Epigenetic drivers of cancer progression

Abstract public domain (NIH RePORTER)

This competing renewal continues our highly productive studies with the long-term goal of identifying the role of the epigenetic landscape in cancer progression, that have been applied under previous periods of the grant to pancreatic ductal adenocarcinoma (PDAC) and leukemia. We have previously shown that human PDAC metastasis is driven epigenetically in the absence of new mutations; and in leukemia, with well-defined independent genetic mutational drivers, the cancer epigenome converges on overlapping genes and pathways that retain an epigenetic cancer memory, even when the initiating mutation is corrected. Here we will focus on genetically engineered mouse models (GEMMs) of pancreatic cancer, in order to define the dynamic epigenomic landscape of PDAC progression in an inherently well-controlled system. In Specific Aim 1, we hypothesize that stepwise progression in PDAC is driven largely, and at some stages entirely, by epigenomic alterations that we can identify systematically in a controlled mouse model system. We will perform comprehensive epigenomic analysis, including spatial multi-omics, using tissues and organoids from existing well-characterized GEMMs. We will perform in vivo imaging to map and isolate GEMM liver metastases to understand the epigenetic steps in this ultimately lethal aspect of the disease. We will also validate epigenomic signatures of GEMM progression in human PDAC development using alternate sectioning and spatial transcriptomics and multi-omics from tissue blocks, in which the histology is registered, reconstructed and annotated at single-cell resolution using novel deep learning methods. In Specific Aim 2, we hypothesize that the ability of PDAC to invade normal tissues is driven in part epigenetically, and that the tumor epigenome can influence its own microenvironment via ECM remodeling in the absence of fibroblasts, as well as be influenced by it before and after fibroblast recruitment, allowing for epigenetically mediated metastasis. We will determine the effects of altering the biomechanical and matrix properties of 2D and 3D cell culture substrates, along with CAF co-culture, on the tumor epigenome, gene expression, and cell migration. We will modify the tumor epigenome using microenvironmental, genetic, pharmacologic and metabolic targeting to test the effect on metastatic colonization and growth. We will also relate epigenomic signatures of the cancer invasive front in human PDAC pathology to the stage-specific microenvironment in mouse models. As a result of this work, we will understand the changes in mean methylation, methylation entropy, chromatin accessibility, and gene expression through well-defined stages of cancer progression, with spatial resolution in tissues, and relate these to human PDAC, helping to define a new epigenomic pathology of human PDAC. We will also understand the effects of the biomechanical and matrix properties, as well as CAF co-culture, on the PDAC epigenome. We believe our highly integrated multimodal approach will answer key questions in PDAC epigenetics that could not be answered without such an interdisciplinary approach.

Public health relevance public domain (NIH RePORTER)

Pancreatic ductal adenocarcinoma (PDAC) has an overall mortality of 95%, even for early-stage disease, in part because, in addition to mutations in the cancer genome, the tumors have an altered epigenome, including chemical changes such as methylation of the DNA component cytosine, and chromatin. We will determine how the epigenome changes from normal to pre-malignant PanIN, to cancer, to metastasis, using well-defined genetically engineered mouse models, and we will determine the role the extracellular environment of the cancer shapes the epigenome and is shaped by it. We will validate this work using human PDAC tissues and cutting-edge methods for visualization of epigenetic marks in tissues, enhancing the value of the project for eventual translation to cancer diagnosis and therapy.