TBEL Project 3

PROJECT 3 - ABSTRACT Pancreatic cancer arises from non-invasive precursor lesions that are curable if detected and treated early. Pancreatic intraepithelial neoplasia (PanIN) is the most common of these precursor lesions and represents a critical target of early detection and cancer prevention approaches. Previous studies from our group have highlighted critical genomic alterations that drive clonal expansion and neoplastic progression in some PanINs. These studies have also demonstrated that expansion and progression can occur without the accumulation of additional driver genomic alterations, suggesting that diverse driver mechanisms operate in different PanINs. The overall hypothesis of this proposal is that the transition to HG PanIN can be driven by genomic or precursor microenvironment (PME) alterations, with distinct drivers dominating in different lesions. To investigate this hypothesis, the proposed studies will evaluate both cell intrinsic and cell extrinsic drivers of neoplastic progression in human PanIN samples. We will employ a novel approach that allows both three-dimensional reconstruction and molecular analysis of human PanIN samples. We will perform multi-region whole exome sequencing and evolutionary reconstruction in order to correlate genomic alterations with expansion and progression of neoplastic cells in three dimensions. In order to identify non-genetic drivers of neoplastic progression, we will analyze immune and stromal cell subsets in the same three-dimensionally reconstructed PanIN samples using imaging mass cytometry, allowing us to determine the variability of key components of the PME across multiple regions of these PanIN samples. This complementary analysis will allow us to correlate the microenvironmental features with the molecular alterations in associated PanIN cells. We will also integrate predicted neoantigens and T-cell receptor sequencing on the same PanIN regions, providing a multi-dimensional analysis of the immune response to PanINs. Taken together, these approaches will systematically evaluate potential drivers of progression in the neoplastic cells and associated immune response, providing crucial biological insights and a rational foundation for novel early detection and prevention approaches.