Prognostic Relevance of Integrated Genetic Profiling in Adult T-Cell Acute Lymphoblastic Leukemia
Authors: Van Vlierberghe Pieter , Ambesi-Impiombato Alberto , Rigo Isaura , Hadler Michael , Paietta Elisabeth , Wiernik Peter H. , Rowe Jacob M , Rue Montserrat , Ferrando Adolfo A. 
Published: October 2019

Abstract
Abstract 294
T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive hematologic tumor associated with poor prognosis. Over the last decade, microarray gene expression studies have shown that T-ALL encompasses distinct molecular groups defined by characteristic gene expression signatures and molecular studies have uncovered major mechanisms of T-cell transformation and numerous oncogenes and tumor suppressors involved in the pathogenesis of T-ALL. This molecular and genetic heterogeneity suggests that distinct groups of T-ALL may respond differently to chemotherapy. However, today there are no well established prognostic markers for patient stratification in this disease and all T-ALL patients are treated under the same therapeutic scheme.
To overcome this obstacle here we performed a comprehensive analysis of the prognostic significance of molecular groups defined gene microarray expression profiling, copy number alterations identified by array-Comparative Genomic Hybridization, immunophenotypic markers and mutation analysis of all major adult T-ALL oncogenes (NOTCH1, IL7R, FLT3, NRAS) and tumor suppressor genes (FBXW7, PTEN, DNM2, PHF6, BCL11B, WT1, EZH2, ETV6, IDH1, IDH2, DNMT3A, GATA3 and RUNX1) in a clinical series of 53 primary leukemia samples uniformly treated according to the Eastern Cooperative Oncology Group (ECOG) E2993 protocol.
Unsupervised analysis of gene expression oligonucleotide microarrays in this series revealed the presence of 2 stable gene expression clusters corresponding to early immature (n = 28) and cortical/mature (n = 25) adult T-ALLs respectively. Early immature T-ALLs show gene expression signatures related to hematopoietic stem cells and myeloid progenitors and are associated with poor prognosis and reduced overall survival compared with cortical/mature adult T-ALLs (P = 0.011). Immunophenotypic analysis showed that CD13 expression was strongly associated with poor survival in our patient series (P=0.002), whereas other early immature or myeloid antigens including CD34 and CD33 showed no clinical impact. Array comparative genomic hybridization (aCGH) analysis in this series identified absence of biallelic deletion of TCRγ, a cytogenetic feature associated with early induction failure and inferior overall survival rates in pediatric T-ALL (Gutierrez et al., JCO, 2010), in 27 out of 53 (51%) adult T-ALL samples analyzed. Notably, 22 of 27 T-ALLs with absence of biallelic deletion of TCRγ were found in the early immature adult T-ALL group, and as in pediatric T-ALL, this molecular marker was associated with inferior overall survival (P = 0.022). In addition, heterozygous deletions of the short arm of chromosome 17 encompassing the TP53 tumor suppressor gene predicted for worse clinical outcome (P = 0.0005); while, homozygous deletions of the CDKN2A/CDKN2B locus on the short arm of chromosome 9 was associated with favorable prognosis (P = 0.012). Most notably, the favorable prognostic effect of homozygous CDKN2A/CDKN2B deletions in our series was restricted to the good prognostic subtype of leukemia samples with a mature/cortical gene expression profile. Finally, comprehensive mutation analysis of adult T-ALL oncogenes and tumor suppressors demonstrated a favorable prognosis for patients with activation of NOTCH1 signaling as result of mutations in NOTCH1 and/or FBXW7 (P = 0.021) and for those harboring heterozygous inactivating mutations or deletions in the BCL11B tumor suppressor gene (P = 0.041). In contrast, somatic mutations in genes targeting the epigenetic regulators DNMT3A (P = 0.003) and IDH1/2 (P = 0.011) were associated with adverse prognosis.
Multivariate analyses highlighted the association of NOTCH1 and/or FBXW7 mutations with favorable outcome and that of TP53 deletions and DNMT3A mutations with poor prognosis in adult T-ALL. Importantly, homozygous CDKN2A/CDKN2B deletions and CD13 expression may serve as prognostic markers to further stratify low-risk cortical/mature adult T-ALL leukemias, whereas DNMT3A mutations might be useful for risk stratification within high-risk early immature adult T-ALLs. Overall, our comprehensive analysis of molecular prognostic markers identify for the first time a subset of adult T-ALLs with very poor response to intensified chemotherapy, highlighting the need to introduce alternative therapies aiming to improve the therapeutic outcome in this group.

Disclosures:
No relevant conflicts of interest to declare.