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ASXL1 and DNMT3A mutation in a cytogenetically normal B3 thymoma.

Belani R, Oliveira G, Erikson GA, Ra S, Schechter MS, Lee JK, Shipman WJ, Haaser SM, Torkamani A - Oncogenesis (2014)

Bottom Line: A stage IVB type B3 thymoma from a 47-year-old male of Asian descent with no history of myasthenia gravis or other autoimmune condition was genomically evaluated.Mutations in known tumor suppressors DNMT3A (p.G728D) and ASXL1 (p.E657fs), consistent with mutations of known consequence in acute myeloid leukemia, were identified.Contrary to a previous report, this finding suggests the genetic etiology of thymomas may not be fundamentally distinct from other tumor types.

View Article: PubMed Central - PubMed

Affiliation: Medical Oncology Associates of San Diego, San Diego, CA, USA.

ABSTRACT
The molecular drivers of thymoma are poorly understood. Outside of the identification of rarely occurring epidermal growth factor receptor and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog mutations via candidate gene sequencing, mutations in common cancer genes have yet to be observed. Only a single thymoma genome sequence has been previously reported, with no mutations in known cancer genes identified. Thus, we attempted to identify somatic driver mutations in a cytogenetically normal thymoma. A stage IVB type B3 thymoma from a 47-year-old male of Asian descent with no history of myasthenia gravis or other autoimmune condition was genomically evaluated. Exome sequencing and low-pass whole-genome sequencing was performed to identify somatic point mutations, copy number changes and structural variants. Mutations in known tumor suppressors DNMT3A (p.G728D) and ASXL1 (p.E657fs), consistent with mutations of known consequence in acute myeloid leukemia, were identified. Contrary to a previous report, this finding suggests the genetic etiology of thymomas may not be fundamentally distinct from other tumor types. Rather, these findings suggest that further sequencing of cytogenetically normal thymoma samples should reveal the specific molecular drivers of thymoma.

No MeSH data available.


Related in: MedlinePlus

The DNMT3A p.G728D mutation observed in this thymoma sample is visualized in the context of other DNMT3A mutations observed in AML genome sequences from TCGA. The protein sequence and functional domains are depicted on the x axis. The number of AML mutations is depicted on the y axis. Red circles correspond to truncating mutations. Green circles correspond to missense mutations. Circle height corresponds to the number of mutations per position, however, the G728D indicator (black) is only meant to indicate position of this mutation. Note the clustering of AML nonsynonymous mutations around position 728. Mutations in this region reduce DNMT3A activity by disrupting the interaction between DNMT3L and DNMT3A. The Sanger sequencing validation trace of p.G7238D is also shown, demonstrating validation of p.G7238D as a homozygous somatic mutation.
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fig2: The DNMT3A p.G728D mutation observed in this thymoma sample is visualized in the context of other DNMT3A mutations observed in AML genome sequences from TCGA. The protein sequence and functional domains are depicted on the x axis. The number of AML mutations is depicted on the y axis. Red circles correspond to truncating mutations. Green circles correspond to missense mutations. Circle height corresponds to the number of mutations per position, however, the G728D indicator (black) is only meant to indicate position of this mutation. Note the clustering of AML nonsynonymous mutations around position 728. Mutations in this region reduce DNMT3A activity by disrupting the interaction between DNMT3L and DNMT3A. The Sanger sequencing validation trace of p.G7238D is also shown, demonstrating validation of p.G7238D as a homozygous somatic mutation.

Mentions: DNMT3A is a DNA methyltransferase required for de novo methylation and mammalian development.16 It is known to act as a tumor suppressor in acute myeloid leukemia (AML) and is observed mutated less frequently in other tumor types.17, 18 The nonsynonymous mutation observed in this thymoma sample leads to a nonconservative substitution of aspartate for glycine at amino-acid 728 (p.G728D) within the DNA methylase domain of DNMT3A. This region is known to be responsible for the hydrophobic interaction between DNMT3A and its regulatory subunit DNMT3L, an interaction that is required for activation of DNMT3A methyltransferase activity and previously shown to be disrupted by mutations in this region.19 Moreover, previously observed nonsynonymous mutations in AML cluster tightly within this region (shown in Figure 2)20, 21, 22. Strikingly and unusually, this somatic mutation was observed in homozygous state in the tumor: 61 of 62 (98.4%) exome sequencing reads from the tumor supported the mutation, 0 of 41 (0%) of exome sequencing reads from the normal sample supported the mutation, the homozygous state was confirmed via Sanger sequencing (Figure 2, inset), and no evidence for loss of heterozygosity was observed in the exome or low-pass whole-genome sequencing data. Moreover, no other somatic mutations were observed at >60% allelic frequency in the tumor, suggesting a specific and early gene conversion event at this locus. Finally, a previously sequenced AML, reported by Hou et al.,22 carried a mutation at this position (p.G728R) and at a nearby position (p.F731L), supporting the notion that homozygous or compound heterozygous mutations at the DNMT3A—DNMT3L interface are required to effectively disrupt methyltransferase activity.23 Thus, the type, location and unusual zygosity of this somatic mutation strongly suggest mutations in DNMT3A have a causal role in the etiology of thymoma.


ASXL1 and DNMT3A mutation in a cytogenetically normal B3 thymoma.

Belani R, Oliveira G, Erikson GA, Ra S, Schechter MS, Lee JK, Shipman WJ, Haaser SM, Torkamani A - Oncogenesis (2014)

The DNMT3A p.G728D mutation observed in this thymoma sample is visualized in the context of other DNMT3A mutations observed in AML genome sequences from TCGA. The protein sequence and functional domains are depicted on the x axis. The number of AML mutations is depicted on the y axis. Red circles correspond to truncating mutations. Green circles correspond to missense mutations. Circle height corresponds to the number of mutations per position, however, the G728D indicator (black) is only meant to indicate position of this mutation. Note the clustering of AML nonsynonymous mutations around position 728. Mutations in this region reduce DNMT3A activity by disrupting the interaction between DNMT3L and DNMT3A. The Sanger sequencing validation trace of p.G7238D is also shown, demonstrating validation of p.G7238D as a homozygous somatic mutation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150211&req=5

fig2: The DNMT3A p.G728D mutation observed in this thymoma sample is visualized in the context of other DNMT3A mutations observed in AML genome sequences from TCGA. The protein sequence and functional domains are depicted on the x axis. The number of AML mutations is depicted on the y axis. Red circles correspond to truncating mutations. Green circles correspond to missense mutations. Circle height corresponds to the number of mutations per position, however, the G728D indicator (black) is only meant to indicate position of this mutation. Note the clustering of AML nonsynonymous mutations around position 728. Mutations in this region reduce DNMT3A activity by disrupting the interaction between DNMT3L and DNMT3A. The Sanger sequencing validation trace of p.G7238D is also shown, demonstrating validation of p.G7238D as a homozygous somatic mutation.
Mentions: DNMT3A is a DNA methyltransferase required for de novo methylation and mammalian development.16 It is known to act as a tumor suppressor in acute myeloid leukemia (AML) and is observed mutated less frequently in other tumor types.17, 18 The nonsynonymous mutation observed in this thymoma sample leads to a nonconservative substitution of aspartate for glycine at amino-acid 728 (p.G728D) within the DNA methylase domain of DNMT3A. This region is known to be responsible for the hydrophobic interaction between DNMT3A and its regulatory subunit DNMT3L, an interaction that is required for activation of DNMT3A methyltransferase activity and previously shown to be disrupted by mutations in this region.19 Moreover, previously observed nonsynonymous mutations in AML cluster tightly within this region (shown in Figure 2)20, 21, 22. Strikingly and unusually, this somatic mutation was observed in homozygous state in the tumor: 61 of 62 (98.4%) exome sequencing reads from the tumor supported the mutation, 0 of 41 (0%) of exome sequencing reads from the normal sample supported the mutation, the homozygous state was confirmed via Sanger sequencing (Figure 2, inset), and no evidence for loss of heterozygosity was observed in the exome or low-pass whole-genome sequencing data. Moreover, no other somatic mutations were observed at >60% allelic frequency in the tumor, suggesting a specific and early gene conversion event at this locus. Finally, a previously sequenced AML, reported by Hou et al.,22 carried a mutation at this position (p.G728R) and at a nearby position (p.F731L), supporting the notion that homozygous or compound heterozygous mutations at the DNMT3A—DNMT3L interface are required to effectively disrupt methyltransferase activity.23 Thus, the type, location and unusual zygosity of this somatic mutation strongly suggest mutations in DNMT3A have a causal role in the etiology of thymoma.

Bottom Line: A stage IVB type B3 thymoma from a 47-year-old male of Asian descent with no history of myasthenia gravis or other autoimmune condition was genomically evaluated.Mutations in known tumor suppressors DNMT3A (p.G728D) and ASXL1 (p.E657fs), consistent with mutations of known consequence in acute myeloid leukemia, were identified.Contrary to a previous report, this finding suggests the genetic etiology of thymomas may not be fundamentally distinct from other tumor types.

View Article: PubMed Central - PubMed

Affiliation: Medical Oncology Associates of San Diego, San Diego, CA, USA.

ABSTRACT
The molecular drivers of thymoma are poorly understood. Outside of the identification of rarely occurring epidermal growth factor receptor and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog mutations via candidate gene sequencing, mutations in common cancer genes have yet to be observed. Only a single thymoma genome sequence has been previously reported, with no mutations in known cancer genes identified. Thus, we attempted to identify somatic driver mutations in a cytogenetically normal thymoma. A stage IVB type B3 thymoma from a 47-year-old male of Asian descent with no history of myasthenia gravis or other autoimmune condition was genomically evaluated. Exome sequencing and low-pass whole-genome sequencing was performed to identify somatic point mutations, copy number changes and structural variants. Mutations in known tumor suppressors DNMT3A (p.G728D) and ASXL1 (p.E657fs), consistent with mutations of known consequence in acute myeloid leukemia, were identified. Contrary to a previous report, this finding suggests the genetic etiology of thymomas may not be fundamentally distinct from other tumor types. Rather, these findings suggest that further sequencing of cytogenetically normal thymoma samples should reveal the specific molecular drivers of thymoma.

No MeSH data available.


Related in: MedlinePlus