Figure 1. Expression levels of PTPRG and PTPRC, but not of PTPN6 at the beginning of nilotinib study treatment are associated with response after 9 months of treatment.

The RNA of total, peripheral blood leukocytes of CML patients in chronic phase was isolated and mRNA expression levels of 38 PTPs (Table S1) were analyzed. GUSB and B2M were used as control genes. (A) 66 patients were grouped according to their individual BCR-ABL1^IS (MR⁴ yes or no) after 9 months of nilotinib treatment. The mRNA levels for three selected PTPs in these patient categories are shown. Since the TIGER study protocol allowed inclusion of patients TKI pretreated for up to six weeks, and up to 6 months with hydroxyurea, we reassessed the actual treatment schedule of all 66 patients after unblinding. We defined two sub-cohorts of patients: (B) in one cohort we excluded 12 of 66 patients that had been TKI pretreated, or discontinued nilotinib within the first 9 months of treatment (n = 54). (C) In the second cohort, we additionally excluded all patients pretreated with hydroxyurea for more than 2 days, and patients that reduced nilotinib dose for more than 3 weeks (n = 35). Each point represents the relative PTP expression value of one patient, bars show mean values +/− standard deviation (SD). Differences in PTP mRNA expression between the patient groups were statistically tested. ns (not significant) if p > 0.05; ^* if p < 0.05; ^** if p < 0.01. P values were calculated using the likelihood ratio test. For details and confidence limits see Table 2.