Identification of novel cluster groups in pediatric high-risk B-precursor acute lymphoblastic leukemia with gene expression profiling: correlation with genome-wide DNA copy number alterations, clinical characteristics, and outcome

Abstract

To resolve the genetic heterogeneity within pediatric high-risk B-precursor acute lymphoblastic leukemia (ALL), a clinically defined poor-risk group with few known recurring cytogenetic abnormalities, we performed gene expression profiling in a cohort of 207 uniformly treated children with high-risk ALL. Expression profiles were correlated with genome-wide DNA copy number abnormalities and clinical and outcome features. Unsupervised clustering of gene expression profiling data revealed 8 unique cluster groups within these high-risk ALL patients, 2 of which were associated with known chromosomal translocations (t(1;19)(TCF3-PBX1) or MLL), and 6 of which lacked any previously known cytogenetic lesion. One unique cluster was characterized by high expression of distinct outlier genes AGAP1, CCNJ, CHST2/7, CLEC12A/B, and PTPRM; ERG DNA deletions; and 4-year relapse-free survival of 94.7% ± 5.1%, compared with 63.5% ± 3.7% for the cohort (P = .01). A second cluster, characterized by high expression of BMPR1B, CRLF2, GPR110, and MUC4; frequent deletion of EBF1, IKZF1, RAG1-2, and IL3RA-CSF2RA; JAK mutations and CRLF2 rearrangements (P < .0001); and Hispanic ethnicity (P < .001) had a very poor 4-year relapse-free survival (21.0% ± 9.5%; P < .001). These studies reveal striking clinical and genetic heterogeneity in high-risk ALL and point to novel genes that may serve as new targets for diagnosis, risk classification, and therapy.

Figure 1

Hierarchical clustering identifies 8 cluster groups in high-risk ALL. Hierarchical clustering using 254 genes (provided in supplemental Table 7A) was used to identify clusters of patients with shared patterns of gene expression. Rows indicate 207 high-risk ALL patients from COG P9906; and columns, 254 probe sets. Shades of red represent expression levels higher than the median; and green, levels lower than the median. The cluster groups are numbered and prefixed by their method of probe set selection: H indicates high CV; C, COPA; and R, ROSE. (A) HC method for selection of probe sets. (B) COPA selection of probe sets. (C) ROSE selection of probe sets.

Figure 2

RFS in gene expression cluster groups. RFS is shown for each of the high CV clusters (A), COPA clusters (B), and ROSE clusters (C). Only the H6, C6, and R6 clusters (curves shown in blue) have a significantly better outcome compared with the entire cohort (dense line), whereas the H8, C8, and R8 clusters (curves shown in red) have a significantly poorer RFS. Hazard ratios and P values are shown in the bottom left of each panel.

Figure 3

Hierarchical clustering identifies similar clusters in an independent high-risk ALL cohort. Hierarchical clustering using 167 probe sets (provided in supplemental Table 7A) was used to identify clusters of patients with shared patterns of gene expression in a second cohort of high-risk ALL patients previously accrued to COG Trial CCG 1961. Rows indicate 99 patients from COG CCG 1961; and columns, 167 probe sets. Shades of red represent expression levels higher than the median; and green represents levels lower than the median. The cluster groups are prefixed by their method of probe set selection: H indicates high CV; C, COPA; and R, ROSE. (A) HC method for selection of probe sets. (B) COPA selection of probe sets. (C) ROSE selection of probe sets.

Figure 4

RFS in an independent high-risk ALL cohort. RFS for the 99 high-risk ALL patients on COG Trial CCG 1961 who were either clustered in cluster 8 or were in the remaining cohort using each different clustering method: HC (A), COPA (B), and ROSE (C). By each method, ALL patients clustered as H8 (A), C8 (B), or R8 (C) had a significantly worse RFS than the remaining patients in the cohort. Hazard ratios and P values are shown in the bottom left of each panel.