003, 198(12):1951. URL http://dx.doi.org/10.1084/jem.20030896. 10.1084/jem.20030896.
10. Milner J.D., Brenchley J.M., Laurence A., Freeman A.F., Hill B.J., Elias K.M., Kanno Y., Spalding C., Elloumi H.Z., Paulson M.L., Davis J., Hsu A., Asher A.I., O'Shea J., Holland S.M., Paul W.E., Douek D.C. Impaired T(H)17 cell differentiation in subjects with autosomal dominant hyper-IgE syndrome. Nature 2008, 452(7188):773. URL http://dx.doi.org/10.1038/nature06764. 10.1038/nature06764.
11. Ma C.S., Chew G.Y., Simpson N., Priyadarshi A., Wong M., Grimbacher B., Fulcher D.A., Tangye S.G., Cook M.C. Deficiency of Th17 cells in hyper IgE syndrome due to mutations in STAT3. J. Exp. Med. 2008, 205(7):1551. URL http://dx.doi.org/10.1084/jem.20080218. 10.1084/jem.20080218.
12. Openshaw P.J., Tregoning J.S. Immune responses and disease enhancement during respiratory syncytial virus infection. Clin. Microbiol. Rev. 2005, 18(3):541. URL http://dx.doi.org/10.1128/CMR.18.3.541-555.2005. 10.1128/CMR.18.3.541-555.2005.
13. Van den Ham H.J., De Jager W., Bijlsma J.W., Prakken B.J., De Boer R.J. Differential cytokine profiles in juvenile idiopathic arthritis subtypes revealed by cluster analysis. Rheumatology. (Oxford). 2009, 48(8):899. URL http://dx.doi.org/10.1093/rheumatology/kep125. 10.1093/rheumatology/kep125.
14. + lymphocytes. J. Immunol. 2003, 171(10):5328.
15. Lund R., Ahlfors H., Kainonen E., Lahesmaa A.M., Dixon C., Lahesmaa R. Identification of genes involved in the initiation of human Th1 or Th2 cell commitment. Eur. J. Immunol. 2005, 35(11):3307. 10.1002/eji.200526079.
16. Lund R.J., Loytomaki M., Naumanen T., Dixon C., Chen Z., Ahlfors H., Tuomela S., Tahvanainen J., Scheinin J., Henttinen T., Rasool O., Lahesmaa R. Genome-wide identification of novel genes involved in early Th1 and Th2 cell differentiation. J. Immunol. 2007, 178(6):3648.
17. Stockis J., Fink W., Francois V., Connerotte T., De Smet C., Knoops L., Van der Bruggen P., Boon T., Coulie P.G., Lucas S. Comparison of stable human Treg and Th clones by transcriptional profiling. Eur. J. Immunol. 2009, 39(3):869. URL http://dx.doi.org/10.1002/eji.200838807. 10.1002/eji.200838807.
18. + T cells. Immunity 2009, 30(1):155. URL http://dx.doi.org/10.1016/j.immuni.2008.12.009. 10.1016/j.immuni.2008.12.009.
19. + T cell recent thymic emigrants are identified by protein tyrosine kinase 7 and have reduced immune function. J. Exp. Med. 2009, 206(2):275. URL http://dx.doi.org/10.1084/jem.20080996. 10.1084/jem.20080996.
20. Millenaar F.F., Okyere J., May S.T., Van Zanten M., Voesenek L.A., Peeters A.J. How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. BMC. Bioinformatics 2006, 7:137. URL http://dx.doi.org/10.1186/1471-2105-7-137. 10.1186/1471-2105-7-137.
21. R: A Language and Environment for Statistical Computing 2008, R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria, URL http://www.R-project.org,.
22. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. URL http://dx.doi.org/10.1186/gb-2004-5-10-r80. 10.1186/gb-2004-5-10-r80.
23. Gautier L., Cope L., Bolstad B.M., Irizarry R.A. Affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20(3):307. URL http://dx.doi.org/10.1093/bioinformatics/btg405. 10.1093/bioinformatics/btg405.
24. Smyth G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 2004, 3. Article3, URL http://dx.doi.org/10.2202/1544-6115.1027. 10.2202/1544-6115.1027.
25. Gett A.V., Hodgkin P.D. Cell division regulates the T cell cytokine repertoire, revealing a mechanism underlying immune class regulation. Proc. Natl. Acad. Sci. U.S.A. 1998, 95(16):9488.
26. Ansel K.M., Djuretic I., Tanasa B., Rao A. Regulation of Th2 differentiation and Il4 locus accessibility. Annu. Rev. Immunol. 2006, 24:607. URL http://dx.doi.org/10.1146/annurev.immunol.23.021704.115821. 10.1146/annurev.immunol.23.021704.115821.
27. Rothenberg E.V., Moore J.E., Yui M.A. Launching the T-cell-lineage developmental programme. Nat. Rev. Immunol. 2008, 8(1):9. URL http://dx.doi.org/10.1038/nri2232. 10.1038/nri2232.
28. Chiang E.Y., Kolumam G.A., Yu X., Francesco M., Ivelja S., Peng I., Gribling P., Shu J., Lee W.P., Refino C.J., Balazs M., Paler-Martinez A., Nguyen A., Young J., Barck K.H., Carano R.A., Ferrando R., Diehl L., Chatterjea D., Grogan J.L. Targeted depletion of lymphotoxin-alpha-expressing TH1 and TH17 cells inhibits autoimmune disease. Nat. Med. 2009, 15(7):766. URL http://dx.doi.org/10.1038/nm.1984. 10.1038/nm.1984.
29. Gao W., Thompson L., Zhou Q., Putheti P., Fahmy T.M., Strom T.B., Metcalfe S.M. Treg versus Th17 lymphocyte lineages are cross-regulated by LIF versus IL-6. Cell Cycle 2009, 8(9):1444.
30. Lai Kwan Lam Q., King Hung Ko O., Zheng B.J., Lu L. Local BAFF gene silencing suppresses Th17-cell generation and ameliorates autoimmune arthritis. Proc. Natl. Acad. Sci. U.S.A. 2008, 105(39):14993. URL http://dx.doi.org/10.1073/pnas.0806044105. 10.1073/pnas.0806044105.
31. Van den Ham H.J., De Boer R.J. From the two-dimensional Th1 and Th2 phenotypes to high-dimensional models for gene regulation. Int. Immunol. 2008, 20(10):1269. URL http://dx.doi.org/10.1093/intimm/dxn093. 10.1093/intimm/dxn093.