Molecular subgroups of T-cell acute lymphoblastic leukemia in adults treated according to pediatric-based GMALL protocols

Abstract

In contrast to B-cell precursor acute lymphoblastic leukemia (ALL), molecular subgroups are less well defined in T-lineage ALL. Comprehensive studies on molecular T-ALL subgroups have been predominantly performed in pediatric ALL patients. Currently, molecular characteristics are rarely considered for risk stratification. Herein, we present a homogenously treated cohort of 230 adult T-ALL patients characterized on transcriptome, and partly on DNA methylation and gene mutation level in correlation with clinical outcome. We identified nine molecular subgroups based on aberrant oncogene expression correlating to four distinct DNA methylation patterns. The subgroup distribution differed from reported pediatric T-ALL cohorts with higher frequencies of prognostic unfavorable subgroups like HOXA or LYL1/LMO2. A small subset (3%) of HOXA adult T-ALL patients revealed restricted expression of posterior HOX genes with aberrant activation of lncRNA HOTTIP. With respect to outcome, TLX1 (n = 44) and NKX2-1 (n = 4) had an exceptionally favorable 3-year overall survival (3y-OS) of 94%. Within thymic T-ALL, the non TLX1 patients had an inferior but still good prognosis. To our knowledge this is the largest cohort of adult T-ALL patients characterized by transcriptome sequencing with meaningful clinical follow-up. Risk classification based on molecular subgroups might emerge and contribute to improvements in outcome.

Fig. 1. Molecular subgroups in adult T-ALL.

Classification of 230 adult T-ALL patients into molecular subgroups based on RNAseq. Clinical data, fusions genes, and oncogene expression are shown.

Fig. 2. Clinical features of molecular subgroups in adult T-ALL.

A Age distribution according to the molecular subtypes. B Immunophenotype according to molecular subgroups. Number of samples varies from (A) and (B) due to missing immunophenotypes for 15 samples. C Gender distribution in the molecular subgroups.

Fig. 3. HOXA13 cluster with recurrent mir181A1HG_HOTTIP fusion.

A Expression of posterior HOXA genes in HOXA13 cluster. B Fusion gene mir181A1HG_HOTTIP with the 5′ fusion partner breakpoint after exon partner and full usage of 3′ fusion partner HOTTIP. C Differentially expressed genes between HOXA13 and HOXA cluster. GSEA enrichment analysis for JAK/STAT and TP53 pathway compared between HOXA13 and HOXA.

Fig. 4. Methylation profile of adult T-ALL samples.

A Principal component analysis of 84 T-ALL samples based on their methylation status using the 2000 most variant CpGs resulting in four stable clusters (M1–M4). B Methylation clusters showed a high concordance with molecular subgroups and immunophenotype. Methylation level of the 2000 most variant CpGs are presented with a clear hypomethylation for cluster M2. Below the graph most prominent molecular subgroups in the methylation clusters are depicted. Samples with an underlying TAL1 fusion are marked. C Number of differentially methylated regions and their methylation status according to the four methylation subgroups. Genes in the differentially methylated regions are reflecting driving oncogenes of molecular T-ALL subgroups.

Fig. 5. Overall survival for molecular subgroups in T-ALL.

(A) Overall survival for the molecular subgroups in 196 adult T-ALL patients independent of their immunophenotype. Unassigned samples are not displayed. Colors for the different subgroups are shown below the figure. B-D Overall survival of adult T-ALL patients according to their molecular risk classification. Good risk group comprises 62 patients: TLX1 (n = 44), NKX2-1 (n = 4) and LMO1 (n = 14); intermediate risk group 47 patients: HOXA (n = 47); poor risk subgroup 76 patients: HOXA13 (n = 5), TLX3 (n = 25), LYL1/LMO2 (n = 29), TAL1/LMO2 (n = 27). E Overall survival for the molecular subgroups in 99 adult T-ALL patients with thymic immunophenotype. Unassigned samples are not displayed. Colors for the different subgroups are shown below the figure.