Elevated GLI1 and PTCH1 transcript levels and trisomy 12 and DHH expression are biomarkers for SMO inhibitor responsiveness in CLL. (A) qPCR for GLI1 and PTCH1 in CLL samples of the different response groups. High GLI1 (n = 24; P = .0260, Cochran-Armitage trend test) or PTCH1 (n = 24; P = .0006, Cochran-Armitage trend test) transcript levels (> 3-fold than the median) compared with GAPDH and relative to the median of all samples are correlated with good response to SMO inhibitor treatment in CLL (single data information in supplemental Table 4, patients 2-11, 13-17, 23-25, 36, 37, 42, 46, 47, and 60). (B) Distribution of trisomy 12 between the different response groups. Presence of trisomy 12 (n = 11; P = .0006, Cochran-Armitage trend test) correlates with good response to SMO inhibitor treatment. (C) Comparison of DHH expression (> 20% positive CLL cells by IHC) or elevated relative PTCH1 and GLI1 transcript levels compared with GAPDH (> 3-fold than the median) between patients positive for trisomy 12 and other patients. Single data for IHC are included in supplemental Table 3, and single data for TaqMan results are included in supplemental Table 4. (D) Percentage of viable cells (annexin V/7-AAD staining) after treatment of primary CLL cells with the SMO inhibitor cyclopamine or the HH-blocking Ab 5E1 for 48 hours compared with control. Patients positive for trisomy 12 (n = 4) show a dose-dependent decrease in viable cells after treatment with SMO inhibitors or the 5E1 Ab, whereas samples positive for del 13q14 (n = 3) show only a decrease in viable cells after SMO inhibitor treatment, but an increase in viable cells after treatment with the 5E1 Ab (analyzed patients 1, 7, 18, 60, 66, 67, and 68).