Clonal architectures and driver mutations in metastatic melanomas.
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.
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.
Li
L
Ding
Donald A. Adam Comprehensive Melanoma Research Center, Moffitt Cancer Center, Tampa, Florida, United States of America.
Minjung
M
Kim
The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Krishna L
KL
Kanchi
The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Nathan D
ND
Dees
The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Charles
C
Lu
The Genome Institute, 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.
Malachi
M
Griffith
Donald A. Adam Comprehensive Melanoma Research Center, Moffitt Cancer Center, Tampa, Florida, United States of America.
David
D
Fenstermacher
Donald A. Adam Comprehensive Melanoma Research Center, Moffitt Cancer Center, Tampa, Florida, United States of America.
Hyeran
H
Sung
The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Christopher A
CA
Miller
Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Brian
B
Goetz
The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Michael C
MC
Wendl
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.
Obi
O
Griffith
Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Lynn A
LA
Cornelius
Department of Medicine, 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.
Gerald P
GP
Linette
The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Joshua F
JF
McMichael
Donald A. Adam Comprehensive Melanoma Research Center, Moffitt Cancer Center, Tampa, Florida, United States of America.
Vernon K
VK
Sondak
Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Ryan C
RC
Fields
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; Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Timothy J
TJ
Ley
Donald A. Adam Comprehensive Melanoma Research Center, Moffitt Cancer Center, Tampa, Florida, United States of America.
James J
JJ
Mulé
The Genome Institute, 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.
Richard K
RK
Wilson
Donald A. Adam Comprehensive Melanoma Research Center, Moffitt Cancer Center, Tampa, Florida, United States of America.
Jeffrey S
JS
Weber
D001483:Base Sequence; D004252:DNA Mutational Analysis; D020558:GTP Phosphohydrolases / Q000235:genetics*; D019942:Genes, p16; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008545:Melanoma / Q000235:genetics*; D008565:Membrane Proteins / Q000235:genetics*; D010749:Phosphoprotein Phosphatases / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics*; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics; D036121:Receptor, EphA3; D017422:Sequence Analysis, DNA; D012878:Skin Neoplasms / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000235:genetics
D008565:Membrane Proteins; D025521:Tumor Suppressor Proteins; C491718:EPHA3 protein, human; D020794:Receptor Protein-Tyrosine Kinases; D036121:Receptor, EphA3; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D010749:Phosphoprotein Phosphatases; D020558:GTP Phosphohydrolases; C579846:NRAS protein, human