Our main goal is to correlate key proteomic and genomic alterations in melanomas with responses to next-generation targeted therapy. The new treatment opportunities and the remarkable heterogeneity of melanoma tumors require better profiling of tumor sub-types to achieve efficient selection of patients for targeted therapies. We will focus on responses to BRAF inhibitors (BRAFi) such as PLX4032/RG7204/ Vemurafenib and GSK2118436. The studies will include novel kinase inhibitors developed by Plexxikon to overcome the "paradoxical effect" of BRAFi (i.e., stimulation of cells with wild type BRAF), termed "paradox breakers" (PLX-PB). Freshly isolated tumors will be characterized at base line before treatment and at the time of disease progression employing multiplex-phosphoproteomic assays, high throughput sequencing of coding regions (Exome-Seq), and gene expression arrays to establish a subset of indicators that correlate with short (<6 months) versus durable (s 12 months) response to the drug. We will assess the characteristics of tumors poorly responsive to BRAFi compared to those with durable response, relapsing over a year after treatment. We expect to identify mechanism(s) of resistance that can be used to devise alternative treatments. The major translational outcome ofthis work is classification of melanomas by phospho-proteomic/genomic/gene expression aberrations that show an association between treatment and response that will lead to development of assays for selection of patients for targeted therapies. In addition, the project will facilitate clinical trials of novel BRAFv600 kinase inhibitors.
Aim 1 : To correlate phosphoproteomic, genomic and gene expression aberrations with resistance to BRAFi.
Aim 2 : To perform functional analyses on the best markers associated with treatment response employing melanoma cells in culture.
Aim 3 : To conduct a Phase I clinical trial with next-generation "paradox-breakers" (PB) BRAFi developed by Plexxikon Inc. We will compare tumor profiles of PLX-PB response to those revealed in Aims 1 and 2.
The experience with PLX4032, an efficient inhibitor of cells harboring the BRAF[V600E/K] mutation, and other targeted therapies demonstrated that while responses have been observed, they are of limited duration due to emergence of tumor resistance. Therefore, there is a need to better define the network of activated kinases and intermediates that may interfere with the selected treatment in order to provide markers for better patient selection and for effective combination therapy.
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