Molecular Characterization of a Novel Subtype of Pediatric Acute Lymphoblastic Leukemia.

Abstract

Gene expression profiling is a powerful tool to classify and predict subtypes of pediatric acute lymphoblastic leukemia (ALL). In addition to accurately classifying known subtypes of ALL, microarray analysis of 327 cases of ALL at our institution using Affymetrix U95 arrays identified a previously uncharacterized novel subgroup of 14 cases of B-ALL with a gene expression signature distinct from other leukemias, suggesting a unique pathogenesis. These cases lacked a recurring cytogenetic anomaly, showed a high frequency of aberrant expression of CD2, lacked molecular markers of other subtypes of ALL, and had a favorable prognosis. We have used several complementary candidate and genome-wide approaches to identify the molecular basis of this novel subtype. Gene expression profiling using Affymetrix U133A and B arrays was used to refine the signature, and when applied to an additional 36 cases of cytogenetically normal B-ALL, 5 cases were identified that share the novel gene expression profile. Intriguingly, the tyrosine kinase PDGFRA was overexpressed in the majority of the novel cases, with 6 novel cases showing exceedingly high levels of PDGFRA expression, which was confirmed by western blotting and flow cytometry. Unexpectedly, 3 of these cases harbored the FIP1L1-PDGFRA fusion characteristic of idiopathic hypereosinophilic syndrome. However, FISH examination demonstrated that this fusion was present in a minor subclone only. RT-PCR and FISH approaches failed to identify alternative PDGFRA fusions, and PDGFRA sequencing failed to identify evidence of activating mutations. Furthermore, in unstimulated cultures or following PDGF-AA stimulation, PDGFRA-overexpressing ALL blasts were not sensitive to imatinib (Gleevec). Other genes in the gene expression profile with potential roles in leukemogenesis, include include the B-cell receptor signaling mediator BRDG1 and the tyrosine phosphatase PTPRM. Using FISH and genomic sequencing of multiple candidates, no potentially leukemogenic abnormality has been identified. To determine if gene amplification, deletion, or copy-neutral loss of heterozygosity is characteristic of this subtype of ALL, genome-wide array-based comparative genomic hybridization and Affymetrix 100K single nucleotide polymorphism arrays were performed on all cases. Deletion of the CDKN2A/2B locus, and deletion of a region at 8p22–23.1 flanking the SPAG11 locus were each found in multiple cases, however no single unifying abnormality was identified. In summary, we have identified and characterized a novel subtype of B-ALL with unique gene expression signature, high incidence of CD2 and PDGFRA overexpression, and favorable outcome. Although no uniform causal molecular lesion has been identified, FIP1L1-PDGFRA fusion may represent one mechanism of PDGFRA overexpression. Further studies and analysis of additional cases may prove informative.