NEW YORK (GenomeWeb News) – In two studies published online in Nature Genetics this past weekend researchers used exome sequencing to identify recurrent or frequent somatic mutations in the MAP kinase family in melanoma.
In the first study, led by researchers from the University of Geneva and the Ludwig Institute for Cancer Research at the University of Lausanne in Switzerland, investigators performed exome sequencing on seven metastases from sporadic cases of cutaneous melanoma. In those seven melanoma exomes they detected a total of 4,933 somatic variants — 3,611 of which were located in protein-coding regions in 2,586 affected genes.
In addition, between 178 and 1,296 somatic alterations were detected in each melanoma, of which between 104 and 761 were missense mutations, between four and 49 were nonsense mutations, between zero and 10 affected splice sites, and between three and seven were short insertions and/or deletions.
Following the exome sequencing, the researchers integrated their data sets of somatic point mutations and somatic copy number alterations with recently reported results from transcriptome sequencing and array comparative genomic hybridization and SNP arrays on the same seven melanomas.
They identified two melanomas with non-canonical BRAF mutations that had somatic G>A transitions at homologous sites in the MAP2K1 and MAP2K2 genes. In an effort to assess the prevalence of these gene mutations in melanoma the researchers performed Sanger sequencing of the MAP2K1, MAP2K2, BRAF, and NRAS coding sequences in 127 additional melanoma samples from 121 affected individuals.
Overall, melanomas from 10 of the 127 samples had mutations in either MAP2K1 or MAP2K2 that "were likely to be damaging," the researchers wrote. They further noted that none of these mutations had been previously reported in melanoma. "Of note, the presence of mutations in MAP2K1 or MAP2K2 did not seem to correlate with BRAF or NRAS mutation status," they added.
The investigators then sought to determine whether melanoma cells that expressed both mutated MAP2K1 or MAP2K2 and BRAF had increased resistance to MEK inhibitors, a class of anti-cancer drugs. Their results "suggest that the sensitivity of melanoma cells containing MAP2K1 or MAP2K2 activating mutations varies depending on the particular combination of MAP2K1 or MAP2K2 and BRAF variants."
The researchers said that the coexistence of mutated BRAF or NRAS with MAP2K1 or MAP2K2 mutations is "particularly puzzling" and that further studies will be needed to address the functional impact of combinations of those variants.
"Our results suggest that MAP2K1 and MAP2K2 mutations may have implications for the treatment of individuals with melanoma and support the currently proposed trials in which melanoma is treated with a combination of BRAF and MEK inhibitors," they concluded.
In a second study, researchers from the Queensland Institute of Medical Research in Brisbane, Australia and elsewhere used the Illumina Genome Analyzer II and Life Technologies SOLiD platforms to sequence eight melanoma exomes in an effort to identify new somatic mutations in metastatic melanoma. They identified 3,215 somatic alterations with a range of 243 to 523 per sample. Of these, 1,076 were synonymous mutations, and 2,139 were predicted to alter protein structure, comprising 1,925 missense, 122 nonsense, 32 splice-site mutations, and 64 small insertions and/or deletions.
The researchers found MAP3K5, MAP3K8, and MAP3K9 each showed somatic mutations in one out of eight melanoma samples. They validated the MAP3K5 and MAP3K9 mutations but said that the MAP3K8 mutation was found to be a false-positive. Eight of 85 melanoma cell lines had nonsynonymous somatic mutations in MAP3K5 and 13 of 85 cells lines had mutations in MAP3K9. Mutations in at least one of these genes occurred in 24 percent of samples, they said.
The investigators also conducted a high-throughput siRNA screen for sensitizers to temozolomide, an alkylating agent that has shown to modestly increase progression-free survivial in phase III studies. They noted that knockdown of MAP3K9 resulted in increased resistance to temozolomide treatment.
The researcher also assessed the effect of attenuating wild-type MAP3K5 and MAP3K9 levels in melanoma cells, looking at whether decreased expression of wild-type kinases can contribute to chemoresistance to temozolomide. Their findings suggest that attenuated MAP3K9 activity can contribute to chemotherapeutic resistance in melanoma.