Absence of biallelic TCRgamma deletion predicts early treatment failure in pediatric T-cell acute lymphoblastic leukemia

Abstract

Purpose: To identify children with T-cell acute lymphoblastic leukemia (T-ALL) at high risk of induction chemotherapy failure by using DNA copy number analysis of leukemic cells collected at diagnosis.

Patients and methods: Array comparative genomic hybridization (CGH) was performed on genomic DNA extracted from diagnostic lymphoblasts from 47 children with T-ALL treated on Children's Oncology Group Study P9404 or Dana-Farber Cancer Institute Protocol 00-01. These samples represented nine patients who did not achieve an initial complete remission, 13 who relapsed, and 25 who became long-term, event-free survivors. The findings were confirmed in an independent cohort of patients by quantitative DNA polymerase chain reaction (DNA-PCR), an assay that is well suited for clinical application.

Results: Analysis of the CGH findings in patients in whom induction chemotherapy failed compared with those in whom induction chemotherapy was successful identified the absence of biallelic TCRgamma locus deletion (ABD), a characteristic of early thymocyte precursors before V(D)J recombination, as the most robust predictor of induction failure (P < .001). This feature was also associated with markedly inferior event-free (P = .002) and overall survival (P < .001) rates: 25% versus 58% and 25% versus 72%, respectively. Using a rapid and inexpensive quantitative DNA-PCR assay, we validated ABD as a predictor of a poor response to induction chemotherapy in an independent series of patients.

Conclusion: Lymphoblasts from children with T-ALL should be evaluated at diagnosis for deletion within the TCRgamma locus. Patients lacking biallelic deletion, which confers a high probability of induction failure with contemporary therapy, should be assigned to alternative therapy in the context of a prospective clinical trial.

Fig 1.

Relationship of absence of biallelic TCRγ locus deletion (ABD) status to clinical outcome. (A) Array comparative genomic hybridization (CGH) data obtained from diagnostic T-cell acute lymphoblastic leukemia (T-ALL) specimens from 47 children with T-ALL treated on Children's Oncology Group (COG) P9404 or Dana-Farber Cancer Institute (DFCI) 00-01 protocols are shown as a dChip plot of CGH segmented log₂ copy number ratios at the TCRγ locus. Red arrows denote patients with ABD, with the threshold for biallelic TCRγ deletion defined as a CGH log₂ ratio of −1.5, corresponding to 35% of normal copy number. The red box denotes the location of the intron between the most 3′ V pseudoexon (TRGV11) and the most 5′ J exon (TRGJP1), which should be involved by any deletion within the TCRγ locus as a result of V-J recombination. Location of the polymerase chain reaction (PCR) primer pairs at TCRγ and at the ANLN control, which were used for the quantitative DNA PCR (Q-PCR) assay to detect ABD, are indicated. (B, C) Kaplan-Meier event-free and overall survival rates for patients with T-ALL classified by ABD status. Tick marks indicate patients still at risk. (D) ABD status by CGH was validated by Q-PCR, with use of the TCRγ and ANLN control primer whose locations are shown in (A). Results of the CGH and DNA PCR analyses were concordant in 97% (37 of 38) samples. IF, induction failure; Chr, chromosome.

Fig 2.

Early T-cell precursor (ETP) gene expression signature identifies a subset of patients with a poor prognosis. (A) Hierarchical clustering analysis of gene expression data based on a set of genes differentially expressed in ETP T-cell acute lymphoblastic leukemia (T-ALL) classifies 14 of our 40 patients as harboring the ETP gene expression signature. (B, C) Kaplan-Meier analyses of event-free survival and overall survival in T-ALL with or without the ETP gene expression signature. Tick marks indicate patients still at risk.

Fig 3.

Overlap between absence of biallelic TCRγ locus deletion (ABD) and early T-cell precursor (ETP) T-cell acute lymphoblastic leukemia patients. (A) ABD versus ETP gene expression signature. (B) ABD versus ETP immunophenotype, which identified only one high-risk patient in this series.

Fig 4.

Kaplan-Meier event-free survival analysis for an independent cohort of children with T-cell acute lymphoblastic leukemia (T-ALL) treated in the Children's Oncology Group AALL0434 and Dana-Farber Cancer Institute 05-01 clinical trials, whose absence of biallelic TCRγ locus deletion (ABD) status was evaluated by quantitative DNA polymerase chain reaction. The diagnostic specimens analyzed represented all of the high-risk patients who were available to us, including patients with treatment failure or with minimal residual disease (MRD) > 1% at the end of induction, and all patients in continuous complete remission > 2.5 years from T-ALL diagnosis. Note that MRD levels ≥ 1% at the end of induction have been associated with outcomes nearly as poor as those of patients with induction failure, with an estimated 5-year relapse-free survival rate of only 14%. Tick marks indicate patients still at risk.