Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21

Abstract

We have previously identified a unique subtype of acute lymphoblastic leukemia (ALL) associated with a poor outcome and characterized by intrachromosomal amplification of chromosome 21 including the RUNX1 gene (iAMP21). In this study, array-based comparative genomic hybridization (aCGH) (n = 10) detected a common region of amplification (CRA) between 33.192 and 39.796 Mb and a common region of deletion (CRD) between 43.7 and 47 Mb in 100% and 70% of iAMP21 patients, respectively. High-resolution genotypic analysis (n = 3) identified allelic imbalances in the CRA. Supervised gene expression analysis showed a distinct signature for eight patients with iAMP21, with 10% of overexpressed genes located within the CRA. The mean expression of these genes was significantly higher in iAMP21 when compared to other ALL samples (n = 45). Although genomic copy number correlated with overall gene expression levels within areas of loss or gain, there was considerable individual variation. A unique subset of differentially expressed genes, outside the CRA and CRD, were identified when gene expression signatures of iAMP21 were compared to ALL samples with ETV6-RUNX1 fusion (n = 21) or high hyperdiploidy with additional chromosomes 21 (n = 23). From this analysis, LGMN was shown to be overexpressed in patients with iAMP21 (P = 0.0012). Genomic and expression data has further characterized this ALL subtype, demonstrating high levels of 21q instability in these patients leading to proposals for mechanisms underlying this clinical phenotype and plausible alternative treatments.

Fig. 1.

Genomic analysis of DNA and cell suspension from patient 5989. (A) BAC aCGH results: chromosome 21 is positioned horizontally, with the centromeric to telomeric positions running from left to right, respectively. Dye swap experiments 1 and 2 are shown by the blue and red lines, respectively. Double deviation of both these experiments from a normal value of 1.00 demonstrates loss or gain of DNA material. Deviation of the red and blue line >1.00 shows loss or gain of copy number, respectively. (B) Examples of the FISH confirmation of aCGH data: each numbered FISH probe corresponds to the same highlighted clone in A. (C) Oligo aCGH data for this patient. Chromosome 21 is positioned as in A. The scatter plot demonstrates mean log intensity ratios at 5,000-bp intervals along chromosome 21. Segmentation analysis is shown as red horizontal lines.

Fig. 2.

Box plot diagrams illustrating LGMN expression (A) and expression of those genes within the CRA (B), compared to other ALL subtypes. On the x axis are shown seven ALL subtypes, BCR-ABL, E2A-PBX1, T-ALL, HD + 21, ETV6-RUNX1, iAMP21, and others. The y axis represents the relative gene expression level of either LGMN or all those genes within the CRA. Each box plot shows the distribution of expression levels from 25th to 75th percentile. The median is shown as a line across the box, whereas the + is the calculated mean expression level for the particular subtype. The dotted line indicates the inner fence, and a value outside the outer fence is shown as an asterisk.