Deciphering the Epigenetic Regulatory Network of Tumors with Single-Molecule Precision

Cell identity in healthy tissues, as well as during malignant transformation, is governed by the dynamics of DNA and chromatin modifications, which expand and diversify phenotypes driven by the same genetic code. At the basis of the chromatin structure are the nucleosomes, in which the double-stranded DNA is wrapped around histone octamers. An aberrant pattern of DNA and histone modifications is a common hallmark of human cancer. Despite extensive research, we currently lack an overarching understanding of the chromatin code, and the implications of its deregulation to tumorigenesis. A recent breakthrough made by Shema and colleagues implements high resolution, single-molecule imaging to map combinatorial histone modifications. Our method enables direct imaging and decoding of various histone marks on individual nucleosomes, followed by single-molecule sequencing of the associated DNA. We now aim to utilize this groundbreaking technology in order to characterize the consequences of cancer-associated chromatin-related alterations on the epigenetic landscapes and transcriptional profiles of tumor cells. Specifically, we are in the processes of implementing our technology to uncover the effects of the extremely common mutation in histone H3 lysine 27 (H3K27M) on the combinatorial chromatin landscape of Pediatric Gliomas. Furthermore, the chromatin related oncogenic consequences of deregulated expression of the Polycomb catalytic subunit EZH2 in different models of breast cancer, will also be examined using our single-molecule resolution assay. Overall this study will delineate the mechanisms by which aberrant Polycomb activity acts as a tumorigenic driving force within different tumorigenic settings, and may serve as paradigm for addressing the contribution of chromatin deregulation to the cancer phenotype.