Whole‐exome sequencing reveals the subclonal expression of NUP214 ‐ ABL1 fusion gene in T‐cell acute lymphoblastic leukemia

2019 ◽  
Vol 67 (1) ◽  
Author(s):  
Yoshinori Tsurusaki ◽  
Jun‐ichi Nagai ◽  
Sachio Fujita ◽  
Masanaka Sugiyama ◽  
Wataru Nakamura ◽  
...  
Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3786-3786
Author(s):  
Masafumi Seki ◽  
Kenichi Yoshida ◽  
Yusuke Sato ◽  
Yuichi Shiraishi ◽  
Kenichi Chiba ◽  
...  

Abstract T-cell acute lymphoblastic leukemia (T-ALL) accounts for 10% to 15% of newly diagnosed cases of childhood acute lymphoblastic leukemia (ALL). Generally, childhood T-ALL patients have a worse prognosis than B cell precursor ALL patients. Recent studies have identified a subtype of T-ALL termed “early T-cell precursor” (ETP) ALL, which is associated with a high risk of treatment failure. In spite of recent improvements of risk stratified multiagent chemotherapy, relapsed patients have a poor prognosis even if they were non-ETP ALL. Recent genome-wide approach revealed frequent NOTCH1 and FBXW7 oncogenic mutations 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 was thought to be one of the novel tumor suppressor gene for adult T-ALL. CNOT3 is part of the CCR4-NOT complex that is the major deadenylase of mRNA. NT5C2, encoding a 5ʹ-nucleotidase was identified as relapse specific mutation, of which mutation is associated with the outgrowth of drug-resistant clones in ALL. However, these mutations have been found in a fraction of childhood T-ALL suggests that the existence of other genetic pathogenesis. To discover new oncogenic gene mutations which involved in the pathogenesis of relapsed T-ALL and to identify novel prognostic markers of childhood T-ALL, we performed genome-wide analysis using whole-exome sequencing and 250K SNP array analyses in 8 cases with relapsed T-ALL and 16 cases with non-relapsed T-ALL. The mean coverage in the whole-exome sequencing of tumor and germline samples was 108× and 100× for the 50-Mb target regions, respectively, by which more than 90% of the coding sequences were represented by more than 20 independent reads on average. A mean of nonsilent mutations per sample at presentation was 18, and sample at 1st relapsed was 19. There were only 16 recurrent mutations in 24 cases; however no shared mutation in 8 relapsed cases other than NOTCH1 and FBXW7. NOTCH1 mutations were found in 50% (12/24), and were frequently identified in relapsed cases (6/8). FBXW7 mutations were also frequently found in 6/24 cases, and 60 % (3/6) 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 two cases with CNOT3 mutations (8.3%). In addition, PHF6 mutation, which is known as X-linked tumor suppressor gene in T-ALL, was recurrent in 3 cases. Other recurrent mutations were shared between 2 cases, respectively. NT5C2 mutation has been reported to a relapse-specific mutation, and we also found NT5C2 mutations in 2 relapsed cases, which detected in only relapsed samples. RPL5 and RPL10 mutations were reported to be found in 10 % of pediatric T-ALL; however there was one mutation in RPL related genes in our study. Furthermore, we found common mutations of acute myeloid leukemia such as TCF7, STAT5A, KIT, RUNX1, and EP300 mutations in a single case. On the other hand, although pediatric T-ALL showed largely normal genomic copy number profiles, homozygous deletions at chromosome 9p21 harboring CDKN2A were frequently detected in our study (17/24 71%). Especially, 9p21 deletions were found in all relapsed cases, suggesting that loss of CDKN2A locus was a critical genetic mechanism of relapsed T-ALL. In conclusion, our results revealed mutations in several known genes, but overall frequency of recurrent somatic mutations in childhood T-ALL is low, even in relapsed samples. Although loss of CDKN2A locus was detected in all relapsed cases, recurrent relapse-specific mutations could not be identified other than NT5C2. These findings suggest that the majority of relapsed T-ALL may be driven by aberrations of CDKN2A and minor clone variants and/or epigenetic modifications during tumor evolution. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3527-3527
Author(s):  
Masafumi Seki ◽  
Kenichi Yoshida ◽  
Shiraishi Yuichi ◽  
Kenichi Chiba ◽  
Hiroko Tanaka ◽  
...  

Abstract 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. Disclosures No relevant conflicts of interest to declare.


Leukemia ◽  
2008 ◽  
Vol 23 (1) ◽  
pp. 125-133 ◽  
Author(s):  
C Graux ◽  
◽  
M Stevens-Kroef ◽  
M Lafage ◽  
N Dastugue ◽  
...  

2012 ◽  
Vol 45 (2) ◽  
pp. 186-190 ◽  
Author(s):  
Kim De Keersmaecker ◽  
Zeynep Kalender Atak ◽  
Ning Li ◽  
Carmen Vicente ◽  
Stephanie Patchett ◽  
...  

Blood ◽  
2005 ◽  
Vol 105 (12) ◽  
pp. 4849-4852 ◽  
Author(s):  
Kim De Keersmaecker ◽  
Carlos Graux ◽  
Maria D. Odero ◽  
Nicole Mentens ◽  
Riet Somers ◽  
...  

Abstract The BCR-ABL1 fusion kinase is frequently associated with chronic myeloid leukemia and B-cell acute lymphoblastic leukemia but is rare in T-cell acute lymphoblastic leukemia (T-ALL). We recently identified NUP214-ABL1 as a variant ABL1 fusion gene in 6% of T-ALL patients. Here we describe the identification of another ABL1 fusion, EML1-ABL1, in a T-ALL patient with a cryptic t(9;14)(q34;q32) associated with deletion of CDKN2A (p16) and expression of TLX1 (HOX11). Echinoderm microtubule-associated protein-like 1-Abelson 1 (EML1-ABL1) is a constitutively phosphorylated tyrosine kinase that transforms Ba/F3 cells to growth factor-independent growth through activation of survival and proliferation pathways, including extracellular signal-related kinase 1/2 (Erk1/2), signal transducers and activators of transcription 5 (Stat5), and Lyn kinase. Deletion of the coiled-coil domain of EML1 abrogated the transforming properties of the fusion kinase. EML1-ABL1 and breakpoint cluster region (BCR)-ABL1 were equally sensitive to the tyrosine kinase inhibitor imatinib. These data further demonstrate the involvement of ABL1 fusions in the pathogenesis of T-ALL and identify EML1-ABL1 as a novel therapeutic target of imatinib. (Blood. 2005;105:4849-4852)


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 141-141
Author(s):  
Jan Cools ◽  
Carlos Graux ◽  
Cindy Melotte ◽  
Hilmar Quentmeier ◽  
Adolfo A. Ferrando ◽  
...  

Abstract The Philadelphia translocation, encoding the BCR-ABL1 (BCR-ABL) fusion gene, is typically found in chronic myeloid leukemia (CML) and precursor B-cell acute lymphoblastic leukemia (B-ALL), but is exceptionally rare in T-cell acute lymphoblastic leukemia (T-ALL). To study the potential involvement of ABL1 gene rearrangements in T-cell malignancies, we screened 90 T-ALL cases by fluorescence in situ hybridization (FISH), using BCR and ABL1 probes. No BCR-ABL1 fusion signals were observed, confirming the low frequency of this rearrangement in T-ALL, but we did observe marked amplification (> 10 signals per nucleus) ABL1 of in 5 of 90 (5.5 %) T-ALL patients. Amplification of ABL1 occurred on small extrachromosomal elements that were not detectable by conventional cytogenetics. and hence are referred to as episomes. FISH, and array-CGH analyses delineated the amplicon as a 500 kb region from chromosome band 9q34, containing the oncogenes ABL1 and NUP214 (CAN). Molecular analysis led to the identification of a NUP214-ABL1 fusion gene, which is generated as result of the circularization of the genomic region between ABL1 and NUP214 to form the episomes. This is the first example of an oncogenic fusion gene generated by extrachromosomal amplification. The NUP214-ABL1 transcript was detected in 5 patients with ABL1 amplification, in 5 of 85 (5.8 %) additional T-ALL patients, and in 3 of 22 T-ALL cell lines. The constitutively phosphorylated tyrosine kinase NUP214-ABL1 is sensitive to the tyrosine kinase inhibitor imatinib mesylate (STI-571). The recurrent cryptic NUP214-ABL1 rearrangement is associated with increased expression TLX1 of (HOX11) or TLX3 (HOX11L2), and with deletion of CDKN2A (p16), consistent with a multi-step pathogenesis of T-ALL. Our results identify a novel mechanism for the generation of a fusion gene on extrachromosomal elements, and indicate the importance of activated tyrosine kinase signaling in the pathogenesis of T-ALL. NUP214-ABL1 expression defines a new subgroup of T-ALL patients that could benefit from imatinib treatment.


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