The significance of PTEN and AKT aberrations in pediatric T-cell acute lymphoblastic leukemia

Abstract

Background: PI3K/AKT pathway mutations are found in T-cell acute lymphoblastic leukemia, but their overall impact and associations with other genetic aberrations is unknown. PTEN mutations have been proposed as secondary mutations that follow NOTCH1-activating mutations and cause cellular resistance to γ-secretase inhibitors.

Design and methods: The impact of PTEN, PI3K and AKT aberrations was studied in a genetically well-characterized pediatric T-cell leukemia patient cohort (n=146) treated on DCOG or COALL protocols.

Results: PTEN and AKT E17K aberrations were detected in 13% and 2% of patients, respectively. Defective PTEN-splicing was identified in incidental cases. Patients without PTEN protein but lacking exon-, splice-, promoter mutations or promoter hypermethylation were present. PTEN/AKT mutations were especially abundant in TAL- or LMO-rearranged leukemia but nearly absent in TLX3-rearranged patients (P=0.03), the opposite to that observed for NOTCH1-activating mutations. Most PTEN/AKT mutant patients either lacked NOTCH1-activating mutations (P=0.006) or had weak NOTCH1-activating mutations (P=0.011), and consequently expressed low intracellular NOTCH1, cMYC and MUSASHI levels. T-cell leukemia patients without PTEN/AKT and NOTCH1-activating mutations fared well, with a cumulative incidence of relapse of only 8% versus 35% for PTEN/AKT and/or NOTCH1-activated patients (P=0.005).

Conclusions: PI3K/AKT pathway aberrations are present in 18% of pediatric T-cell acute lymphoblastic leukemia patients. Absence of strong NOTCH1-activating mutations in these cases may explain cellular insensitivity to γ-secretase inhibitors.

Figure 1.

PTEN aberrations result in low PTEN expression in pediatric T-ALL patients. (A) Schematic representation of identified mutations in the phosphatase- and C2-domains of the PTEN gene. Missense mutations are indicated by open triangles, whereas a silent mutation is presented as a filled gray triangle. Nonsense mutations due to insertions and/or deletions are indicated by a filled black triangle. (B) Total PTEN and (C) phosphorylated PTEN (S380) expression levels in wild-type and PTEN-mutated pediatric T-ALL patient samples and T-ALL cell lines, analyzed by reverse-phase protein microarray. Patients with a PTEN deletion are represented by a filled circle and patients with PTEN missense or nonsense mutations by an open circle. Wild-type patients that lack PTEN protein expression are indicated by a black square. *Patient sample #335; this patient bears a PTEN R129G missense mutation.

Figure 2.

Defective splicing of PTEN transcripts. Analysis of alternative PTEN splicing in 2 wild-type PTEN patients and PTEN expression (#419 and #914), seven PTEN wild-type patients and cell lines without PTEN expression (#768, #8628, #9243, HPBALL, LOUCY, HSB2 and KE37), 5 patients with silent or intronic mutations (#2720, #2698, #2845, #2790 and #540) and 7 patients with mono-allelic PTEN mutations or deletions (#9160, #9919, #9963, #2759, #2852, #321 and #8815). RT-PCR I covers wild-type and alternative PTEN transcripts from exon 1 through exon 6, whereas RT-PCR II covers wild-type and alternative PTEN transcripts from exon 6 through 9. *Patients and cell lines expressing aberrant transcripts.

Figure 3.

T-ALL patients without PTEN/AKT and/or NOTCH1-activating mutations have a good outcome. Cumulative incidence of relapse (CIR) (A) and event-free survival (EFS) (B) for DCOG and COALL pediatric T-ALL patients. Different patient groups are indicated in the legend. Log rank P values in a stratified analysis for DCOG and COALL protocols have been indicated for indicated mutation groups relative to PTEN/AKT and NOTCH1/FBXW7 non-mutated patients (i.e. wild-type patients).