Modeling genomic diversity and tumor dependency in malignant melanoma.
The classification of human tumors based on molecular criteria offers tremendous clinical potential; however, discerning critical and "druggable" effectors on a large scale will also require robust experimental models reflective of tumor genomic diversity. Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative "driver" events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors. When annotated according to these lesions, melanomas cluster into subgroups suggestive of distinct oncogenic mechanisms. Integrating gene expression data suggests novel candidate effector genes linked to recurrent copy gains and losses, including both phosphatase and tensin homologue (PTEN)-dependent and PTEN-independent tumor suppressor mechanisms associated with chromosome 10 deletions. Finally, sample-matched pharmacologic data show that FGFR1 mutations and extracellular signal-regulated kinase (ERK) activation may modulate sensitivity to mitogen-activated protein kinase/ERK kinase inhibitors. Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors.
Lin
William M
WM
Department of Medical Oncology, Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
Baker
Alissa C
AC
Beroukhim
Rameen
R
Winckler
Wendy
W
Feng
Whei
W
Marmion
Jennifer M
JM
Laine
Elisabeth
E
Greulich
Heidi
H
Tseng
Hsiuyi
H
Gates
Casey
C
Hodi
F Stephen
FS
Dranoff
Glenn
G
Sellers
William R
WR
Thomas
Roman K
RK
Meyerson
Matthew
M
Golub
Todd R
TR
Dummer
Reinhard
R
Herlyn
Meenhard
M
Getz
Gad
G
Garraway
Levi A
LA
D000465:Algorithms; D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D002872:Chromosome Deletion; D002879:Chromosomes, Human, Pair 10; D016000:Cluster Analysis; D004273:DNA, Neoplasm / Q000235:genetics; D048049:Extracellular Signal-Regulated MAP Kinases / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D006801:Humans; D019656:Loss of Heterozygosity; D008545:Melanoma / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D020928:Mitogen-Activated Protein Kinases / Q000235:genetics / Q000378:metabolism; D051059:PTEN Phosphohydrolase / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D051496:Receptor, Fibroblast Growth Factor, Type 1 / Q000235:genetics; D048490:raf Kinases / Q000235:genetics
D004273:DNA, Neoplasm; C496348:FGFR1 protein, human; D051496:Receptor, Fibroblast Growth Factor, Type 1; D048490:raf Kinases; D048049:Extracellular Signal-Regulated MAP Kinases; D020928:Mitogen-Activated Protein Kinases; D051059:PTEN Phosphohydrolase; C494929:PTEN protein, human