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Whole genome sequence analysis links chromothripsis to EGFR, MDM2, MDM4, and CDK4 amplification in glioblastoma.

Furgason JM, Koncar RF, Michelhaugh SK, Sarkar FH, Mittal S, Sloan AE, Barnholtz-Sloan JS, Bahassi el M - Oncoscience (2015)

Bottom Line: The data derived from this study was further expanded on using fluorescence in situ hybridization (FISH) analysis and susceptibility studies with colony formation assays.We show that primary GBMs are associated with higher chromothripsis scores and establish a link between chromothripsis and gene amplification of receptor tyrosine kinases (RTKs), as well as modulators of the TP53 and RB1 pathways.Utilizing a newly introduced bioinformatic tool, we provide evidence that chromothripsis is associated with the formation of amplicons containing several oncogenes involved in key pathways that are likely essential for post-chromothriptic cell survival.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, Division of Hematology/Oncology and UC Brain Tumor Center, University of Cincinnati, Cincinnati OH, USA.

ABSTRACT

Background: Findings based on recent advances in next-generation sequence analysis suggest that, in some tumors, a single catastrophic event, termed chromothripsis, results in several simultaneous tumorigenic alterations. Previous studies have suggested that glioblastoma (GBM) may exhibit chromothripsis at a higher rate (39%) than other tumors (9%). Primary glioblastoma is an aggressive form of brain cancer that typically appears suddenly in older adults. With aggressive treatment, the median survival time is only 15 months. Their acute onset and widespread genomic instability indicates that chromothripsis may play a key role in their initiation and progression. GBMs are often characterized by EGFR amplification, CDKN2A and PTEN deletion, although approximately 20% of GBMs harbor additional amplifications in MDM2 or MDM4 with CDK4.

Methods: We used the chromothripsis prediction tool, Shatterproof, in conjunction with a custom whole genome sequence analysis pipeline in order to generate putative regions of chromothripsis. The data derived from this study was further expanded on using fluorescence in situ hybridization (FISH) analysis and susceptibility studies with colony formation assays.

Results: We show that primary GBMs are associated with higher chromothripsis scores and establish a link between chromothripsis and gene amplification of receptor tyrosine kinases (RTKs), as well as modulators of the TP53 and RB1 pathways.

Conclusions: Utilizing a newly introduced bioinformatic tool, we provide evidence that chromothripsis is associated with the formation of amplicons containing several oncogenes involved in key pathways that are likely essential for post-chromothriptic cell survival.

No MeSH data available.


Related in: MedlinePlus

Amplification of key regulators of the TP53 and RB1 pathways are tied to EGFR and 2 other tyrosine kinase amplification in Glioblastoma(A) Circos diagram depicting a chromothriptic event that occurred in TCGA-06-0157 which resulted in the recombination of discrete regions of chromosomes 1, 7, and 12, leading to the co-amplification of MDM4, EGFR, and CDK4, respectively. Tracks are organized, from outside to inside: karyotype data, cosmic database cancer associated genes, intra-chromosomal translocations (light green links), copy number data (0>cn<10, >10 is indicated by size of point), and inter-chromosomal translocation (central links). (B) cBioPortal OncoPrint visualization of TCGA Glioblastoma tumor alterations showing the mutual exclusivity of MDM2, MDM4, and TP53 paired with CDK4, RB1, and to a lesser extent, CDKN2A. (C) Specific TCGA tumors analyzed by this study were selected from the population of MDM2/MDM4 amplified tumors depicted in figure 1b and include the tyrosine kinase receptors that are amplified. A more detailed table of these alterations is included in figure 2c.
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Figure 1: Amplification of key regulators of the TP53 and RB1 pathways are tied to EGFR and 2 other tyrosine kinase amplification in Glioblastoma(A) Circos diagram depicting a chromothriptic event that occurred in TCGA-06-0157 which resulted in the recombination of discrete regions of chromosomes 1, 7, and 12, leading to the co-amplification of MDM4, EGFR, and CDK4, respectively. Tracks are organized, from outside to inside: karyotype data, cosmic database cancer associated genes, intra-chromosomal translocations (light green links), copy number data (0>cn<10, >10 is indicated by size of point), and inter-chromosomal translocation (central links). (B) cBioPortal OncoPrint visualization of TCGA Glioblastoma tumor alterations showing the mutual exclusivity of MDM2, MDM4, and TP53 paired with CDK4, RB1, and to a lesser extent, CDKN2A. (C) Specific TCGA tumors analyzed by this study were selected from the population of MDM2/MDM4 amplified tumors depicted in figure 1b and include the tyrosine kinase receptors that are amplified. A more detailed table of these alterations is included in figure 2c.

Mentions: Recently, using whole genome sequencing datasets generated in our laboratory and by TCGA, we identified a population of GBM tumors that exhibited MDM4 amplifications that appeared to be mutually exclusive with the MDM2 amplification that was previously reported. Our analysis of MDM2 and MDM4 amplified tumors has revealed that, in many cases, these amplifications are directly tied to trans-chromosomal rearrangements, often in and around the EGFR gene or another RTK. Indeed, it is likely that these translocations are responsible for positioning MDM2 or MDM4, along with CDK4, within the same amplicon that results in EGFR amplification. Our analysis revealed that four out of 12 TCGA tumors exhibited this co-amplification (Figures 1a, S1, S2). In one MDM4-amplified tumor, TCGA-06-0157, CDK4 has been translocated to the same amplicon as MDM4, while MDM2 is unaltered, indicating that CDK4 is selectively amplified in conjunction with these TP53 regulators (Figure 1a). A similar phenomenon involving the MDM2/CDK4 locus was observed in the 3 other tumors. Amplifications of CDK4 and either MDM2 or MDM4 can be found in nearly 20% of all GBM tumors in TCGA (Figure 1b). In the case of MDM2-amplified tumors, it appears that amplification of CDK4 is the primary mechanism of modulating RB1 function. This is likely due to the close proximity of the CDK4 gene to MDM2.


Whole genome sequence analysis links chromothripsis to EGFR, MDM2, MDM4, and CDK4 amplification in glioblastoma.

Furgason JM, Koncar RF, Michelhaugh SK, Sarkar FH, Mittal S, Sloan AE, Barnholtz-Sloan JS, Bahassi el M - Oncoscience (2015)

Amplification of key regulators of the TP53 and RB1 pathways are tied to EGFR and 2 other tyrosine kinase amplification in Glioblastoma(A) Circos diagram depicting a chromothriptic event that occurred in TCGA-06-0157 which resulted in the recombination of discrete regions of chromosomes 1, 7, and 12, leading to the co-amplification of MDM4, EGFR, and CDK4, respectively. Tracks are organized, from outside to inside: karyotype data, cosmic database cancer associated genes, intra-chromosomal translocations (light green links), copy number data (0>cn<10, >10 is indicated by size of point), and inter-chromosomal translocation (central links). (B) cBioPortal OncoPrint visualization of TCGA Glioblastoma tumor alterations showing the mutual exclusivity of MDM2, MDM4, and TP53 paired with CDK4, RB1, and to a lesser extent, CDKN2A. (C) Specific TCGA tumors analyzed by this study were selected from the population of MDM2/MDM4 amplified tumors depicted in figure 1b and include the tyrosine kinase receptors that are amplified. A more detailed table of these alterations is included in figure 2c.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 1: Amplification of key regulators of the TP53 and RB1 pathways are tied to EGFR and 2 other tyrosine kinase amplification in Glioblastoma(A) Circos diagram depicting a chromothriptic event that occurred in TCGA-06-0157 which resulted in the recombination of discrete regions of chromosomes 1, 7, and 12, leading to the co-amplification of MDM4, EGFR, and CDK4, respectively. Tracks are organized, from outside to inside: karyotype data, cosmic database cancer associated genes, intra-chromosomal translocations (light green links), copy number data (0>cn<10, >10 is indicated by size of point), and inter-chromosomal translocation (central links). (B) cBioPortal OncoPrint visualization of TCGA Glioblastoma tumor alterations showing the mutual exclusivity of MDM2, MDM4, and TP53 paired with CDK4, RB1, and to a lesser extent, CDKN2A. (C) Specific TCGA tumors analyzed by this study were selected from the population of MDM2/MDM4 amplified tumors depicted in figure 1b and include the tyrosine kinase receptors that are amplified. A more detailed table of these alterations is included in figure 2c.
Mentions: Recently, using whole genome sequencing datasets generated in our laboratory and by TCGA, we identified a population of GBM tumors that exhibited MDM4 amplifications that appeared to be mutually exclusive with the MDM2 amplification that was previously reported. Our analysis of MDM2 and MDM4 amplified tumors has revealed that, in many cases, these amplifications are directly tied to trans-chromosomal rearrangements, often in and around the EGFR gene or another RTK. Indeed, it is likely that these translocations are responsible for positioning MDM2 or MDM4, along with CDK4, within the same amplicon that results in EGFR amplification. Our analysis revealed that four out of 12 TCGA tumors exhibited this co-amplification (Figures 1a, S1, S2). In one MDM4-amplified tumor, TCGA-06-0157, CDK4 has been translocated to the same amplicon as MDM4, while MDM2 is unaltered, indicating that CDK4 is selectively amplified in conjunction with these TP53 regulators (Figure 1a). A similar phenomenon involving the MDM2/CDK4 locus was observed in the 3 other tumors. Amplifications of CDK4 and either MDM2 or MDM4 can be found in nearly 20% of all GBM tumors in TCGA (Figure 1b). In the case of MDM2-amplified tumors, it appears that amplification of CDK4 is the primary mechanism of modulating RB1 function. This is likely due to the close proximity of the CDK4 gene to MDM2.

Bottom Line: The data derived from this study was further expanded on using fluorescence in situ hybridization (FISH) analysis and susceptibility studies with colony formation assays.We show that primary GBMs are associated with higher chromothripsis scores and establish a link between chromothripsis and gene amplification of receptor tyrosine kinases (RTKs), as well as modulators of the TP53 and RB1 pathways.Utilizing a newly introduced bioinformatic tool, we provide evidence that chromothripsis is associated with the formation of amplicons containing several oncogenes involved in key pathways that are likely essential for post-chromothriptic cell survival.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, Division of Hematology/Oncology and UC Brain Tumor Center, University of Cincinnati, Cincinnati OH, USA.

ABSTRACT

Background: Findings based on recent advances in next-generation sequence analysis suggest that, in some tumors, a single catastrophic event, termed chromothripsis, results in several simultaneous tumorigenic alterations. Previous studies have suggested that glioblastoma (GBM) may exhibit chromothripsis at a higher rate (39%) than other tumors (9%). Primary glioblastoma is an aggressive form of brain cancer that typically appears suddenly in older adults. With aggressive treatment, the median survival time is only 15 months. Their acute onset and widespread genomic instability indicates that chromothripsis may play a key role in their initiation and progression. GBMs are often characterized by EGFR amplification, CDKN2A and PTEN deletion, although approximately 20% of GBMs harbor additional amplifications in MDM2 or MDM4 with CDK4.

Methods: We used the chromothripsis prediction tool, Shatterproof, in conjunction with a custom whole genome sequence analysis pipeline in order to generate putative regions of chromothripsis. The data derived from this study was further expanded on using fluorescence in situ hybridization (FISH) analysis and susceptibility studies with colony formation assays.

Results: We show that primary GBMs are associated with higher chromothripsis scores and establish a link between chromothripsis and gene amplification of receptor tyrosine kinases (RTKs), as well as modulators of the TP53 and RB1 pathways.

Conclusions: Utilizing a newly introduced bioinformatic tool, we provide evidence that chromothripsis is associated with the formation of amplicons containing several oncogenes involved in key pathways that are likely essential for post-chromothriptic cell survival.

No MeSH data available.


Related in: MedlinePlus