Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia

Abstract

Most children with acute lymphoblastic leukemia (ALL) can be cured, but the prognosis is dismal for the minority of patients who relapse after treatment. To explore the genetic basis of relapse, we performed genome-wide DNA copy number analyses on matched diagnosis and relapse samples from 61 pediatric patients with ALL. The diagnosis and relapse samples typically showed different patterns of genomic copy number abnormalities (CNAs), with the CNAs acquired at relapse preferentially affecting genes implicated in cell cycle regulation and B cell development. Most relapse samples lacked some of the CNAs present at diagnosis, which suggests that the cells responsible for relapse are ancestral to the primary leukemia cells. Backtracking studies revealed that cells corresponding to the relapse clone were often present as minor subpopulations at diagnosis. These data suggest that genomic abnormalities contributing to ALL relapse are selected for during treatment, and they point to new targets for therapeutic intervention.

Figure 1. Deletions of CDKN2A/B and ETV6 in relapsed ALL

A, Log₂ ratio SNP 6.0 copy number data (median smoothed with a window of five markers; blue is deletion and red is gain) of chromosome 9p flanking CDKN2A/B for 9 representative cases showing new or more extensive deletions at this locus at relapse. Deletions in selected cases were confirmed by quantitative genomic PCR (table S17). B coverage of the locus for one case. Each vertical red line represents the genomic position and log₂ ratio copy number of an individual marker. This case has acquired a homozygous deletion extending involving exon 2 of CDKN2B and all of CDKN2A at relapse. C-H Backtracking of CNAs using lesion-specific genomic PCR assays in ALL. C-E ADD3, E-H C20orf94. Log₂ ratio copy number heatmaps for diagnosis and relapse samples are shown in panels C and F; the genomic location of SNP probes and regions of deletion are shown in D and G; E and H: PCR for each lesion was performed for diagnosis, relapse, and where available, germline DNA samples. In each case, a CNA-specific PCR product was observed at diagnosis as well as relapse, indicating that each CNA was present at diagnosis.

Figure 2

Clonal relationship of diagnosis and relapse samples in ALL. The majority of relapse cases have a clear relationship to the presenting diagnosis leukemic clone, either arising through the acquisition of additional genetic lesions, or more commonly, arising from a ancestral (pre-diagnosis) clone. In the latter scenario, the relapse clone retains some but not all of the lesions found in the diagnostic sample, while acquiring new lesions. Lesion specific backtracking studies revealed that in most cases the relapse clone exists as a minor sub-clone within the diagnostic sample prior to the initiation of therapy. In only a minority of ALL cases does the relapse clone represent the emergence of a genetically distinct and thus unrelated second leukemia.