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In Western countries, gene alterations involving the CRLF2‐JAK signaling pathway are identified in approximately 50–60% of patients with Down syndrome‐associated acute lymphoblastic leukemia (DS‐ALL), and this pathway is considered a potential therapeutic target. The frequency of BTG1 deletions in DS‐ALL is controversial. IKZF1 deletions, found in 20–30% of DS‐ALL patients, are associated with a poor outcome and EBF1 deletions are very rare (∼2%). We analyzed 38 patients to determine the frequencies and clinical implications of CRLF2‐JAK pathway genetic alterations and recurrent gene deletions in Japanese DS‐ALL patients. We confirmed a high incidence of P2RY8‐CRLF2 (29%) and JAK2 mutations (16%), though the frequency of P2RY8‐CRLF2 was slightly lower than that in Western countries (∼50%). BTG1 deletions were common in our cohort (25%). IKZF1 deletions were detected in 25% of patients and associated with shorter overall survival (OS). EBF1 deletions were found at an unexpectedly high frequency (16%), and at a significantly higher level in P2RY8‐CRLF2‐positive patients than in P2RY8‐CRLF2‐negative patients (44% vs. 4%, P = 0.015). Deletions of CDKN2A/B and PAX5 were common in P2RY8‐CRLF2‐negative patients (48 and 39%, respectively) but not in P2RY8‐CRLF2‐positive patients (11% each). Associations between these genetic alterations and clinical characteristics were not observed except for inferior OS in patients with IKZF1 deletions. These results suggest that differences exist between the genetic profiles of DS‐ALL patients in Japan and in Western countries, and that P2RY8‐CRLF2 and EBF1 deletions may cooperate in leukemogenesis in a subset of Japanese DS‐ALL patients. © 2014 Wiley Periodicals, Inc.

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Introduction: Children with Down syndrome (DS) have a higher incidence of acute lymphoblastic leukemia (ALL) than children without DS. DS-ALL patients have poorer survival than non-DS-ALL patients due to both a high relapse rate and increased treatment-related mortality. DS-ALL is characterized by increased incidence of gene alterations involving CRLF2-JAK pathway. We previously confirmed a high incidence of the P2RY8-CRLF2 fusion (29%) and JAK2 mutations (16%) in Japanese DS-ALL patients, though the frequency of P2RY8-CRLF2 was slightly lower than that in Western populations (~50%). Recently, a European group reported that driver mutations in RAS (KRAS and NRAS) recurred to a similar extent (36%) as JAK2 mutations (29%) or P2RY8-CRLF2 (33%) in DS-ALL patients, and RAS mutations were almost completely mutually exclusive with JAK2 mutations. However, there have been no studies on RAS pathway mutations in Asian patients with DS-ALL. Objective: To clarify the incidence of RAS pathway mutations and their prognostic value in Japanese patients with DS-ALL. Patients and methods: In this study, we performed mutation analyses of 32 genes encoding signal-transducing molecules, receptor tyrosine kinases, epigenetic regulators and components of the cohesin complex in 32 DS-ALL patients (8 with P2RY8-CRLF2 and 24 without P2RY8-CRLF2) using target deep sequencing. Target regions were enriched using the HaloPlex Target Enrichment System and sequencing was performed on an Illumina MiSeq instrument. Kaplan-Meier estimates were used to calculate event-free survival (EFS) and overall survival (OS). Results: We identified JAK2 and RAS pathway mutations in 6 (19%) and 12 [KRAS (n=4), PTPN11 (n=2), NRAS (n=1), FLT3 (n=1), KRAS and NRAS (n=1), NRAS and PTPN11 (n=1), NRAS and FLT3 (n=1), and NRAS and NF1 (n=1); 38%] patients, respectively. All 6 patients with JAK2 mutation were positive for P2RY8-CRLF2, whereas only 1 of 12 patients with RAS pathway mutations were positive for P2RY8-CRLF2. No patients had mutations in both JAK2 and RAS pathway, indicating that JAK2 and RAS pathway mutations are mutually exclusive. In total, 19 RAS pathway mutations were found in 12 patients, and 8 of 19 mutations had low variant allele frequencies between 1 and 10%, suggesting that these mutations are involved in the progression rather than the initiation of DS-ALL. There were no statistically significant differences in gender, age at diagnosis, initial white blood cell count, NCI risk group, recurrent cytogenetic abnormalities, EFS (5-year EFS, 77.8% vs. 66.1%, p =0.48) and OS (5-year OS, 79.0% vs. 66.7%, p =0.75) between patients with and without RAS pathway mutations. Conclusions: RAS pathway mutations were identified in Japanese DS-ALL patients at a similar frequency to that in Western populations, and this pathway could be a potential therapeutic target. RAS pathway mutations had no clinical impact in the present cohort, and more patients need to be evaluated to clarify the exact clinical implications of RAS pathway mutations in DS-ALL patients. Disclosures No relevant conflicts of interest to declare.