Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia

Abstract

Changes in gene dosage are a major driver of cancer, known to be caused by a finite, but increasingly well annotated, repertoire of mutational mechanisms. This can potentially generate correlated copy-number alterations across hundreds of linked genes, as exemplified by the 2% of childhood acute lymphoblastic leukaemia (ALL) with recurrent amplification of megabase regions of chromosome 21 (iAMP21). We used genomic, cytogenetic and transcriptional analysis, coupled with novel bioinformatic approaches, to reconstruct the evolution of iAMP21 ALL. Here we show that individuals born with the rare constitutional Robertsonian translocation between chromosomes 15 and 21, rob(15;21)(q10;q10)c, have approximately 2,700-fold increased risk of developing iAMP21 ALL compared to the general population. In such cases, amplification is initiated by a chromothripsis event involving both sister chromatids of the Robertsonian chromosome, a novel mechanism for cancer predisposition. In sporadic iAMP21, breakage-fusion-bridge cycles are typically the initiating event, often followed by chromothripsis. In both sporadic and rob(15;21)c-associated iAMP21, the final stages frequently involve duplications of the entire abnormal chromosome. The end-product is a derivative of chromosome 21 or the rob(15;21)c chromosome with gene dosage optimized for leukaemic potential, showing constrained copy-number levels over multiple linked genes. Thus, dicentric chromosomes may be an important precipitant of chromothripsis, as we show rob(15;21)c to be constitutionally dicentric and breakage-fusion-bridge cycles generate dicentric chromosomes somatically. Furthermore, our data illustrate that several cancer-specific mutational processes, applied sequentially, can coordinate to fashion copy-number profiles over large genomic scales, incrementally refining the fitness benefits of aggregated gene dosage changes.

Figure 1. Rearrangements of chromosome 21 in patient PD9020a

A: Rearrangement and copy number pattern. The temporal order of the three major rearrangement events are marked ①, ② and ③. Rearrangements are separated based on their orientation: D, deletion-type; TD, tandem duplication-type; HH, head-to-head inverted; TT, tail-to-tail inverted. B: Copy number jump distribution, showing the copy number at each end of each rearrangement. C: Copy number step distribution, showing the distribution in magnitude of copy number change at copy number segmentation breakpoints. D: Metaphase showing multiple signals for RUNX1 clustered on a single chromosome (large green signal) compared to the normal chromosome 21 (small paired green signals). The red signals indicate two normal copies of ETV6 on the chromosomes 12. Inset shows a partial G-banded karyotype of chromosomes 21. E: Model for the evolution of the iAMP21 chromosome. At each stage, newly synthesized sister chromatids are distinguished by a blue outline.

Figure 2. Rearrangements of der(15;21) in patient PD7170a

A: Rearrangement and copy number pattern. The temporal order of the two major rearrangement events are marked ① and ②. Rearrangements are separated based on their orientation: D, deletion-type; TD, tandem duplication-type; HH, head-to-head inverted; TT, tail-to-tail inverted. B: Copy number jump distribution, showing the copy number at each end of each rearrangement. C: copy number step distribution, showing the distribution in magnitude of copy number change at copy number segmentation breakpoints. D: Representative metaphases: Left-hand cell shows multiple signals for RUNX1 (large red signals) clustered on two regions on the abnormal chromosome. And normal copies of ETV6 on chromosome 12 (green). Right-hand cell has been painted for chromosomes 15 (green) and 21 (red). Inset shows partial G-banded karyotype: normal chromosome 15, normal chromosome 21 and isochromosome der(15;21). E: Left-hand cell shows representative metaphase from a non-leukaemic cell in patient PD10009a with rob(15;21)c, hybridized with centromere-specific probes for chromosomes 15 (green) and 13 and 21 (red), confirming that the Robertsonian chromosome is dicentric. Right-hand cell shows a leukaemia metaphase in which der(15;21) iAMP21 chromosome retains the chromosome 21 centromere (red), but not the chromosome 15 centromere (green). F: Model for evolution of iAMP21 in rob(15;21)c. Newly synthesized sister chromatids are indicated by a blue outline.

Figure 3. Rearrangement patterns of the iAMP21 chromosome in the remaining patients

Rearrangement and copy number patterns for chromosome 21 of sporadic iAMP21 ALL patients (A) and der(15;21) rearrangements in der(15;21) iAMP21 ALL patients (B). The inferred temporal orders of the major rearrangement events are shown with symbols ①, ② and ③. In patients PD4117a and PD9021a, the fold-back rearrangement demarcating the second BFB repair breakpoint have probably been lost or obscured due to subsequent rearrangement events, and a ‘?’ symbol is used to denote the uncertainty of their location. Inferred evolution of the derivative iAMP21 chromosomes are shown in the bottom panel. WCD – whole-chromosome duplication, WC – whole chromosome. Events with incomplete understanding are labeled ‘?’.

Figure 4. Chromothripsis alters the copy number landscape of chromosome 21 in a non-random fashion

Chromosome arm-level (A) and zoomed-in view (B) of chromosome 21, showing gene expression, copy number (CN) distribution, chromothripsis effect and distribution of rearrangement breakpoints. In the gene expression panels, positive strand genes are shown in blue and negative strand genes are shown in red. C: Correlation between average rate of deletion in the Beroukhim et al. dataset and chromothripsis effect for chromosome 21. IQR – inter-quartile range.