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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

Comparison of Circos plots of the metastatic samples from two tissue sites of the same individuals (MEL5 and MEL13).In MEL5, pancreas tumor specific structural variants (inversions and deletions) are clustered on chromosomes 2 and 5, and pancreas or lung enriched rearrangements are drawn in yellow. In MEL13, highly similar copy number and structural variant patterns between lung and chest wall metastases are shown. No purity-based copy number corrections were used for plotting copy number.
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pone-0111153-g005: Comparison of Circos plots of the metastatic samples from two tissue sites of the same individuals (MEL5 and MEL13).In MEL5, pancreas tumor specific structural variants (inversions and deletions) are clustered on chromosomes 2 and 5, and pancreas or lung enriched rearrangements are drawn in yellow. In MEL13, highly similar copy number and structural variant patterns between lung and chest wall metastases are shown. No purity-based copy number corrections were used for plotting copy number.

Mentions: Among the 28 paired cases, 8 (2 WGS and 6 extension cases) had multiple metastasis samples, allowing the examination of relationships of different tumors from the same individual. First, we investigated the two WGS cases (MEL5 and MEL13) with two metastasis samples each. The rearrangement and copy number patterns were almost identical for the MEL13 paired metachronous tumors from chest wall and lung (Figure 5). In MEL5, a significant number of inversions on chromosome 3 were found to be present in the pancreatic metastasis but not the lung metastasis (Figure 5). Clonality analysis using point mutations from selected copy number neutral regions revealed at least two clusters each in the lung (22.2% and 14.3%) and pancreas (45.6% and 39.4%) metastasis from MEL5 (Figure 6and Table S12b–c in File S2). The MEL5 lung metastasis has two distinct mutation clusters, while the pancreas metastasis harbors two clusters with overlapping boundaries. A comparison of genome-wide tier 1 mutations in the pancreas versus lung metastases (Figure 6and Table S12f in File S2) shows that greater than 99% of the tier 1 mutations (1127/1139) are shared between these two samples, indicating they likely emerged from the same progenitor clone in the primary tumor. Many MEL5 mutations appear to be enriched in the pancreas sample. Additionally, a wider range of VAFs present in the pancreas sample indicates that numerous copy number altering events occurred after the initial development of the pancreas metastasis. Both the lung and chest wall metastatic tumors in MEL13 have a very similar clonal pattern (Figure 6and Table S12d–e in File S2), with one dominant higher VAF peak (24.9% and 32.4%, respectively) shouldered by less distinct clusters of mutations. The slight difference in the peak VAFs of the dominant clusters in these two metastases suggests that the chest wall biological specimen has a higher purity (64.8% tumor) than that of the lung metastasis (49.8% tumor). Consistent with the kernel density plots (Figure 6), an analysis of VAFs of genome-wide tier 1 mutations in MEL13 (Figure 6and Table S12g in File S2) shows similar clonal architecture in the two metastasis samples, as most occur at comparable VAFs. Again, over 99% of the mutations are shared between the two metastases (503 of 505) in MEL13, with only 2 mutations being sample specific. This result suggests that both MEL13 metastases are derived from the same clone/subclone in the primary tumor.


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)

Comparison of Circos plots of the metastatic samples from two tissue sites of the same individuals (MEL5 and MEL13).In MEL5, pancreas tumor specific structural variants (inversions and deletions) are clustered on chromosomes 2 and 5, and pancreas or lung enriched rearrangements are drawn in yellow. In MEL13, highly similar copy number and structural variant patterns between lung and chest wall metastases are shown. No purity-based copy number corrections were used for plotting copy number.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111153-g005: Comparison of Circos plots of the metastatic samples from two tissue sites of the same individuals (MEL5 and MEL13).In MEL5, pancreas tumor specific structural variants (inversions and deletions) are clustered on chromosomes 2 and 5, and pancreas or lung enriched rearrangements are drawn in yellow. In MEL13, highly similar copy number and structural variant patterns between lung and chest wall metastases are shown. No purity-based copy number corrections were used for plotting copy number.
Mentions: Among the 28 paired cases, 8 (2 WGS and 6 extension cases) had multiple metastasis samples, allowing the examination of relationships of different tumors from the same individual. First, we investigated the two WGS cases (MEL5 and MEL13) with two metastasis samples each. The rearrangement and copy number patterns were almost identical for the MEL13 paired metachronous tumors from chest wall and lung (Figure 5). In MEL5, a significant number of inversions on chromosome 3 were found to be present in the pancreatic metastasis but not the lung metastasis (Figure 5). Clonality analysis using point mutations from selected copy number neutral regions revealed at least two clusters each in the lung (22.2% and 14.3%) and pancreas (45.6% and 39.4%) metastasis from MEL5 (Figure 6and Table S12b–c in File S2). The MEL5 lung metastasis has two distinct mutation clusters, while the pancreas metastasis harbors two clusters with overlapping boundaries. A comparison of genome-wide tier 1 mutations in the pancreas versus lung metastases (Figure 6and Table S12f in File S2) shows that greater than 99% of the tier 1 mutations (1127/1139) are shared between these two samples, indicating they likely emerged from the same progenitor clone in the primary tumor. Many MEL5 mutations appear to be enriched in the pancreas sample. Additionally, a wider range of VAFs present in the pancreas sample indicates that numerous copy number altering events occurred after the initial development of the pancreas metastasis. Both the lung and chest wall metastatic tumors in MEL13 have a very similar clonal pattern (Figure 6and Table S12d–e in File S2), with one dominant higher VAF peak (24.9% and 32.4%, respectively) shouldered by less distinct clusters of mutations. The slight difference in the peak VAFs of the dominant clusters in these two metastases suggests that the chest wall biological specimen has a higher purity (64.8% tumor) than that of the lung metastasis (49.8% tumor). Consistent with the kernel density plots (Figure 6), an analysis of VAFs of genome-wide tier 1 mutations in MEL13 (Figure 6and Table S12g in File S2) shows similar clonal architecture in the two metastasis samples, as most occur at comparable VAFs. Again, over 99% of the mutations are shared between the two metastases (503 of 505) in MEL13, with only 2 mutations being sample specific. This result suggests that both MEL13 metastases are derived from the same clone/subclone in the primary tumor.

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