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.

Advantages and Limitations of SNP Array in the Molecular Characterization of Pediatric T-Cell Acute Lymphoblastic Leukemia

“…Similar concomitance between particular gene deletions (WT1, IFNA, RB1, and CTCF) was previously reported by Zhang et al (51). We did not observe the co-occurrence between SUZ12 and CDKN2AB alterations, although Noronha et al (4) indicate such concomitance in their study. The study of Karrman et al (15) revealed that CDKN2A deletions were significantly associated with a high WBC count, but we did not find a similar association in our cohort.…”

“…The lack or reduced expression of RUNX1 also affects the activity of MYB, MYC , and GATA3 oncogenes, which confirms the key role of RUNX1 in the pathogenesis of T-ALL ( 24 ). In the described cohort of patients, RUNX1, MYB , and GATA3 changes affected 8.1% ( n = 7), 12.8% ( n = 11), and 1.2% ( n = 1) of cases, respectively, which corresponds to the results that have been previously reported ( 4 , 9 , 25 ).…”

“…The activity of this signaling pathway is closely related to the normal course of hematopoiesis; thus, the disturbed expression of key Wnt pathway molecules is characteristic of leukemias (26). Other studies reported a similar frequency of LEF1 alterations in T-ALL (4,27,28). Moreover, Wang and Zhang (29) indicated that lower expression of LEF1 is associated with ETP-ALL, but we cannot compare our data to published results because of the limited number of ETP-ALL cases (n = 2) in our cohort.…”

“…T-cell acute lymphoblastic leukemia has been divided into four subtypes according to the European Group for the Immunological Classification of Leukemia (EGIL): pro-T EGIL T-I (cCD3 + , CD7 + ), pre-T EGIL T-II (cCD3 + , CD7 + , and CD5/CD2 + ), cortical T EGIL T-III (cCD3 + , Cd1a + , sCD3 +/− ), and mature-T EGIL T-IV (cCD3 + , sCD3 + , CD1a − ) ( 2 ). Early T-cell precursor (ETP)–ALL is characterized as an additional subtype of T-cell ALL with blasts usually negative for CD1a and CD8, weak expression of CD5, and the presence of one or more myeloid or stem cell markers ( 3 , 4 ). The prognostic factors and risk stratification are different in T-ALL when compared to B-lineage leukemia.…”

Facts and Challenges in Immunotherapy for T-Cell Acute Lymphoblastic Leukemia

“…Unique gene expression profiles were later found to be associated with leukemic arrest of thymocytes at different developmental stages [ 15 ], leading to the definition of new T-ALL subgroups characterized by the driver oncogenes or oncogene fusions ( TAL/LMO, TLX1, TLX3 , HOXA , and MYB genes), denoted as type A aberrations, present at diagnosis [ 16 ]. Other genetic alterations, denoted as type B, are recurrently detected in T-ALL patients and include point mutations, insertions and deletions (INDELs), and chromosomal gains or losses, which result in activation of the NOTCH1 T-cell fate specification pathway ( NOTCH1/FBXW7 ) in more than 60% of T-ALL cases [ 17 ], activation of cytokine signaling pathways ( IL7R, JAK1/3, FLT3, CKIT, PI3K/AKT/PTEN, ABL1, N/KRAS ) and transcription factors ( RUNX1, ETV6, BCL11B, WT1, TCF7, LEF1, CTNNB1, GATA3, IKZF1 ), inactivation of cell cycle inhibitors ( CDKN2A/B, CDKN1B, CDKN1C, CCND3, RB ), or deregulation of chromatin modifiers and remodeling factors ( PHF6 , CTCF, KDM6A, SETD2, KMT2A/2D/2C, DNMT3A, IDH1/2 ) (reviewed in [ 18 , 19 , 20 , 21 , 22 ]).…”