Integrating Genomic and Epigenomic Alterations in Cancer and its Microenvironment

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Despite knowing the importance of the role of the microenvironment in tumor development, genetic studies of solid tumors, whether sporadic or hereditary, to date, have treated them as single amorphous entities. Genetic and epigenetic analyses of breast carcinomas are no exception. Using 381-microsatellite marker loss-of-heterozygosity (LOH) scan in 135 distinct sporadic invasive breast cancers, we have identified 19 key loci on 15 chromosomes with significant LOH in the epithelium and 38 key loci on 19 chromosomes with significant LOH in the stroma (chromosome-wise modeling). We therefore initially hypothesize that these regions which when loss would play a role in breast cancer progression; we also hypothesize that these regions act as signposts for genes which when epigenetically modified which together with structural loss play some role in breast cancer progression as germane to epithelial-stromal interactions. We believe therefore that the tumor microenvironment, especially the stroma plays an essential, but largely undefined role, in breast carcinogenesis. Bringing together experimental and computational biologists, Project 2 will use a rolling model iterative, integrative approach of directed genetic and epigenetic analysis and validation as well as informatics model building to understand breast cancer progression. This will involve hypothesis generation and testing, with the initial hypothesis that LOH and/or epigenetic inactivation of genes within the 19 epithelial loci would occur in initiation or earlier in progression and the multiple stromal targets would be involved to facilitate progression, invasion and metastases. We will take a directed SNP-based LOH and hypermethylation-based strategy to examine the 58 initial target regions in stroma and epithelium of 150 invasive breast carcinomas for key genes undergoing LOH and/or hypermethylation during progression. These experimental data will be used for model building, one taking a phylogenetics-type approach and the other utilizing a network-like approach to help integrate genetic and epigenetic alterations in tumor progression in the context of the epithelium and stroma. Model building and experimentation will continue until a model(s) are derived that can accurately predict the alterations in the 2 compartments as they relate to progression. In the near future, these somatic genetic and epigenetic progression-related alterations in epithelium and stroma will be correlated with clinical outcomes. Elucidation of novel regions of LOH and hypermethylation relevant in the stromal compartment might ultimately reveal novel targets for prevention and therapy.