Figure 4. Whole genome transcriptome analysis of Th22 compared with Th1, Th2, and Th17 cells reveals unique functional profiling of Th22.

Th22 clones (n = 3) and Th1, Th2, and Th17 clones (n = 5) were stimulated for 6 hours with a TCR stimulus, and the mRNA expression profile was analyzed in a whole genome microarray approach. (A) Differential Th22 transcriptome, shown as a dLogPlot of Th22 pool genes that were upregulated or downregulated compared with Th1, Th2, and Th17 pools. (B) Th22 transcriptome separation, shown by total up- and downregulated genes in the Th22 pool compared with the single subsets of Th1, Th2, and Th17 clones. (C) Clonal phenotypes. Intensity of immunologically relevant genes of T cell subsets is shown as a heatmap. The Agilent array (single color, technology 14850) contains multiple probe sets for some genes that were empirically observed to differ in intensity from a gene-covering selection of probes. The differential abundance of these probes can originate from alternative splice variants or differential mRNA stability, for example. Alternative probes showing differences in intensity in the present study are indicated by Roman numerals; probe set sequences are available at http://www.agilent.com. Compared with CCL15^I (A_23_P218369), CCL15^II (A_24_P301501) recognizes an additional splice variant. For FGF1, 16 splice variants are already suggested, and the difference between Th1 and Th22 may originate in differential exon usage (shown are FGF1^I, A_23_P136433; FGF1^II, A_24_P251969; FGF1^III, A_24_P111106; FGF1^IV, A_23_P213336). For FGF12, 11 different splice variants are known, and differential signals could reflect differential splicing (shown are FGF12^I, A_24_P334300; FGF12^II, A_23_P211727). Probe RORC2^II (A_23_P372910) binds in the 3′ untranslated region, whereas RORC2^I (A_23_P324107) binds in the coding region. FOXO4^II (A_24_P379165) binds the 3′ end of the gene, for which up to 3 splice variants may exist (also shown is FOXO4^I, A_24_P911066). The more sensitive BNC-2^I (A_23_P43690) binds exon 6, whereas BNC-2^II (A_23_P43684) binds to the C-terminal exon 7. For CCL23, 2 splice variants are known, of which variant 1 is recognized by CCL23^I (A_24_P319088) and both variants by CCL23^II (A_24_P133905). (D) Overview of the Th22 phenotype.