The Profile of Immunophenotype and Genotype Aberrations in Subsets of Pediatric T-Cell Acute Lymphoblastic Leukemia

Abstract

T-cell acute lymphoblastic leukemia (T-ALL) is a biologically heterogeneous malignancy, which reflects distinctive stages of T-cell differentiation arrest. We have revisited a cohort of pediatric T-ALL, in order to test if immunophenotypes associated with molecular alterations would predict the patient's outcome. Genetic mutations, translocations and copy number alterations were identified through Sanger sequencing, RT-PCR, FISH and multiplex ligation-dependent probe amplification (MLPA). We defined 8 immunophenotypic T-ALL subtypes through multiparametric flow cytometry: early T-cell precursor (ETP, n = 27), immature (n = 38), early cortical (n = 15), cortical (n = 50), late cortical (n = 53), CD4/CD8 double negative mature (n = 31), double positive mature (n = 35) and simple positive mature (n = 31) T-ALL. Deletions (del) or amplifications (amp) in at least one gene were observed in 87% of cases. The most frequent gene alterations were CDKN2A/B^del (71.4%), NOTCH1^mut (47.6%) and FBXW7^mut (17%). ETP-ALL had frequent FLT3^mut (22.2%) and SUZ12^del (16.7%) (p < 0.001), while CDKN2A/B^del were rarely found in this subtype (p < 0.001). The early cortical T-ALL subtype had high frequencies of NOTCH1^mut and IL7R^mut (71%, 28.6%, respectively), whereas, mature T-ALL with double positive CD4/CD8 had the highest frequencies of STIL-TAL1 (36.7%), LEF1^del (27.3%) and CASP8AP2^del (22.7%). The co-existence of two groups of T-ALL with NOTCH1^mut/IL7R^mut, and with TLX3/SUZ12^del/NF1^del/IL7R^mut, were characterized with statistical significance (p < 0.05) but only STIL-TAL1 (pOS 47.5%) and NOTCH1^WT/FBXW7^WT (pOS 55.3%) are predictors of poor T-ALL outcomes. In conclusion, we have observed that 8 T-ALL subgroups are characterized by distinct molecular profiles. The mutations in NOTCH1/FBXW7 and STIL-TAL1 rearrangement had a prognostic impact, independent of immunophenotype.

Keywords: T-cell acute lymphoblastic leukemia; childhood; early T-cell precursor acute lymphoblastic leukemia; immunophenotypic subtypes; molecular alterations; overall survival.

Figure 1

The frequencies and the concomitance of molecular alterations in 168 pediatric T-ALL cases. (A) Circos plot showing the overall co-occurrence of mutations, rearrangements, and CNA assessed through MLPA. Outer segments proportionally represent the alterations found in T-ALL. Interior lines connecting the outer segments proportionally demonstrate the concomitances among genetic alterations. (B) Number of cases with each molecular alteration in gray squares, and number of cases with concomitances between two alterations in white, green and red squares. Green squares represent positive while the red squares negative associations. Alterations ordered by type of abnormality. Rearrangements in blue, mutations in pink, CNA deletions in brown and amplifications in yellow.

Figure 2

Overview of molecular alterations identified in 168 samples according to T-ALL subtypes and grouped into recurrently altered pathways. ETP, early T cell precursror; DP, douple positive for CD4/CD8; SP, single positive for CD4/CD8; DN, double negative for CD4/CD8; mut, mutation; del, deletion; pos, positive; amp, amplification. Vertical lines represent each patient.

Figure 3

Overall survival curves in 60 months according to NOTCH1/FBXW7 (A) and STIL-TAL1 (B) status. Mut, Mutated; WT, Wild Type; pOS, probability of overall survival; CI, confidential interval; pos, positive.