Genome-wide approach to identify risk factors for therapy-related myeloid leukemia

Abstract

Using a target gene approach, only a few host genetic risk factors for treatment-related myeloid leukemia (t-ML) have been defined. Gene expression microarrays allow for a more genome-wide approach to assess possible genetic risk factors for t-ML. We assessed gene expression profiles (n ¼ 12 625 probe sets) in diagnostic acute lymphoblastic leukemic cells from 228 children treated on protocols that included leukemogenic agents such as etoposide, 13 of whom developed t-ML. Expression of 68 probes, corresponding to 63 genes, was significantly related to risk of t-ML. Hierarchical clustering of these probe sets clustered patients into three groups with 94, 122 and 12 patients, respectively; 12 of the 13 patients who went on to develop t-ML were overrepresented in the latter group (Po0.0001). A permutation test indicated a low likelihood that these probe sets and clusters were obtained by chance (Po0.001). Distinguishing genes included transcription-related oncogenes (v-Myb, Pax-5), cyclins (CCNG1, CCNG2 and CCND1) and histone HIST1H4C. Common transcription factor recognition elements among similarly up-or downregulated genes included several involved in hematopoietic differentiation or leukemogenesis (Maz, PU.1, ARNT). This approach has identified several genes whose expression distinguishes patients at risk of t-ML, and suggests targets for assessing germline predisposition to leukemogenesis.

Genome scan implicates adhesion biological pathways in secondary leukemia

“…We also compared allele frequencies in the larger group of controls (n ¼ 169) to allele frequencies in the 13 cases. We compared ALL blast gene expression from microarrays in cases vs controls (as previously reported), 16 as variation in gene expression is partially reflective of germline genomic variability, 24,25 which could reflect inherited susceptibility to secondary leukemia.…”

“…We hypothesized that there might be common pathways whose genes are 'hit' by various mechanisms (that is, LOH, increased or decreased copy number or expression, or germline genotypes), with an ultimate functional consequence that could lead to secondary leukemia. Genes that distinguished cases from controls identified from SNP and gene expression analyses included 1695 genes, and each was classified as to the method by which it had been invoked (that is, allele frequency differences in cases vs controls, LOH or copy number differences in secondary leukemia blasts vs germline, or via gene expression differences 16 ). For each gene, we tabulated the number of cases harboring the 'high-risk' genotype associated with the development of secondary leukemia (Supplementary Table 3).…”

“…We combined these genes with those from our previous analysis of genes whose expression differentiated cases from controls. 16 We queried the KEGG database 31 to determine which pathways were overrepresented by genetic alteration in cases of secondary leukemia. Independently, we performed a pathway analysis on the basis of genes from our experiments in cell lines whose SNP frequencies predicted high levels of etoposide-induced MLL rearrangements.…”

“…16 Genotyping DNA (500 ng) was digested with XbaI and HindIII restriction enzymes, amplified, labeled and hybridized to the Affymetrix GeneChip Human Mapping100K Set according to the manufacturer's instructions. The chips were scanned, and genotype calls were made using GeneChip DNA Analysis Software.…”

“…For our clinical studies, we compared 116 204 single nucleotide polymorphisms (SNPs) in germline vs secondary leukemia blast DNA (Figure 1), and germline SNPs in cases of secondary leukemia vs identically treated controls. The DNA polymorphism data were merged with genome-wide microarray expression data from a separate, partially overlapping cohort of cases and controls 16 to identify high-risk pathways associated with secondary leukemia. For our experimental studies, we conducted a genome-wide survey of polymorphisms that predict the in vitro formation of leukemogenic chromosomal translocations.…”