Contributions
Abstract: PB1598
Type: Publication Only
Background
T-acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy that accounts for approximately 20% of all cases of ALL. It tends to be more common in adults than children.Understanding the disease pathogenesis and expected biological behavior of T-ALL on the basis of genetic profiles is essential if T-ALLis to be successfully treated.
Aims
In this study, we explored the association of pathogenesis and biology based on genetic aberrations in T-ALLbyintegrative genetic analyses using massive parallel sequencing as well as copy number analysis of T-ALL patients.
Methods
The study included 102 T-ALL patients (69 male and 33 females comprising 42 children and 60 adults. Massive parallel sequencing of the exons of 11 genes (NOTCH1, DNMT3A, FBXW7, RUNX1, PHF6, PTEN, GATA3, KRAS, EZH2, NRAS, and SH2B3) was performed to comprehensively characterize the patterns ofsomatic mutations in T-ALL. Multiplex ligation-dependent probe amplification (MLPA) was done for detection of commonly deleted genes in T-ALL.In addition, CDKN2A and CDKN2B mRNA expressionand promoter methylation were analyzed usingRT-qPCRand pyrosequencing, respectively.
Results
We identified principal genetic alterations in 97.1%(99/102) cases of T-ALL using integrativegenetic analyses including massive parallel sequencing and MLPA. A total of 134 mutations were found in descending order of genes: NOTCH1(66.7%), FBXW7(19.6%), PHF6(15.7%), RUNX1(12.7%), NRAS(10.8%), and DNMT3A(9.8%).Copy number alterations were most frequently detected CDKN2B,CDKN2A and genes on 9p21.3 in T-ALL(45.1%). Gene expression data demonstratedthe downregulation of CDKN2B in most cases of T-ALL, while CDKN2A downregulation was mainly restricted to deletions. Additional quantitative methylation analysis demonstrated that CDKN2B downregulation stemmed from deletion and hypermethylation. Analysis of 64 patients with CDKN2B hypermethylation indicated relationships with older age of onset and early T-cell precursor ALL, which involved very early arrest of T-cell differentiation. Genes associated with methylation and myeloid neoplasms including DNMT3A and NRAS were more commonly mutated in T-ALL with CDKN2Bhypermethylation. Especially, CDKN2Bbiallelic deletion or high methylationlevel(≥ 45%) was a poor prognostic factor, as was age of onset, GATA3 and SH2B3 mutations.
Conclusion
This study clarifies one of the most important genetic events in T-ALL, CDKN2B downregulation, via the mechanisms of deletion and hypermethylation. Different susceptible genetic backgrounds exist according to CDKN2B downregulation mechanism.
Session topic: 1. Acute lymphoblastic leukemia – Biology & Translational Research
Keyword(s): Methylation, T-ALL, Gene expression
Abstract: PB1598
Type: Publication Only
Background
T-acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy that accounts for approximately 20% of all cases of ALL. It tends to be more common in adults than children.Understanding the disease pathogenesis and expected biological behavior of T-ALL on the basis of genetic profiles is essential if T-ALLis to be successfully treated.
Aims
In this study, we explored the association of pathogenesis and biology based on genetic aberrations in T-ALLbyintegrative genetic analyses using massive parallel sequencing as well as copy number analysis of T-ALL patients.
Methods
The study included 102 T-ALL patients (69 male and 33 females comprising 42 children and 60 adults. Massive parallel sequencing of the exons of 11 genes (NOTCH1, DNMT3A, FBXW7, RUNX1, PHF6, PTEN, GATA3, KRAS, EZH2, NRAS, and SH2B3) was performed to comprehensively characterize the patterns ofsomatic mutations in T-ALL. Multiplex ligation-dependent probe amplification (MLPA) was done for detection of commonly deleted genes in T-ALL.In addition, CDKN2A and CDKN2B mRNA expressionand promoter methylation were analyzed usingRT-qPCRand pyrosequencing, respectively.
Results
We identified principal genetic alterations in 97.1%(99/102) cases of T-ALL using integrativegenetic analyses including massive parallel sequencing and MLPA. A total of 134 mutations were found in descending order of genes: NOTCH1(66.7%), FBXW7(19.6%), PHF6(15.7%), RUNX1(12.7%), NRAS(10.8%), and DNMT3A(9.8%).Copy number alterations were most frequently detected CDKN2B,CDKN2A and genes on 9p21.3 in T-ALL(45.1%). Gene expression data demonstratedthe downregulation of CDKN2B in most cases of T-ALL, while CDKN2A downregulation was mainly restricted to deletions. Additional quantitative methylation analysis demonstrated that CDKN2B downregulation stemmed from deletion and hypermethylation. Analysis of 64 patients with CDKN2B hypermethylation indicated relationships with older age of onset and early T-cell precursor ALL, which involved very early arrest of T-cell differentiation. Genes associated with methylation and myeloid neoplasms including DNMT3A and NRAS were more commonly mutated in T-ALL with CDKN2Bhypermethylation. Especially, CDKN2Bbiallelic deletion or high methylationlevel(≥ 45%) was a poor prognostic factor, as was age of onset, GATA3 and SH2B3 mutations.
Conclusion
This study clarifies one of the most important genetic events in T-ALL, CDKN2B downregulation, via the mechanisms of deletion and hypermethylation. Different susceptible genetic backgrounds exist according to CDKN2B downregulation mechanism.
Session topic: 1. Acute lymphoblastic leukemia – Biology & Translational Research
Keyword(s): Methylation, T-ALL, Gene expression