Identification of fusion genes and characterization of transcriptome features in T-cell acute lymphoblastic leukemia

Significance

To get more insights into the disease mechanism of T-cell acute lymphoblastic leukemia (T-ALL), particularly in an adult group, we addressed the genomic landscape in 130 patients, including 61 cases of adult T-ALL. A number of new genetic aberrations were identified using integrated transcriptome and genomic analysis. Distinct T-ALL subgroups were defined according to the interplay among different genetic abnormalities and gene transcription patterns. Characterization of genomic features of T-ALL is valuable not only for a better understanding of leukemogenesis, but also for patient stratification and tailored therapy.

Abstract

T-cell acute lymphoblastic leukemia (T-ALL) is a clonal malignancy of immature T cells. Recently, the next-generation sequencing approach has allowed systematic identification of molecular features in pediatric T-ALL. Here, by performing RNA-sequencing and other genomewide analysis, we investigated the genomic landscape in 61 adult and 69 pediatric T-ALL cases. Thirty-six distinct gene fusion transcripts were identified, with SET-NUP214 being highly related to adult cases. Among 18 previously unknown fusions, ZBTB16-ABL1, TRA-SALL2, and involvement of NKX2-1 were recurrent events. ZBTB16-ABL1 functioned as a leukemogenic driver and responded to the effect of tyrosine kinase inhibitors. Among 48 genes with mutation rates >3%, 6 were newly found in T-ALL. An aberrantly overexpressed short mRNA transcript of the SLC17A9 gene was revealed in most cases with overexpressed TAL1, which predicted a poor prognosis in the adult group. Up-regulation of HOXA, MEF2C, and LYL1 was often present in adult cases, while TAL1 overexpression was detected mainly in the pediatric group. Although most gene fusions were mutually exclusive, they coexisted with gene mutations. These genetic abnormalities were correlated with deregulated gene expression markers in three subgroups. This study may further enrich the current knowledge of T-ALL molecular pathogenesis.