Our primary research interests are the study of the genes that are altered in cancer and the cellular pathways these genes perturb. Identifying the genetic alterations and understanding how they work provides the foundation for novel approaches to the prevention, diagnosis and treatment of cancer. To fulfill these goals, we are using a sequence-based mutational analysis to evaluate genetic alterations in cutaneous malignant melanoma. Melanoma develops from the malignant transformation of melanocytes. It is the most common fatal skin cancer, and its incidence has increased at a more rapid rate than any other malignancy in the US. Unlike early-stage disease, late stage melanoma has few therapeutic options;hence our studies focus on late stage disease. The clinical progression is assumed to correspond to the accumulation of genetic mutations. In order to develop treatments for advanced disease, it is important to understand the genetic alterations leading to melanoma as such understanding will permit personalized design of treatments for melanoma. In the FY2013 we worked on a multitude of projects generated from our whole-genome/whole-exome sequencing of our metastatic melanoma samples as well as merged data published by others in the field. The projects were broken down into examining functionally, hotspot mutations (synonymous or non-synonymous) and highly mutated genes. Using whole-genome and whole-exome sequencing we identified somatic mutations in 29 melanoma samples. Validation of one synonymous somatic mutation in BCL2L12 in 285 samples identified 12 cases that harbored the recurrent F17F mutation. This led to increased BCL2L12 mRNA and protein levels, due to differential targeting of wild-type and mutant BCL2L12 by hsa-miR-671-5p. Protein made from mutant BCL2L12 transcript bound p53, inhibited UV-induced apoptosis more efficiently than wild-type BCL2L12 and reduced endogenous p53 target gene transcription. This was the first report of positive selection of a recurrent somatic synonymous mutation in cancer. Next, we studied the effect a non-synonyomus mutation imparts on the Mitogen Activated Protein Kinase Kinase Kinase 5 (MAP3K5 or ASK1) in metastatic melanoma. Upon further analysis of our whole-genome and whole-exome sequencing data of samples, we identified several genes that harbor recurrent non-synonymous mutations. These included MAP3K5, which in a prevalence screen of 288 melanomas was found to harbor a R256C substitution in 5 cases. All MAP3K5 mutated samples were wild-type for BRAF, suggesting a mutual exclusivity for these mutations. Functional analysis of the MAP3K5 R256C mutation revealed attenuation of MKK4 activation through increased binding of the inhibitory protein thioredoxin (TXN/TRX-1/Trx);resulting in increased proliferation and anchorage-independent growth of melanoma cells. This mutation represents a potential target for the design of new therapies to treat melanoma. Finally we focused our efforts on examining highly mutated genes originally discovered in our previous whole-exome screen. Identification and functional characterization of putative mutations is ongoing. Our work provides a strong rationale for development of therapeutic and diagnostic approaches for individuals harboring the various discovered mutations. Using these tools, one could envision tailored therapeutics based on the mutations in an individuals cancer.

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Prickett, Todd D; Zerlanko, Brad; Gartner, Jared J et al. (2014) Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin. J Invest Dermatol 134:452-460
Robbins, Paul F; Lu, Yong-Chen; El-Gamil, Mona et al. (2013) Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells. Nat Med 19:747-52
Lu, Yong-Chen; Yao, Xin; Li, Yong F et al. (2013) Mutated PPP1R3B is recognized by T cells used to treat a melanoma patient who experienced a durable complete tumor regression. J Immunol 190:6034-42
Hansen, Nancy F; Gartner, Jared J; Mei, Lan et al. (2013) Shimmer: detection of genetic alterations in tumors using next-generation sequence data. Bioinformatics 29:1498-503
Hill, Victoria K; Gartner, Jared J; Samuels, Yardena et al. (2013) The genetics of melanoma: recent advances. Annu Rev Genomics Hum Genet 14:257-79
Walia, Vijay; Mu, Euphemia W; Lin, Jimmy C et al. (2012) Delving into somatic variation in sporadic melanoma. Pigment Cell Melanoma Res 25:155-70
Prickett, Todd D; Samuels, Yardena (2012) Molecular pathways: dysregulated glutamatergic signaling pathways in cancer. Clin Cancer Res 18:4240-6
Parker, Stephen C J; Gartner, Jared; Cardenas-Navia, Isabel et al. (2012) Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. PLoS Genet 8:e1002871
Gartner, Jared J; Davis, Sean; Wei, Xiaomu et al. (2012) Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics 13:505
Wei, Xiaomu; Walia, Vijay; Lin, Jimmy C et al. (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 43:442-6

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