WT1 mutations in T-ALL

The molecular mechanisms involved in disease progression and relapse in T-cell acute lymphoblastic leukemia (T-ALL) are poorly understood. We used single nucleotide polymorphism (SNP) array analysis to analyze paired diagnostic and relapsed T-ALL samples to identify recurrent genetic alterations in T-ALL. This analysis showed a notorious absence of acquired chromosomal changes at relapse. In addition, we identified deletions and associated mutations in the WT1 tumor suppressor gene in 2/9 samples. Subsequent analysis showed WT1 mutations in 28/211 (13.2%) of pediatric and 10/85 (11.7%) of adult T-ALL cases. WT1 mutations present in T-ALL are predominantly heterozygous frameshift mutations resulting in truncation of the C-terminal zinc finger domains of this transcription factor. WT1 mutations are most prominently found in T-ALL cases with aberrant rearrangements of the oncogenic TLX1, TLX3 and HOXA transcription factor oncogenes. Survival analysis demonstrated that WT1 mutations do not confer adverse prognosis in pediatric and adult T-ALL. Overall these results show that overt chromosomal instability does not seem to be a major mutagenic mechanism contributing to disease progression in T-ALL and the presence of WT1 mutations as a recurrent genetic alteration in T-ALL. DNA samples from pediatric T-ALL patients (n=9) obtained at diagnosis, remission and relapse were analyzed with the GeneChip Human Mapping 250K Sty Array (Affymetrix, Santa Clara, California), which contains 238,000 SNPs. Copy number and LOH analysis was performed with dCHIP. Probe intensity data for each array was normalized to a baseline array with median signal intensity using the “invariant set” model, as previously described 11. We used matched remission samples as a reference for copy number estimation and loss of heterozygosity (LOH) analysis. LOH was analyzed using a Hidden Markov Model in dChip and an inferred LOH call threshold of 0.5.