THE GENETICS OF OCULAR MELANOMA

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Abstract: Metastasis is a defining feature of malignant tumors and is the most common cause of cancer-related death. However, the genetics of metastasis are poorly understood. Uveal melanoma (UM) is the most common primary cancer of the eye and the second most common form of melanoma. UMs have a highly characteristic pattern of metastasis to the liver that is resistant to conventional chemotherapy and is usually fatal. UMs have remarkably little genomic instability, few cytogenetic alterations, and rare genetic mutations. Thus, when mutations are found in these tumors, they are highly likely to be driver rather than passenger mutations. UMs can be grouped according to risk of metastatic death into class 1 (low risk) and class 2 (high risk) based on a validated gene expression signature. A major focus of research has been to identify the specific genetic changes that confer metastatic competency in UM. The class 2 signature is usually accompanied by loss of one copy of chromosome 3 (monosomy 3), which has led to the widespread expectation that loss of one copy of chromosome 3 in UM cells unmasks recessive inactivating mutations in a gene (or genes) on the remaining copy of chromosome 3 that confer metastatic capacity. Other changes include gain of chromosome 8q and loss of chromosome 8p. In the class of class 1 tumors, gain of chromosome 6p is common. The)investigators of this proposal are pioneers in the analysis of the molecular genetics of UM. We were the first group to apply the recently described technique of exome capture followed by massively parallel sequencing to identify BAP1 as the metastasis suppressor mapping to chromosome 3 in UM. In the current study we will capitalize on our recent success with these technologies to identify additional tumor suppressor genes and oncogenes mutated in UM. In Aim 1 we will generate additional exome sequences of both class 1 and class 2 tumors, comparing them with their matched germline DNA. Potential tumor suppressor genes harboring deleterious mutations, and oncogenes harboring potential activating mutations driving the development of UM will be confirmed with Sanger sequencing and evaluated in an additional 10-30 class 1 and class 2 tumors and matched germline DNA. In Aim 2 we will use targeted capture to re-sequence newly identified additional mutations within these genes in additional samples (>100 of each tumor type) to determine their contribution to UM. In Aim 3 we will perform limited functional studies of 5 newly identified genes in cell lines. We will perform binding assays to evaluate the effects of mis-sense and in-frame coding changes on interactions with known and novel partners, and over-express activating oncogenes and knockdown tumor suppressors to determine their effect on cell morphology and gene expression. Information on molecular alterations in tumors will then be incorporated with clinical information to begin to develop a prognostic classification of UM. This is a collaborative proposal from a multidisciplinary collaborative group from the departments of Ophthalmology and Genetics that has the proven expertise to complete the aims of this proposal. )