Genome-wide copy number profiling reveals molecular evolution from diagnosis to relapse in childhood acute lymphoblastic leukemia

Abstract

The underlying pathways that lead to relapse in childhood acute lymphoblastic leukemia (ALL) are unknown. To comprehensively characterize the molecular evolution of relapsed childhood B-precursor ALL, we used human 500K singlenucleotide polymorphism arrays to identify somatic copy number alterations (CNAs) in 20 diagnosis/relapse pairs relative to germ line. We identified 758 CNAs, 66.4% of which were less than 1 Mb, and deletions outnumbered amplifications by approximately 2.5:1. Although CNAs persisting from diagnosis to relapse were observed in all 20 cases, 17 patients exhibited differential CNA patterns from diagnosis to relapse. Of the 396 CNAs observed in 20 relapse samples, only 69 (17.4%) were novel (absent in the matched diagnosis samples). EBF1 and IKZF1 deletions were particularly frequent in this relapsed ALL cohort (25.0% and 35.0%, respectively), suggesting their role in disease recurrence. In addition, we noted concordance in global gene expression and DNA copy number changes (P ‫؍‬ 2.2 ؋ 10 ؊16 ). Finally, relapse-specific focal deletion of MSH6 and, consequently, reduced gene expression were found in 2 of 20 cases. In an independent cohort of children with ALL, reduced expression of MSH6 was associated with resistance to mercaptopurine and prednisone, thereby providing a plausible mechanism by which this acquired deletion contributes to drug resistance at relapse. (Blood. 2008;112: 4178-4183) IntroductionOwing to advances in risk-adapted combination chemotherapy, the great majority of children with acute lymphoblastic leukemia (ALL) will survive beyond 5 years after initial presentation of leukemia. 1 However, 15% to 20% of ALL patients will have a relapse, making relapsed ALL the fifth most common childhood cancer in the United States. 2 Unlike newly diagnosed ALL, the prognosis of relapsed ALL is relatively poor, even with aggressive retrieval therapies. Five-year event-free survival of relapsed ALL is only 10% to 40%, depending on the length of first remission. 3 Consistent with clinical observations, Klumper et al have demonstrated that leukemia cells obtained at relapse were dramatically more resistant to many chemotherapeutic agents compared with cells from the initial tumor of the same person. 4 For example, the drug concentration of prednisone needed to kill 50% of leukemia cells (LC 50 ) increased by as much as 357-fold from diagnosis to relapse.Analyses of antigen receptor gene rearrangements indicate that, in almost all cases, the relapsed population of cells is clonally related to the original diagnostic sample. 5 Thus, whereas 50% of relapsed leukemia samples exhibit a novel clonal marker that was absent at diagnosis, 94% of relapse samples share at least one marker with the corresponding initial leukemia. Similar studies comparing genetic lesions between diagnosis and relapse provide evidence for the evolution or selection of the relapse leukemic clone. 6,7 Lesions specific to relapse are of particular importance because they constitute strong candidates responsible for drug resis...

Deletions of IKZF1 and SPRED1 are associated with poor prognosis in a population-based series of pediatric B-cell precursor acute lymphoblastic leukemia diagnosed between 1992 and 2011

“…First, we investigated a population-based series, not focusing solely on high risk ALL, 4 T-ALL, 15 specific cytogenetic subgroups in BCP ALL, 16,17 or excluding some subgroups. 13 Also, none of our patients was lost to follow-up in contrast to several prior studies and for some of our cases the observation time was close to 20 years with a median follow-up of 10 years, whereas the maximum follow-up time has been 10 years or less in earlier studies, 14,17,18,20,21 (Figures 1 and 2). Furthermore, the SNP arrays used provide higher resolution (>1 M SNPs) compared with prior SNP array-based ALL studies (250K-500K), 4,[13][14][15][16][17][18] making it possible to delineate imbalances in greater detail and to identify previously unknown gene targets, as exemplified below.…”

“…The reason for this may partly be due to the smaller number of samples analyzed in most previous studies, because when reviewing the supplementary data from published SNP array analyses of ALL, 4,13,14,16 we identified only one relapse sample, reported by Mullighan et al 4 , with a deletion including SPRED1 among other genes; this is the only prior study comprising a similar number of patients as our study. Furthermore, it is possible that the higher resolution of our SNP arrays could be an additional reason, since two of our SPRED1 deletions were small focal deletions that could have escaped detection in previous studies.…”

“…A number of studies aiming at elucidating the underlying mechanisms for relapse has compared genetic features in paired diagnostic and relapse samples using conventional cytogenetic, 7,8 clone-specific polymerase chain reaction (PCR), 9,10 fluorescence in situ hybridization (FISH), 11,12 and single nucleotide polymorphism (SNP) array analyses, 4,[13][14][15][16][17] revealing that the relapsed clones can be identical to the ones seen at diagnosis, display additional changes (clonal evolution), or harbor both additional, identical as well as fewer changes (evolution from a preleukemic/ancestral clone). The two latter evolution patterns indicate outgrowth of therapy-resistant minor subclones.…”

“…4,[9][10][11][12]16,17 In addition, high-resolution genomic profiling has identified genes, for example CDKN2A, ETV6, IKZF1, and EBF1, that are more frequently deleted in samples from patients who subsequently relapse than in samples from those remaining in fist complete remission (CR1). 4,13,14,18 However, whether these deletions serve as independent prognostic markers is still unclear. 13,14,18,19 4 In the present study, SNP array analyses were performed on diagnostic, CR1, relapse (R), and induction failure (IF) samples from pediatric ALL patients to identify copy number aberrations and uniparental isodisomies (UPDs) associated with R/IF.…”

“…25 Although these genes have not been reported to be deleted in ALL or otherwise associated with this disease, the observed 6p imbalances overlap to some extent with 6p deletions reported in Down syndrome-associated ALL and other histone clusters on 6p have been shown be deleted in pediatric ALL, with methylation arrays suggesting that histone deletions are associated with methylation alterations. 26,27 Thus, HIST1H2BD and HIST1H1E may be added to the growing list of acute leukemia-associated genes, for example DNMT3, EZH2, HOX family, and MLL, that 13 contribute to the leukemogenic process through deregulated CpG methylation or histone modification. [28][29][30][31] Among the other recurrent gene targets, most -CDKN2A, EBF1, ETV6, IKZF1, PAX5, RAG1, and TBL1XR1 -have been thoroughly discussed previously.…”