A COMBINED APPROACH TO DETECT RARE FUSION EVENTS IN ACUTE MYELOID LEUKEMIA
(Abstract release date: 05/19/16)
EHA Library. Padella A. 06/09/16; 134528; PB1628
Ms. Antonella Padella
Contributions
Contributions
Abstract
Abstract: PB1628
Type: Publication Only
Background
A complex network of events characterizes Acute Myeloid Leukemia (AML), including point mutations, epigenetic modification, copy-number alterations, gene-expression alterations and fusion events. A recent study revealed that 45% of AML patients carry one fusion gene and 50% of detected fusions were novel and not recurrent events (TCGA, N Engl J Med; 2013). However, the leukemogenic potential of these fusions and their prognostic role are still unknown.
Aims
The aim of the study was to identify rare gene fusions having a causative role in leukemogenesis and which may be a target for personalized therapy in AML cases with rare chromosomal translocations.
Methods
RNAseq was performed on 4 AML patients (#59810, #20, #84 and #21, Hiseq1000 Illumina) and deFuse and Chimerascan was used to detect fusions. Putative chimeras were prioritized according to cytogenetic analysis. In addition, we exploited Pegasus and Oncofuse to select biologically relevant fusions cryptic at cytogenetic analysis. Selected fusions were validated with Sanger sequencing.
Results
The reliability of our bioinformatic analysis was confirmed thanks to the detection of the CBFβ-MYH11 transcript in the sample #84 associated to the inv(16).We detected two in-frame fusion genes in sample #20: CPD-PXT1 which appeared as the reciprocal fusion product of t(6;17) translocation, and SAV1-GYPB, which remained cryptic at cytogenetic analysis. The first chimera involved a metallocarboxypeptidase and a partner whose biological function is unknown. The second chimera involved the oncogene SAV1, a central player of the Hippo pathway, which controls the proliferation and promotes the apoptosis. The fusion event causes the loss of the protein-protein interaction domain of SAV1, which is fundamental for its stability.Sample #21 carried an in-frame fusion transcript involving the genes OAZ1 and MAFK. The first gene is involved in the polyamine synthesis, while the latter one is a transcriptional regulator. The putative fusion protein was formed by the cis-acting elements sensitive to polyamine levels of OAZ1 and the bZIP domain of MAFK.We detected two fusion transcripts in sample #59810: ZEB2-BCL11B, associated with translocation t(2;14), and CNOT2-WT1, associated with t(11;12). In particular, three different isoforms of the in-frame chimera ZEB2-BCL11B were expressed: the full length (Isoform 1), the Isoform 2 with one exon of BCL11B spliced and the Isoform 3 with 2 exons of BCL11B spliced. Gene expression profiling showed an upregulation of ZEB2 and BCL11B transcripts in the patient’s blasts, compared to 53 AML samples with no chromosomal aberrations in the 14q32 region. On the contrary, CNOT2-WT1 was an out-of-frame gene fusion and the reciprocal of the fusion revealed the intron retention of CNOT2.
Conclusion
Our data suggest that fusion events are frequent in AML and different approaches, including G-banding, molecular biology, bioinformatics and statistics, need to be integrated in order to better understand AML pathogenesis. The lack of recurrence in the landscape of AML gene fusions confers heterogeneity to the pathogenesis of the disease and we are further investigating the pathogenetic potential of the identified translocations, in order to identify common patterns of oncogenic events, which may be exploited to stratify patients and tailor personalized therapies.Acknowledgements: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Fusion, Targeted therapy, Translocation
Type: Publication Only
Background
A complex network of events characterizes Acute Myeloid Leukemia (AML), including point mutations, epigenetic modification, copy-number alterations, gene-expression alterations and fusion events. A recent study revealed that 45% of AML patients carry one fusion gene and 50% of detected fusions were novel and not recurrent events (TCGA, N Engl J Med; 2013). However, the leukemogenic potential of these fusions and their prognostic role are still unknown.
Aims
The aim of the study was to identify rare gene fusions having a causative role in leukemogenesis and which may be a target for personalized therapy in AML cases with rare chromosomal translocations.
Methods
RNAseq was performed on 4 AML patients (#59810, #20, #84 and #21, Hiseq1000 Illumina) and deFuse and Chimerascan was used to detect fusions. Putative chimeras were prioritized according to cytogenetic analysis. In addition, we exploited Pegasus and Oncofuse to select biologically relevant fusions cryptic at cytogenetic analysis. Selected fusions were validated with Sanger sequencing.
Results
The reliability of our bioinformatic analysis was confirmed thanks to the detection of the CBFβ-MYH11 transcript in the sample #84 associated to the inv(16).We detected two in-frame fusion genes in sample #20: CPD-PXT1 which appeared as the reciprocal fusion product of t(6;17) translocation, and SAV1-GYPB, which remained cryptic at cytogenetic analysis. The first chimera involved a metallocarboxypeptidase and a partner whose biological function is unknown. The second chimera involved the oncogene SAV1, a central player of the Hippo pathway, which controls the proliferation and promotes the apoptosis. The fusion event causes the loss of the protein-protein interaction domain of SAV1, which is fundamental for its stability.Sample #21 carried an in-frame fusion transcript involving the genes OAZ1 and MAFK. The first gene is involved in the polyamine synthesis, while the latter one is a transcriptional regulator. The putative fusion protein was formed by the cis-acting elements sensitive to polyamine levels of OAZ1 and the bZIP domain of MAFK.We detected two fusion transcripts in sample #59810: ZEB2-BCL11B, associated with translocation t(2;14), and CNOT2-WT1, associated with t(11;12). In particular, three different isoforms of the in-frame chimera ZEB2-BCL11B were expressed: the full length (Isoform 1), the Isoform 2 with one exon of BCL11B spliced and the Isoform 3 with 2 exons of BCL11B spliced. Gene expression profiling showed an upregulation of ZEB2 and BCL11B transcripts in the patient’s blasts, compared to 53 AML samples with no chromosomal aberrations in the 14q32 region. On the contrary, CNOT2-WT1 was an out-of-frame gene fusion and the reciprocal of the fusion revealed the intron retention of CNOT2.
Conclusion
Our data suggest that fusion events are frequent in AML and different approaches, including G-banding, molecular biology, bioinformatics and statistics, need to be integrated in order to better understand AML pathogenesis. The lack of recurrence in the landscape of AML gene fusions confers heterogeneity to the pathogenesis of the disease and we are further investigating the pathogenetic potential of the identified translocations, in order to identify common patterns of oncogenic events, which may be exploited to stratify patients and tailor personalized therapies.Acknowledgements: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Fusion, Targeted therapy, Translocation
Abstract: PB1628
Type: Publication Only
Background
A complex network of events characterizes Acute Myeloid Leukemia (AML), including point mutations, epigenetic modification, copy-number alterations, gene-expression alterations and fusion events. A recent study revealed that 45% of AML patients carry one fusion gene and 50% of detected fusions were novel and not recurrent events (TCGA, N Engl J Med; 2013). However, the leukemogenic potential of these fusions and their prognostic role are still unknown.
Aims
The aim of the study was to identify rare gene fusions having a causative role in leukemogenesis and which may be a target for personalized therapy in AML cases with rare chromosomal translocations.
Methods
RNAseq was performed on 4 AML patients (#59810, #20, #84 and #21, Hiseq1000 Illumina) and deFuse and Chimerascan was used to detect fusions. Putative chimeras were prioritized according to cytogenetic analysis. In addition, we exploited Pegasus and Oncofuse to select biologically relevant fusions cryptic at cytogenetic analysis. Selected fusions were validated with Sanger sequencing.
Results
The reliability of our bioinformatic analysis was confirmed thanks to the detection of the CBFβ-MYH11 transcript in the sample #84 associated to the inv(16).We detected two in-frame fusion genes in sample #20: CPD-PXT1 which appeared as the reciprocal fusion product of t(6;17) translocation, and SAV1-GYPB, which remained cryptic at cytogenetic analysis. The first chimera involved a metallocarboxypeptidase and a partner whose biological function is unknown. The second chimera involved the oncogene SAV1, a central player of the Hippo pathway, which controls the proliferation and promotes the apoptosis. The fusion event causes the loss of the protein-protein interaction domain of SAV1, which is fundamental for its stability.Sample #21 carried an in-frame fusion transcript involving the genes OAZ1 and MAFK. The first gene is involved in the polyamine synthesis, while the latter one is a transcriptional regulator. The putative fusion protein was formed by the cis-acting elements sensitive to polyamine levels of OAZ1 and the bZIP domain of MAFK.We detected two fusion transcripts in sample #59810: ZEB2-BCL11B, associated with translocation t(2;14), and CNOT2-WT1, associated with t(11;12). In particular, three different isoforms of the in-frame chimera ZEB2-BCL11B were expressed: the full length (Isoform 1), the Isoform 2 with one exon of BCL11B spliced and the Isoform 3 with 2 exons of BCL11B spliced. Gene expression profiling showed an upregulation of ZEB2 and BCL11B transcripts in the patient’s blasts, compared to 53 AML samples with no chromosomal aberrations in the 14q32 region. On the contrary, CNOT2-WT1 was an out-of-frame gene fusion and the reciprocal of the fusion revealed the intron retention of CNOT2.
Conclusion
Our data suggest that fusion events are frequent in AML and different approaches, including G-banding, molecular biology, bioinformatics and statistics, need to be integrated in order to better understand AML pathogenesis. The lack of recurrence in the landscape of AML gene fusions confers heterogeneity to the pathogenesis of the disease and we are further investigating the pathogenetic potential of the identified translocations, in order to identify common patterns of oncogenic events, which may be exploited to stratify patients and tailor personalized therapies.Acknowledgements: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Fusion, Targeted therapy, Translocation
Type: Publication Only
Background
A complex network of events characterizes Acute Myeloid Leukemia (AML), including point mutations, epigenetic modification, copy-number alterations, gene-expression alterations and fusion events. A recent study revealed that 45% of AML patients carry one fusion gene and 50% of detected fusions were novel and not recurrent events (TCGA, N Engl J Med; 2013). However, the leukemogenic potential of these fusions and their prognostic role are still unknown.
Aims
The aim of the study was to identify rare gene fusions having a causative role in leukemogenesis and which may be a target for personalized therapy in AML cases with rare chromosomal translocations.
Methods
RNAseq was performed on 4 AML patients (#59810, #20, #84 and #21, Hiseq1000 Illumina) and deFuse and Chimerascan was used to detect fusions. Putative chimeras were prioritized according to cytogenetic analysis. In addition, we exploited Pegasus and Oncofuse to select biologically relevant fusions cryptic at cytogenetic analysis. Selected fusions were validated with Sanger sequencing.
Results
The reliability of our bioinformatic analysis was confirmed thanks to the detection of the CBFβ-MYH11 transcript in the sample #84 associated to the inv(16).We detected two in-frame fusion genes in sample #20: CPD-PXT1 which appeared as the reciprocal fusion product of t(6;17) translocation, and SAV1-GYPB, which remained cryptic at cytogenetic analysis. The first chimera involved a metallocarboxypeptidase and a partner whose biological function is unknown. The second chimera involved the oncogene SAV1, a central player of the Hippo pathway, which controls the proliferation and promotes the apoptosis. The fusion event causes the loss of the protein-protein interaction domain of SAV1, which is fundamental for its stability.Sample #21 carried an in-frame fusion transcript involving the genes OAZ1 and MAFK. The first gene is involved in the polyamine synthesis, while the latter one is a transcriptional regulator. The putative fusion protein was formed by the cis-acting elements sensitive to polyamine levels of OAZ1 and the bZIP domain of MAFK.We detected two fusion transcripts in sample #59810: ZEB2-BCL11B, associated with translocation t(2;14), and CNOT2-WT1, associated with t(11;12). In particular, three different isoforms of the in-frame chimera ZEB2-BCL11B were expressed: the full length (Isoform 1), the Isoform 2 with one exon of BCL11B spliced and the Isoform 3 with 2 exons of BCL11B spliced. Gene expression profiling showed an upregulation of ZEB2 and BCL11B transcripts in the patient’s blasts, compared to 53 AML samples with no chromosomal aberrations in the 14q32 region. On the contrary, CNOT2-WT1 was an out-of-frame gene fusion and the reciprocal of the fusion revealed the intron retention of CNOT2.
Conclusion
Our data suggest that fusion events are frequent in AML and different approaches, including G-banding, molecular biology, bioinformatics and statistics, need to be integrated in order to better understand AML pathogenesis. The lack of recurrence in the landscape of AML gene fusions confers heterogeneity to the pathogenesis of the disease and we are further investigating the pathogenetic potential of the identified translocations, in order to identify common patterns of oncogenic events, which may be exploited to stratify patients and tailor personalized therapies.Acknowledgements: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project.
Session topic: E-poster
Keyword(s): Acute myeloid leukemia, Fusion, Targeted therapy, Translocation
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