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Genetic Landscape of High Hyperdiploid Childhood Acute Lymphoblastic Leukemia

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Genetic Landscape of High Hyperdiploid Childhood Acute Lymphoblastic Leukemia Genetic landscape of high hyperdiploid childhood acute lymphoblastic leukemia Kajsa Paulssona,1, Erik Forestierb, Henrik Lilljebjörna, Jesper Heldrupc, Mikael Behrendtzd, Bryan D. Younge, and Bertil Johanssona aDepartment of Clinical Genetics, University and Regional Laboratories, and cDepartment of Pediatrics, Skåne University Hospital, Lund University, SE-221 85 Lund, Sweden; bDepartment of Clinical Sciences, Pediatrics, University of Umeå, SE-901 85 Umeå, Sweden; dDepartment of Pediatrics, Linköping University Hospital, SE-581 85 Linköping, Sweden; and eInstitute of Cancer, Barts and the Royal London School of Medicine, London EC1M 6BQ, United Kingdom Edited* by Janet D. Rowley, University of Chicago, Chicago, IL, and approved October 12, 2010 (received for review May 21, 2010) High hyperdiploid acute lymphoblastic leukemia (ALL) is one of the however, it is possible that as yet unidentified primary aberra- most common malignancies in children. It is characterized by gain tions are present but are not detected because of the low reso- of chromosomes, typically +X, +4, +6, +10, +14, +17, +18, and +21, lution of most genetic screening techniques. Such hidden primary +21; little is known about additional genetic aberrations. Approx- events have been reported previously in aneuploid tumors, e.g., fi imately 20% of the patients relapse; therefore it is clinically im- the recent identi cation of structural rearrangements resulting in CRLF2 portant to identify risk-stratifying markers. We used SNP array deregulation of cytokine receptor-like factor 2 ( )ina analysis to investigate a consecutive series of 74 cases of high large proportion of ALL in patients with Down syndrome and microdeletions leading to the transmembrane protease, serin 2 hyperdiploid ALL. We show that the characteristic chromosomal TMPRSS2 gains are even more frequent than previously believed, indicating ( )/v-ets erythroblastosis virus E26 oncogene homolog (ERG) hybrid gene in prostate cancer (16, 17). Identification of a that karyotyping mistakes are common, and that almost 80% of fusion gene in high hyperdiploid ALL would be of major clinical the cases display additional abnormalities detectable by SNP array importance, possibly simplifying diagnostic procedures and pro- analysis. Subclonality analysis strongly implied that the numerical viding novel treatment options. aberrations were primary and arose before structural events, Although high hyperdiploidy generally confers a favorable suggesting that step-wise evolution of the leukemic clone is com- prognosis in childhood ALL, ∼20% of the patients suffer a re- mon. An association between duplication of 1q and +5 was seen (P = lapse, and 10% succumb to the disease (5, 7). Identification of 0.003). Other frequent abnormalities included whole-chromosome additional recurrent changes could aid in the identification of the uniparental isodisomies (wUPIDs) 9 and 11, gain of 17q not associ- high-risk cases and would be of great clinical importance. The ated with isochromosome formation, extra gain of part of 21q, only specific genetic markers that now are used for risk stratifi- deletions of ETS variant 6 (ETV6), cyclin-dependent kinase inhibitor cation in some centers are the “triple trisomies” (i.e., +4, +10, 2A (CKDN2A) and paired box 5 (PAX5), and PAN3 poly(A) specific and +17), which denote a lower-risk group in the Children’s ribonuclease subunit homolog (PAN3) microdeletions. Comparison Oncology Group (COG) protocol (18, 19). None of the other of whole-chromosome and partial UPID9 suggested different path- genetic abnormalities that have been shown to be recurrent in ogenetic outcomes, with the former not involving CDKN2A. Finally, addition to the chromosomal gains—including point mutations two cases had partial deletions of AT rich interactive domain 5B of fms-related tyrosine kinase 3 (FLT3), neuroblastoma RAS (ARID5B), indicating that acquired as well as constitutional variants viral oncogene homolog (NRAS), v-Ki ras2 Kirsten rat sarcoma KRAS in this locus may be associated with pediatric ALL. Here we provide viral oncogene homolog ( ), and protein tyrosine phos- PTPN11 a comprehensive characterization of the genetic landscape of high phatase, non receptor type 11 ( ), microdeletions of, e.g., cyclin-dependent kinase inhibitor 2A (CDKN2A) (9p21.3), ETS hyperdiploid childhood ALL, including the heterogeneous pattern of ETV6 PAX5 secondary genetic events. variant 6 ( ) (12p13.2), and paired box 5 ( ) (9p13.2), and structural aberrations such as dup(1q) and i(17q)—has proved to affect outcome, and hence there is a need for novel cute lymphoblastic leukemia (ALL) is the most common prognostic markers in high hyperdiploid childhood ALL (2). ∼ form of childhood malignancy, with a yearly incidence of 4/ In the present study, we used SNP array analyses to investigate A – 100,000 person-years in children 1 14 y old (1). Twenty to the genomes of a consecutive series of high hyperdiploid child- fi – twenty- ve percent display high hyperdiploidy (51 67 chromo- hood ALL. We show that the pattern of chromosomal gains is somes), making high hyperdiploid cases one of the largest sub- even more specific than indicated by standard cytogenetic anal- groups of pediatric cancer (2). Clinically, high hyperdiploid ALL ysis and that there is a genetic heterogeneity in this subgroup – is associated with age of 3 5 y, a relatively low WBC count, and regarding the additional genetic events. a B-cell precursor immunophenotype (3–7). The prognosis is favorable, with 5-y overall survival rates (OS) close to 90% (5, 7). Results MEDICAL SCIENCES Several lines of evidence suggest that the initiating transforming – Chromosomal Gains in High Hyperdiploid ALL. The SNP array event may occur in utero (8 10), but the etiology remains un- analysis showed that the median modal number was 55 (range known. Recently, two independent, large, genome-wide associ- 51–63) among the 74 cases. Chromosome 21 was gained in 100% ation studies reported linkage to a locus in the gene AT rich of the cases, followed by chromosome X in 95%, chromosomes 6 interactive domain 5B (ARID5B) at 10q21.2, but it is unclear and 14 in 91%, chromosome 18 in 86%, chromosome 4 in 80%, how this region affects the risk of developing high hyperdiploid chromosome 17 in 77%, chromosome 10 in 76%, chromosome 8 childhood ALL (11, 12). in 36%, and chromosome 5 in 26% (Figs. 1 and 2 and Table S1; Genetically, high hyperdiploid ALL is characterized by mas- sive aneuploidy, manifesting as a nonrandom gain of chromo- somes, typically including some or all of +X, +4, +6, +10, +14, +17, +18, and +21,+21, but other trisomies and tetrasomies are Author contributions: K.P., B.D.Y., and B.J. designed research; K.P., H.L., J.H., and M.B. seen also. Monosomies, on the other hand, are exceedingly rare performed research; K.P., E.F., and B.J. analyzed data; and K.P. and B.J. wrote the paper. (2, 13). The pathogenetic consequences of the chromosomal The authors declare no conflict of interest. gains remain poorly understood, but it generally is believed that *This Direct Submission article had a prearranged editor. gene dosage effects are of importance (2, 14, 15). No other 1To whom correspondence should be addressed. E-mail: [email protected]. characteristic genetic abnormality, such as a fusion gene, has This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. been found in the vast majority of high hyperdiploid ALL cases; 1073/pnas.1006981107/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1006981107 PNAS | December 14, 2010 | vol. 107 | no. 50 | 21719–21724 Downloaded by guest on October 1, 2021 Fig. 1. Chromosome gains detected by SNP array analysis in 74 cases of high hyperdiploid childhood ALL. Xf denotes gain of the X chromosome in females; Xm in males. “Trisomy” and “Tetrasomy” of Xm and Y correspond to one and two extra copies of these chromosomes, respectively. Chromo- somes X, 4, 6, 10, 14, 17, 18, and 21 were all gained in more than 70% of the cases; chromosome 21 was gained in 100% of the cases. Extra copies of chromosomes 8 and 5 were present in 36% and 26% of the cases, re- spectively, whereas all other chromosomes were gained in <20% of the 74 cases. Tetrasomies were seen for chromosomes 4, 8, 10, 14, 18, 21, and X, and pentasomy was seen for chromosome 21 only. for examples of SNP array results, see Fig. 3). The remaining chromosomes were all gained in less than 20% of the cases (range 0–17%); extra chromosomes 1 and 19 were not present in any of the cases (Fig. 1). The majority of the gains were tri- somies, but tetrasomies were detected for chromosomes 21 (72% of the 74 cases), 14 (16%), 10 (11%), 18 (8.1%), X (6.1% of Fig. 2. Overview of acquired genetic imbalances and UPIDs detected by SNP girls), 8 (2.7%), and 4 (1.4%), and pentasomy was seen for array analysis in 74 cases of high hyperdiploid childhood ALL. Each line chromosome 21 (6.8%) (Fig. 1). All but one tetrasomy were corresponds to an aberration in the chromosome on the left. Thin lines “2:2”; i.e., both homologs had been duplicated. Thirty-nine cases correspond to aberrations detected in one case; thicker lines indicate aber- (53%) had concurrent gains of chromosomes 4, 10, and 17 [i.e., rations detected in eight cases. Blue lines denote gains, red lines denote fi were positive for the “triple trisomies” (18, 19)]. There were no losses, and green lines denote UPIDs. This gure was made using the fi Genome-Wide Viewer software, freely available at http://www.well.ox.ac. signi cant differences in event-free survival (EFS) or OS be- ∼ tween cases with and without the triple trisomies or between uk/ jcazier/GWA_View.html. cases positive and negative for gain of chromosome 18, as pre- viously has been debated (5) (Fig.
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