Whole Exome and Transcriptome Analyses in Pediatric T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) accounts for 10% to 15% of newly diagnosed cases of childhood acute lymphoblastic leukemia (ALL). Recent genome-wide approach revealed frequent NOTCH1 and FBXW7 oncogenic mutations in T-ALL. In addition, previous whole-exome sequencing disclosed novel CNOT3 mutations in approximately 10% of adult T-ALL cases, and thus, CNOT3 is thought to be one of the novel tumor suppressor gene for adult T-ALL. However, somatic mutations in these genes have been found in a fraction of childhood T-ALL, suggesting that the existence of other genetic pathogenesis. Although chromosomal translocations are the most frequent genetic abnormalities detected in other types of leukemia, recurrent translocations except for SIL-TAL1 rearrangement have been poorly defined in T-ALL.

To discover driver mutations or fusion genes which involved in the pathogenesis of pediatric T-ALL and to identify novel prognostic markers of childhood T-ALL, we performed whole-exome sequencing (WES) and transcriptome sequencing (WTS) in 25 cases with T-ALL. Diagnostic total DNA from 25 cases and RNA from 15 cases were analyzed for both WES and WTS, and 8 relapsed samples were also analyzed for WES. Median age at diagnosis was 9 years old (1–15), and male to female ratio was 20 to 5. Libraries for WES and WTS were generated using the SureSelect (Agilent) or TruSeq RNA Sample Preparation kit (Illumina), respectively. High throughput sequencing was performed using the Illumina HiSeq 2000 platform. To detect somatic mutations or fusion transcripts, we used our pipeline “Genomon-exome” and “Genomon-fusion” algorithm. Subsequently, somatic mutations were validated using deep amplicon sequencing. Candidate fusion transcripts were validated by reverse - transcription polymerase-chain-reaction (RT-PCR) and Sanger sequencing.

Most frequent mutation was NOTCH1, which was detected in 52% (13/25) by WES. FBXW7 mutations were also frequently found in 28% (7/25), and 43 % (3/7) were compound heterozygous mutations. In those 6 cases, only one case with FBWX7 mutation had a NOTCH1 mutation. CNOT3 mutations were reported to be frequent in adult T-ALL; however we found only 2 cases with CNOT3 mutations (8.0%). In addition, PHF6 mutation, which is known as X-linked tumor suppressor gene in T-ALL, was recurrently detected in 4 cases (16%). Other recurrent mutations were shared between 2 cases, respectively.

We identified previously known fusion genes, such as MLL-ENL and FGFROP1-FGFR1 in 2 cases. MLL-ENL is one of the frequent translocation for infant multilineage leukemia (MLL), but also reported in non-infant B cell precursor ALL or T-ALL. FGFR1OP is ubiquitously expressed, and the predicted chimeric FGFR1OP-FGFR1 protein contains the catalytic domain of FGFR1. It is thought to be promote hematopoietic stem cell proliferation and leukemogenesis through a constitutive phosphorylation and activation of the downstream pathway of FGFR1.

In conclusion, although NOTCH1 and FBXW7 mutations were relatively frequently detected in our series, we could not detect frequent additional mutations in this study. Consistent with other reports, frequent translocations were not observed in T-ALL, suggesting the genetic differences between T-ALL and other hematological malignancies. Further studies will be necessary to unravel oncogenic mechanisms that implicated in new therapeutic strategy for pediatric T-ALL.