PTEN microdeletions in T-cell acute lymphoblastic leukemia are caused by illegitimate RAG-mediated recombination events

Abstract

Key Points• Microdeletions represent an additional inactivation mechanism for PTEN in human T-cell acute lymphoblastic leukemia.• PTEN microdeletions are RAG-mediated aberrations.Phosphatase and tensin homolog (PTEN)-inactivating mutations and/or deletions are an independent risk factor for relapse of T-cell acute lymphoblastic leukemia (T-ALL) patients treated on Dutch Childhood Oncology Group or German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia protocols. Some monoallelic mutated or PTEN wild-type patients lack PTEN protein, implying that additional PTEN inactivation mechanisms exist. We show that PTEN is inactivated by small deletions affecting a few exons in 8% of pediatric T-ALL patients. These microdeletions were clonal in 3% and subclonal in 5% of patients. Conserved deletion breakpoints are flanked by cryptic recombination signal sequences (cRSSs) and frequently have non-template-derived nucleotides inserted in between breakpoints, pointing to an illegitimate RAG recombination-driven activity. Identified cRSSs drive RAG-dependent recombination in a reporter system as efficiently as bona fide RSSs that flank gene segments of the T-cell receptor locus. Remarkably, equivalent microdeletions were detected in thymocytes of healthy individuals. Microdeletions strongly associate with the TALLMO subtype characterized by TAL1 or LMO2 rearrangements. Primary and secondary xenotransplantation of TAL1-rearranged leukemia allowed development of leukemic subclones with newly acquired PTEN microdeletions. Ongoing RAG activity may therefore actively contribute to the acquisition of preleukemic hits, clonal diversification, and disease progression. (Blood. 2014;124(4):567-578)

The relevance of PTEN-AKT in relation to NOTCH1-directed treatment strategies in T-cell acute lymphoblastic leukemia

“…21,35 Similar results were reported for other cohorts of pediatric T-ALL patients treated using other protocols. 32,33 In the Berlin-Frankfurt-Munster study, the presence of NOTCH1-activating mutations in addition to PTEN-inactivating mutations predicts for good outcome similar to that of patients harboring NOTCH1-activating mutations only, 32 suggesting that NOTCH1-mutations can antagonize the unfavorable effect of PTEN aberrations.…”

“…26,27 Restoring PTEN levels in these cell lines decreased cell size and induced apoptosis by suppressing the PI3K-AKT pathway. 28 Studies by others [29][30][31][32][33][34] and our group 21,35 revealed aberrations in the PTEN-PI3K-AKT pathway in approximately 23% of primary samples obtained from pediatric T-ALL patients. With respect to T-ALL subtypes, we have shown that PTEN aberrations are strongly associated with TAL-or LMO-rearranged leukemia in children 21 and the same was observed in adult T-ALL cohorts.…”

“…38 Recently, we reported that approximately 8% of T-ALL patients have a RAG-mediated microdeletion in the phosphatase domain that disrupts the reading frame ( Figure 1). 35 In addition, mutations have been identified in PI3K and AKT; specifically, 9% of pediatric T-ALL patients have a mutation in either the catalytic (PIK3CA) or regulatory (PIK3R1) subunit of PI3K, and 2% of patients have a mutation in AKT itself (Figure 2A). 21,30 Many T-ALL patients with a heterozygous PTEN mutation also acquire a deletion 21 or microdeletion 35 in their remaining wild-type allele in leukemic subclones 29 that may give rise to relapse.…”

“…35 In addition, mutations have been identified in PI3K and AKT; specifically, 9% of pediatric T-ALL patients have a mutation in either the catalytic (PIK3CA) or regulatory (PIK3R1) subunit of PI3K, and 2% of patients have a mutation in AKT itself (Figure 2A). 21,30 Many T-ALL patients with a heterozygous PTEN mutation also acquire a deletion 21 or microdeletion 35 in their remaining wild-type allele in leukemic subclones 29 that may give rise to relapse. This phenomenon was demonstrated functionally by Clappier et al who used an elegant human T-ALL xenograft transplantation model in mice and found the selection and preferential outgrowth of PTEN-inactivated leukemic cells.…”

Oncogenetic mutations combined with MRD improve outcome prediction in pediatric T-cell acute lymphoblastic leukemia

“…27,30 We did not search for microdeletions. 31 In brief, the oncogenetic low-risk (gLoR) group was defined by the presence of an N/F mutation and the absence of an R/P mutation, and the oncogenetic high-risk (gHiR) group was defined by N/F germ line (GL) and R/P GL or altered N/F mutations and R/P altered, as for adult GRAALL patients. 27 MRD status and outcome MRD analysis was conducted with a sensitivity threshold of 10…”