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Clonal architectures and driver mutations in metastatic melanomas.

Ding L, Kim M, Kanchi KL, Dees ND, Lu C, Griffith M, Fenstermacher D, Sung H, Miller CA, Goetz B, Wendl MC, Griffith O, Cornelius LA, Linette GP, McMichael JF, Sondak VK, Fields RC, Ley TJ, Mulé JJ, Wilson RK, Weber JS - PLoS ONE (2014)

Bottom Line: Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2).Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature.Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor.

View Article: PubMed Central - PubMed

Affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America.

ABSTRACT
To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2). Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic and mutational relationships among four metastatic samples from different sites of the same individuals (MEL 174).Geographic locations and CT scans of metastasis samples in MEL 174 with 2 samples from liver (liver tumor 1, liver tumor 2), one from omentum, and one from portal nodule. Phylogenetic relationships among 4 metastatic tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis. Increased variant allele frequency of BRAF (V600E) in liver 2 and portal module, both tumors showed resistance to vemurafinib treatment. BRAF amplifications were also shown in liver 2 and portal module tumors.
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pone-0111153-g008: Phylogenetic and mutational relationships among four metastatic samples from different sites of the same individuals (MEL 174).Geographic locations and CT scans of metastasis samples in MEL 174 with 2 samples from liver (liver tumor 1, liver tumor 2), one from omentum, and one from portal nodule. Phylogenetic relationships among 4 metastatic tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis. Increased variant allele frequency of BRAF (V600E) in liver 2 and portal module, both tumors showed resistance to vemurafinib treatment. BRAF amplifications were also shown in liver 2 and portal module tumors.

Mentions: We also analyzed a quartet of synchronous tumors from MEL174: two from the liver (liver tumors 1 and 2), one omentum tumor, and one portal nodule tumor (Figure 8). Liver tumor 2 shows some similarities to the portal nodule tumor, with both having major amplifications on chromosomes 7 and 8, while liver tumor 1 and omentum tumor show a “quieter” overall copy number landscape. Copy number alterations and mutation-based phylogenetic largely agree on the relationship between these tumors (Table S13 in File S1and Figure S3 in File S1). Liver tumor 1 and the omentum tumor responded to treatment with the BRAF inhibitor vemurafinib, while the others continued growing/progressing during treatment. We found that both BRAF (V600E) and CTNNA2 (R755*) have much higher variant/mutant allele frequencies in the non-reponsive portal nodule (BRAF: 65.2%; CTNNA2: 15.6%) and liver tumor 2 (33.3%; 16.1%) than in the omentum nodule (8.2%; 1.1%) and liver tumor 1(14.3%; 2.8%). The CTNNA2 mutation is almost undetectable in the omentum nodule with only one read, out of 94 total reads, supporting the mutant allele. A MAP2K1 (E203K) mutation is only detected in liver tumor 2 despite the high coverage (>40X) in all 4 metastases (Table S14 in File S2). After applying purity-based VAF adjustments, the portal nodule has the highest adjusted VAF at 72.47%, followed by liver tumor 2, liver tumor 1, omentum nodule at 55.55%, 47.63%, and 41% respectively. Our data indicate that sample-specific genetic alterations and variable frequencies of mutations might contribute to differential treatment responses among metastasis samples from the same patients, consistent with a previous report [39] (Figure 8). Moreover, our analysis shows that all four metastatic tumors from both patients were derived from the same primary tumor but their patterns of mutations diverged considerably during evolution and metastatic growth.


Clonal architectures and driver mutations in metastatic melanomas.

Ding L, Kim M, Kanchi KL, Dees ND, Lu C, Griffith M, Fenstermacher D, Sung H, Miller CA, Goetz B, Wendl MC, Griffith O, Cornelius LA, Linette GP, McMichael JF, Sondak VK, Fields RC, Ley TJ, Mulé JJ, Wilson RK, Weber JS - PLoS ONE (2014)

Phylogenetic and mutational relationships among four metastatic samples from different sites of the same individuals (MEL 174).Geographic locations and CT scans of metastasis samples in MEL 174 with 2 samples from liver (liver tumor 1, liver tumor 2), one from omentum, and one from portal nodule. Phylogenetic relationships among 4 metastatic tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis. Increased variant allele frequency of BRAF (V600E) in liver 2 and portal module, both tumors showed resistance to vemurafinib treatment. BRAF amplifications were also shown in liver 2 and portal module tumors.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230926&req=5

pone-0111153-g008: Phylogenetic and mutational relationships among four metastatic samples from different sites of the same individuals (MEL 174).Geographic locations and CT scans of metastasis samples in MEL 174 with 2 samples from liver (liver tumor 1, liver tumor 2), one from omentum, and one from portal nodule. Phylogenetic relationships among 4 metastatic tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis. Increased variant allele frequency of BRAF (V600E) in liver 2 and portal module, both tumors showed resistance to vemurafinib treatment. BRAF amplifications were also shown in liver 2 and portal module tumors.
Mentions: We also analyzed a quartet of synchronous tumors from MEL174: two from the liver (liver tumors 1 and 2), one omentum tumor, and one portal nodule tumor (Figure 8). Liver tumor 2 shows some similarities to the portal nodule tumor, with both having major amplifications on chromosomes 7 and 8, while liver tumor 1 and omentum tumor show a “quieter” overall copy number landscape. Copy number alterations and mutation-based phylogenetic largely agree on the relationship between these tumors (Table S13 in File S1and Figure S3 in File S1). Liver tumor 1 and the omentum tumor responded to treatment with the BRAF inhibitor vemurafinib, while the others continued growing/progressing during treatment. We found that both BRAF (V600E) and CTNNA2 (R755*) have much higher variant/mutant allele frequencies in the non-reponsive portal nodule (BRAF: 65.2%; CTNNA2: 15.6%) and liver tumor 2 (33.3%; 16.1%) than in the omentum nodule (8.2%; 1.1%) and liver tumor 1(14.3%; 2.8%). The CTNNA2 mutation is almost undetectable in the omentum nodule with only one read, out of 94 total reads, supporting the mutant allele. A MAP2K1 (E203K) mutation is only detected in liver tumor 2 despite the high coverage (>40X) in all 4 metastases (Table S14 in File S2). After applying purity-based VAF adjustments, the portal nodule has the highest adjusted VAF at 72.47%, followed by liver tumor 2, liver tumor 1, omentum nodule at 55.55%, 47.63%, and 41% respectively. Our data indicate that sample-specific genetic alterations and variable frequencies of mutations might contribute to differential treatment responses among metastasis samples from the same patients, consistent with a previous report [39] (Figure 8). Moreover, our analysis shows that all four metastatic tumors from both patients were derived from the same primary tumor but their patterns of mutations diverged considerably during evolution and metastatic growth.

Bottom Line: Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2).Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature.Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor.

View Article: PubMed Central - PubMed

Affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America.

ABSTRACT
To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2). Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma.

No MeSH data available.


Related in: MedlinePlus