Detection of Cytogenetic Abnormalities Associated with Outcome Differences in Acute Myeloid Leukemia Using Array-Based Comparative Genomic Hybridization (aCGH) Analysis.

The presence of abnormal cytogenetic findings at diagnosis is an independent indicator of the outcome in patients with acute myeloid leukemias (AML). Recent availability of high-resolution analysis by aCGH technology has facilitated rapid detection of cytogenetic abnormalities previously undetected by the conventional G-banded karyotyping. Aim: To determine whether specific cytogenetic abnormalities, as detected by the aCGH analysis, are associated with differences in clinical outcomes in a group of patients with AML treated uniformly with the standard chemotherapy regimen of Idarubicin and Cytarabine.

A total of 111 patients with newly diagnosed AML (Median age: 55 years; range, 22 to 73 years) were enrolled in the study. All patients were treated with Idarubicin 12 mg/m² IV daily x 3 days and Cytarabine 1.5 g/m² by continuous IV infusion daily x 4 days (3 days in patients older than 60). The diagnostic bone marrow samples from 48 of these patients were analyzed by aCGH using a 44K CGH array with a spatial resolution of 50-75 kb (Agilent Inc). The aberrations detected by aCGH using CGH Analytics (Agilent Inc, Santa Clara, CA) and the Nexus Copy Number Software (Biodiscovery Inc, El Segundo, CA) were compared to conventional G-banded karyotyping results. Correlation of aCGH-detected aberrations with clinical outcome was performed by Kaplan-Meier analysis and log-rank test.

Complete remission (CR) was achieved in 34/48 (71%) patients, out of which 16 (47%) patients relapsed in less than 1 year (Median: 18.5 weeks, range: 1-44 weeks) and the remaining 18 (53%) patients sustained CR beyond one year (Median: 89 weeks, range: 58-132 weeks). The comparison of aCGH findings between the patients achieving CR and the resistant patients showed significant association of loss of a 155 kilobase region on 5q33.3 with achievement of CR (p<0.05). This 5q33.3 locus harboring two genes, transcription factor EBF1 and transmembrane protein RNF145, was deleted in 9/34 (26.5%) patients achieving CR, but not in the resistant patients (0/14, 0%). Additionally, the loss of 17p11.2-q11.1 spanning 3194 kilobases was associated with poor overall survival (Kaplan-Meier analysis, p=0.0096). This deleted region involved 342 genes and 12 microRNAs. Conventional karyotyping detected loss of 17p in 10/48 (21%) patients, whereas the aCGH analysis detected 17p losses in two additional patients (12/48, 25%). By allowing delineation of the precise boundaries of the aberrations, aCGH demonstrated that deletion of 17p did not involve the TP53 gene in 3/12 (25%) patients, although these three patients showed genetic instability and poor clinical outcome. Overall, the aCGH findings were in concordance with the conventional karyotyping results. The aCGH analysis was able to detect aberrations in samples containing blast count as low as 5%. In addition, aCGH identified previously undetected aberrations, as small as 5 kb, of currently unknown significance.

The aCGH analysis indicates that the loss of 5q33.3 is associated with achievement of complete remission and the loss of 17p11.2-q11.1 is associated with poor overall survival in AML patients treated with Idarubicin and Cytarabine. Array CGH analysis provides a useful and rapid diagnostic tool for identifying these high-risk patients. The biologic roles of EBF1 and RNF145 in therapy response warrant further investigation.

No relevant conflicts of interest to declare.