C20orf94 deletion Is Strongly Associated with TEL/AML1 Rearrangement and Links Illegitimate V(D)J Recombination with Gender Bias In Childhood Acute Lymphoblastic Leukemia

Abstract 1718

Childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent structural and/or numeric genetic aberrations and has been consistently reported to occur with a 20% higher incidence in males relative to females. We performed 100k Affymetrix SNP-array analysis in a selected set of 20 ALL samples. In five out of these 20 patients, a previously described deletion of the 5' region of C20orf94 – a gene coding for an uncharacterized DNA repair-associated protein – was observed. The results were validated by high-resolution custom-made CGH array analysis. As the breakpoints within C20orf94 were defined to recurrent positions, we next applied a PCR assay to screen diagnostic leukemic specimens of a representative cohort of 513 patients enroled into the German multicenter trial ALL-BFM 2000 on treatment of childhood ALL. Here, C20orf94 deletions were detected in 164 patients (32.0%). None of 134 available remission samples exhibited the deletion as well as none of 145 healthy blood donors. Sequencing analysis in 40 patients revealed specific breakpoint junctions with typical characteristics of illegitimate V(D)J recombination in all samples. When analyzing the association of C20orf94 deletion with clinical characteristics in the entire screening cohort, the most significant interrelationships were observed for male gender (75.6% of positives; P < 0.001) and TEL/AML1-rearranged ALL (43.3% of positives; P < 0.001). A negative association was observed for a DNA index of ≥1.16 (3.0% of positives; P < 0.001). In contrast, C20orf94 deletion did not show any effect on treatment outcome. Additional screening of an independent cohort of 232 TEL/AML1-rearranged ALLs identified 145 positive samples and not only confirmed the high incidence of C20orf94 deletion in this subgroup, but also allowed validation of its specific association with male gender (55.9% of positives; P = 0.049). In 21 of 22 (17 TEL/AML1-positive and 5 other pre B cell ALLs) paired initial and relapse leukemic samples C20orf94 deletions were maintained at relapse. Breakpoint sequencing of paired initial and relapse leukemic samples revealed a stable monoclonal breakpoint sequence in 9 patients indicating stability of C20orf94 deletions during disease progression. The remaining samples either developed heterogeneity of C20orf94 breakpoints at relapse after monoclonality at initial diagnosis or initially already showed a polyclonal pattern. Backtracking of C20orf94 deletions to birth in seven TEL/AML1-positive patients using material derived from Guthrie cards did not yield any positive results. In conclusion, we describe the frequent and uniform deletion of the 5' part of C20orf94 in childhood ALL - particularly in males and the TEL/AML1-rearranged subtype. These findings suggest a potential role for C20orf94 deletion in the pathogenesis of childhood ALL and point to differences in illegitimate V(D)J recombination as one potential explanation for the observed and currently only poorly understood gender bias in childhood ALL.