Project 2: Dissection of clonal architecture and evolution in solid tumors

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TITLE Project 2: Dissection of clonal architecture and evolution in solid tumors ABSTRACT Increasing evidence in solid tumors suggests that drug resistance and therapeutic failure results from natural selection of resistant subclones during the disease course. Intra-tumor heterogeneity and cancer subclonal diversity is the key driving force of the high failure rate of oncology drugs relative to other medical specialties where drugs are applied to stable somatic genomes rather than the unstable genomes found in human cancer. In this proposal, we focus on one of the most incurable and genetically heterogeneous tumors (human glioblastoma), to predict and validate the landscape of driver alterations that mark initiation, founder evolution, and therapy adaptation within individual patients. We will develop and apply novel technologies for high-throughput transcription and genomic analysis of individual cells within malignant glioma tissues. Our current system is capable of single cell mRNA capture, cDNA barcoding, and on-chip amplification, generating amplicons for direct conversion into a standard, pooled sequencing library. We will adapt the same device for massively parallel, on-chip capture of genomic DNA from individual cells for whole genome amplification and exome capture. Next, we will functionally validate the single-cell glioma models in orthotopic mouse and human systems in vitro and in vivo. The successful outcome of this proposal will be to deliver an integrated computational-experimental pipeline that will be able to predict the forthcoming evolutionary moves of any solid tumor in the presence of a defined set of selective pressures. This information will be of invaluable significance to decipher evolving tumor dependencies and provide the most accurate therapeutic predictions.