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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 167).Geographic locations and CT scans of metastasis samples in MEL167 with three tumor samples from small bowel (mass 1, mass 2, and mass 3) and one from mensenteric lymph node. Phylogenetic relationships, mutation patterns, and copy number landscape in all four tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis.
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pone-0111153-g007: Phylogenetic and mutational relationships among four metastatic samples from different sites of the same individuals (MEL 167).Geographic locations and CT scans of metastasis samples in MEL167 with three tumor samples from small bowel (mass 1, mass 2, and mass 3) and one from mensenteric lymph node. Phylogenetic relationships, mutation patterns, and copy number landscape in all four tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis.

Mentions: Two cases (MEL167 and MEL174) with 4 synchronous metastatic samples were sequenced with a targeted extension panel. MEL167 has three tumor samples from small bowel and one from a lymph node. The relative locations of small bowel tumors 1, 2, and 3 from MEL167 are shown in Figure 7. Copy number analysis using VarScan 2 shows that small bowel tumors 2 and 3 share amplifications on chromosomes 7q, 13q, and 20, consistent with their close proximity in location. The lymph node tumor shared amplifications on chromosomes 2 and 3 with small bowel tumor 2 while small bowel tumor 1 showed no major amplifications genome-wide (Figure 7). Phylip-based phylogenetics analysis (Supplementary Materials and Methods in File S1) using mutations and their purity-corrected frequencies (Table S13 In File S1 and Figure S3 in File S1) recapitulated the copy number analysis-based findings and identified small bowel tumors 2 and 3 as closely related and most divergent from the normal. The lymph node and small bowel tumor 1 are more similar to each other and appear to be less divergent from the the normal tissue (Figure 7). Mutations in TP53 (H179Y), NRAS (Q61K), ATR (G2120C), and EPHA3 (P317S) are shared by all four tumors, suggesting they are likely founding mutations from the primary tumor (Figure 7 and Table S14 in File S2). On the other hand, PREX2 (P614S) and ZNF831 (P1639S) are only present in some tumors.


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 167).Geographic locations and CT scans of metastasis samples in MEL167 with three tumor samples from small bowel (mass 1, mass 2, and mass 3) and one from mensenteric lymph node. Phylogenetic relationships, mutation patterns, and copy number landscape in all four tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111153-g007: Phylogenetic and mutational relationships among four metastatic samples from different sites of the same individuals (MEL 167).Geographic locations and CT scans of metastasis samples in MEL167 with three tumor samples from small bowel (mass 1, mass 2, and mass 3) and one from mensenteric lymph node. Phylogenetic relationships, mutation patterns, and copy number landscape in all four tumors were shown. Purity based VAF corrections were applied prior to phylogenetic analysis.
Mentions: Two cases (MEL167 and MEL174) with 4 synchronous metastatic samples were sequenced with a targeted extension panel. MEL167 has three tumor samples from small bowel and one from a lymph node. The relative locations of small bowel tumors 1, 2, and 3 from MEL167 are shown in Figure 7. Copy number analysis using VarScan 2 shows that small bowel tumors 2 and 3 share amplifications on chromosomes 7q, 13q, and 20, consistent with their close proximity in location. The lymph node tumor shared amplifications on chromosomes 2 and 3 with small bowel tumor 2 while small bowel tumor 1 showed no major amplifications genome-wide (Figure 7). Phylip-based phylogenetics analysis (Supplementary Materials and Methods in File S1) using mutations and their purity-corrected frequencies (Table S13 In File S1 and Figure S3 in File S1) recapitulated the copy number analysis-based findings and identified small bowel tumors 2 and 3 as closely related and most divergent from the normal. The lymph node and small bowel tumor 1 are more similar to each other and appear to be less divergent from the the normal tissue (Figure 7). Mutations in TP53 (H179Y), NRAS (Q61K), ATR (G2120C), and EPHA3 (P317S) are shared by all four tumors, suggesting they are likely founding mutations from the primary tumor (Figure 7 and Table S14 in File S2). On the other hand, PREX2 (P614S) and ZNF831 (P1639S) are only present in some tumors.

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