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, <i>n</i> = 27), immature (<i>n</i> = 38), early cortical (<i>n</i> = 15), cortical (<i>n</i> = 50), late cortical (<i>n</i> = 53), CD4/CD8 double negative mature (<i>n</i> = 31), double positive mature (<i>n</i> = 35) and simple positive mature (<i>n</i> = 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 <i>CDKN2A/B</i>^del (71.4%), <i>NOTCH1</i>^mut (47.6%) and <i>FBXW7</i>^mut (17%). ETP-ALL had frequent <i>FLT3</i>^mut (22.2%) and <i>SUZ12</i>^del (16.7%) (<i>p</i> < 0.001), while <i>CDKN2A/B</i>^del were rarely found in this subtype (<i>p</i> < 0.001). The early cortical T-ALL subtype had high frequencies of <i>NOTCH1</i>^mut and <i>IL7R</i>^mut (71%, 28.6%, respectively), whereas, mature T-ALL with double positive CD4/CD8 had the highest frequencies of <i>STIL-TAL1</i> (36.7%), <i>LEF1</i>^del (27.3%) and <i>CASP8AP2</i>^del (22.7%). The co-existence of two groups of T-ALL with <i>NOTCH1</i>^mut<i>/IL7R</i>^mut, and with <i>TLX3/SUZ12</i>^del<i>/NF1</i>^del/<i>IL7R</i>^mut, were characterized with statistical significance (<i>p</i> < 0.05) but only <i>STIL-TAL1</i> (pOS 47.5%) and <i>NOTCH1</i>^WT/<i>FBXW7</i>^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 <i>NOTCH1/FBXW7</i> and <i>STIL-TAL1</i> rearrangement had a prognostic impact, independent of immunophenotype.