TAL1 Super Enhancer Aberration and Stil-TAL1 Fusion in Pediatric T Cell Acute Lymphoblastic Leukemia

Background

Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic cancer accounting for 10 to 15% of newly diagnosed pediatric ALL cases, and is associated with a poor treatment outcome compared with B-cell ALL especially in relapsed cases despite recent improvement with an intensive treatment. TAL1 deletion on chromosome 1p33 which is also known as STIL-TAL1, is found in 20-25% of cases with T-ALL, which results in overexpression of TAL1 under the control of the promoter of STIL located next to TAL1. Recently, TAL1 super enhancer aberration (TAL1-SE) was reported, which introduce binding motifs for the MYB transcription factor in a noncoding region. This somatic mutation results in aberrant expression of TAL1 without STIL-TAL1. Clinical features of TAL1-SE and its difference with STIL-TAL1 cases have been poorly studied, and this could be a new instrument of treatment stratification in T-ALL.

Methods

Targeted capture sequencing for coding regions of 151 genes using a custom-made bait including the TAL1-SE region was performed in 132 Japanese T-ALL cases under 15 years old to detect somatic mutations. For the further analysis, whole transcriptome sequencing (WTS) was performed in 88 cases. Screening for STIL-TAL1 fusion by reverse transcription PCR was also performed in additional 44 cases. All cases of TAL1-SE and STIL-TAL1 were validated by Sanger sequencing. Our pipelines,"Genomon 2" algorithm, were used for detection of somatic mutations and fusions. Most samples of DNA and RNA were offered from Tokyo Children's Cancer Study Group (TCCSG), and available clinical data were mainly based on the TCCSG clinical study treated with BFM-based ALL treatment protocol.

Results

TAL1-SE and STIL-TAL1 were found mutually exclusive in 6 (4.5%) and 24 cases (18.1%), respectively. All patients with TAL1-SE were under 10 years old. TAL1-SE cases showed a favorable 3-year overall survival (3y-OS) compared with STIL-TAL1 cases which were reported to show a good prognosis (83.3% vs 85.9% respectively, p = 0.71). However, 3-year disease free survival (3y-DFS) was 22.2% and 72.3% respectively (p = 0.04), indicating higher relapse rate in TAL1-SE cases, and they were probably rescued by second line treatment. Patients with STIL-TAL1 showed significantly poorer prednisolone response (over 1,000 /µl of blast at day 8, p < 0.05), though they showed favorable 3y-OS, which might be resulted from frequent high WBC counts at diagnosis (> 100×10⁶/l, 59%). Comparison of TAL1 expression using read counts of WTS revealed significantly higher TAL1 expression in TAL1-SE cases than STIL-TAL1 cases (p < 0.05). To reveal the difference of gene expression profile between STIL-TAL1 and TAL1-SE, unsupervised consensus clustering of gene expression data in 24 cases performed WTS (6 cases of TAL1-SE and 18 cases of STIL-TAL1) divided into 2 clusters. All cases with TAL1-SE were grouped into the same cluster with 10 STIL-TAL1 cases (Cluster 1). The other 8 STIL-TAL1 cases were classified as Cluster 2. A genetic landscape of these 24 cases showed more frequent NOTCH1 and/or FBXW7 mutations in Cluster 1 (87.5% vs 37.5%, p = 0.02), whereas mutations in genes encoding transcription factor such as RUNX1 and BCL11B were found only in Cluster 1 (n = 1, n = 3, respectively). There was a tendency of better 3y-OS and 3y-DFS in Cluster 2 (73.9% vs 100%, p = 0.14, 55.6% vs 85.7%, p = 0.15, respectively).

Conclusion

TAL1-SE and STIL-TAL1 showed a relatively good prognosis, though high relapse rate in TAL1-SE and a poor prednisolone response in STIL-TAL1 were observed. STIL-TAL1 cases were biologically divided into 2 groups based on the expression profile (with TAL1-SE and STIL-TAL1 only), and these 2 groups showed different clinical and genetic features such as 3y-OS or frequency of NOTCH1/FBXW7 mutations. Our findings illustrate the clinicopathological differences between STIL-TAL1 and TAL1-SE cases, and thus, it might be helpful for development a new therapeutic strategy for these patients with TAL1 overexpression T-ALL.