In Acute Myeloid Leukemia with Complex Karyotype TP53 Alterations Are Associated with Specific Genomic Aberrations and Predict Inferior Survival.

Abstract 2632

Poster Board II-608

In acute myeloid leukemia (AML) complex karyotype is defined as the presence of ≥3 chromosome abnormalities in the absence of one of the chromosomal rearrangements listed in the category “AML with recurrent genetic abnormalities” (WHO 2008). This subset of AML accounts for approximately 10 to 15 % of all AML and it is characterized by a very poor prognosis. To identify novel genomic regions of interest in this AML subgroup, we recently applied microarray-based techniques (array-comparative genomic hybridization [CGH] and single nucleotide polymorphism [SNP] analysis) allowing high-resolution genome-wide screening of genomic imbalances in 245 patients; 171 of the 245 (70%) patients were enrolled in clinical protocols using intensive chemotherapy. Applying these techniques, we identified deletions of 17p13 encompassing the TP53 locus in 94 of 245 (38%) cases. Based on these findings and the fact that TP53 is a frequently affected gene in numerous malignancies, we aimed to investigate its role in complex karyotype AML. Therefore, we screened 188 of the 245 patients forTP53 mutations either by direct sequencing of exon 5 to 9 or by denaturating high-performance liquid chromatography of exon 4 to 10 on a WAVE® system followed by direct sequencing of the positive cases. In total, we identified 137 mutations (exon 4 [e4] n=2; e5 n=41; e6 n=26; e7 n=35; e8 n=26; e10 n=1; splice sites n=6) in 106 patients (56%) with a maximum of four mutations per case. Of these 137 mutations, 108 were missense mutations, 15 frame shift mutations, 8 nonsense mutations, and 6 were located at intronic splice sites.

Combining the findings from array-based and mutation analyses, TP53 gene alterations were identified in 129 of 188 (69%) patients. Of note, 29% of these cases showed biallelic TP53 gene alterations with deletion of one allele and at least one mutation in the remaining allele.

When correlating TP53 alterations (mutations and/or deletions) with genomic data from array-based analyses, we found positive correlations with the presence of 5q and 7q losses (Chi-square test P < .001 and P = .001, respectively), total number of deletions (P < .001), gains (P = .002), high-level DNA amplifications (P < .001), and genomic complexity as measured by total number of aberrations per case (P < .001). Correlation of TP53 alterations with clinical characteristics revealed that patients with TP53 alterations were older (median age 60 versus 55 years, P = .01) and showed in trend a lower WBC (median, 6.6 versus 14.2 × 10⁹/L, P = .14); there was no difference in bone marrow and blood blast counts, in platelet counts, or in type of AML (de novo vs. secondary vs. treatment-related). Clinical outcome analyses were restricted to patients enrolled in prospective clinical trials (n=171). AML exhibiting a TP53 alteration had significantly lower complete remission (CR) rates [25% (26/104) versus 56% (24/43), P < .001], inferior event-free survival (EFS, P = .009), relapse-free survival (RFS, P = .02), and overall survival (OS, P < .001) compared with TP53 wild type AML. In multivariate models for achievement of CR, RFS, and OS, TP53 alteration retained its significance as an independent risk factor (CR: OR 0.38, P < .001; RFS: HR 1.65, P = .02; OS: HR: 2.15, P = .002).

In conclusion, TP53 is the most frequently known affected gene in complex karyotype AML. We found that the TP53 status is associated with specific genomic aberrations as well as the degree of genomic complexity, a finding that fits well into the TP53 pathomechanism of genomic instability. Importantly, among AML with complex karyotype TP53 alterations significantly predicted inferior outcome allowing for a further refinement of this AML subgroup.