CD4⁺T-cell gene-expression signature at aGVHD onset. For this analysis, samples from the 2 cohorts were pooled. All recipients without aGVHD or with grade ≥2 aGVHD were included in the analysis (No GVHD, n = 35; GVHD, n = 24). (A) Gene-expression profiles of CD4⁺ T cells from 24 patients at aGVHD onset compared with 35 patients without aGVHD in cohorts 1 and 2. Orange and light blue dots represent transcripts that were significantly up- and downregulated in recipients at aGVHD onset compared with No GVHD recipients, respectively, with FDR < 0.05. P values were calculated using an unpaired Student t test. Adjusted P values (FDR) were calculated using the Benjamini-Hochberg method to correct for multiple comparisons. (B) Results of QuSAGE conducted on CD4⁺ T-cell gene-expression profiles from aGVHD and No GVHD recipients. Plotted is the negative logarithm to the base 10 of the P values for the 6 modules with significantly different pathway activity (FDR < 0.05) at GVHD onset compared with No GVHD recipients. (C) Transcript levels of TGFBR1, SMAD3, and IGF2R in CD4⁺ T cells from recipients without aGVHD (No GVHD) and at aGVHD onset (GVHD). These genes showed decreased expression at aGVHD onset compared with recipients without GVHD (P < .05; FDR < 0.1). (D) Transcript levels of BCL3, BCL10, ICOS, and PSMD7 in CD4⁺ T cells from recipients without aGVHD and at aGVHD onset. These genes showed increased expression at aGVHD onset compared with recipients without aGVHD (P < .05; FDR < 0.1). P values were calculated using an unpaired Student t test. Adjusted P values (FDR) were calculated using the Benjamini-Hochberg method to correct for multiple comparisons. Nominal P values are shown in panels B and D.