Abstract #LB-92: Frequent JAK mutations in pediatric acute lymphoblastic leukemia with poor outcome: A new therapeutic target in resistant disease.

Introduction: Relapsed acute lymphoblastic leukemia (ALL) is one of the most common childhood malignancies and carries a poor prognosis. To identify genetic determinants of outcome and potential therapeutic targets, we performed integrated genomic analysis in a cohort of 221 children with B-progenitor ALL at high risk of relapse who lacked known high-risk genetic alterations[e.g., BCR-ABL1 and hypodiploidy (Children\#8217;s Oncology Group P9906 study)]. We identified a group of cases characterized by very high incidence of relapse, genetic alteration of IKZF1, and a gene expression profile similar to BCR-ABL1 ALL, raising the possibility of the activation of an unidentified tyrosine kinase in these patients (Mullighan et al.; N Engl J Med 2009;360:470-80). Methods: We performed genomic resequencing of JAK1, JAK2, JAK3, and TYK2 in 187 cases in this cohort with available DNA. We examined the functional consequences of JAK mutations in murine pro-B cells and examined associations between JAK mutations and DNA copy number alterations, gene expression profile, and outcome. Results: Twenty patients (10.7%) harbored somatic, heterozygous, non-silent coding mutations in JAK1, JAK2, and JAK3, all of whom lacked known recurring translocations. Sixteen JAK2 mutations were identified, most commonly at or near R683 in the JAK2 pseudokinase domain (R683G: n=10; R683S, I682F, and QGinsR683: n=1). We also identified novel mutations in the JAK2 kinase domain (R867Q, D873N, and P933R), JAK1 pseudokinase domain (L624_R629>W, S646F, and V658F), and JAK3 (S789P). In contrast to previous studies suggesting that JAK2 mutations in ALL are exclusively observed in patients with Down syndrome (DS-ALL), only two mutations involved DS-ALL patients (n=9 sequenced). With the exception of JAK3 S789P, each mutation involved highly conserved residues in the kinase or pseudokinase JAK domains. The JAK2 mutations are likely to affect the interlobe interface of the pseudokinase domain, and the protein-protein interaction domain and active site of the kinase domain. Expression of JAK1 and JAK2 mutant alleles in Ba/F3 cells transduced with the murine erythropoietin receptor conferred growth factor independence, and flow cytometric phosphosignaling analysis demonstrated activation of JAK-STAT signaling following the expression of each mutant JAK allele. This in vitro transformation and JAK-STAT activation was abrogated by pharmacologic JAK inhibitors. The presence of JAK mutations was associated with deletion of IKZF1 and CDKN2A/B and poor outcome. The 4-year incidence of relapse was 71% for patients with JAK and IKZF1 alterations, compared to 23% for patients with neither lesion (P=0.0004). The gene expression profile of JAK-mutated ALL was highly similar to that of BCR-ABL1 ALL, which also has a high frequency of IKZF1 deletion and poor prognosis. Conclusions: These results expand the range of diseases associated with JAK mutations and show that lesions targeting multiple pathways, including lymphoid development (IKZF1), tumor suppression (CDKN2A/B), and tyrosine kinases (BCR-ABL1 or JAK), cooperate to induce aggressive ALL. JAK inhibition warrants clinical evaluation in this subset of high risk pediatric ALL.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr LB-92.