Grant Number:	1R01CA292936-01 Interpret this number
Primary Investigator:	Muzumdar, Mandar
Organization:	Yale University
Project Title:	3d Genome Reorganization Drives Cancer Development
Fiscal Year:	2024

PROJECT SUMMARY/ABSTRACT The three-dimensional (3D) genome folding organization within the nucleus of cells plays a key role in epigenomic regulation in both normal physiology and disease. Sequencing-based 3D genomics technologies – such as high-throughput chromosome conformation capture (Hi-C) – have reported systematically altered genome organization in cancer cells. Yet, these studies relied on population averaging of cells and indirect inference of genome organization based on chromatin contacts. As a result, how the genome is folded in true 3D in individual cancer cells in vivo, how this folding organization evolves and is regulated during cancer progression from normal to preinvasive to invasive tumor cells within the native tissue environment, and how alterations in genome organization drive tumorigenesis remain elusive. To address these gaps in knowledge, we applied an image-based 3D genomics method that we pioneered termed chromatin tracing to a faithful Kras- driven mouse model (K-MADM-Trp53) of lung adenocarcinoma (LUAD) and developed the first in situ single-cell 3D genome atlas of any cancer. We observed stereotypical 3D genome alterations during cancer development, including a striking structural bottleneck in preinvasive adenomas prior to progression to LUAD, indicating a stringent selection on the 3D genome early in tumorigenesis. We further found that 3D genome organization correlates with distinct histologic cancer states in single cells and shifts in this organization reveal potential drivers of LUAD progression. In this proposal, we aim to test the hypothesis that changes in the 3D organization of the cancer genome drive tumorigenesis. The studies in Aim 1 utilize a sophisticated multiplexed in vivo CRISPR knockout screen to establish the functional importance of 3D genome-regulated candidate driver genes in LUAD progression and confirm that similar alterations occur in human LUAD biospecimens. The proposed work in Aim 2 uses genetic and pharmacologic manipulation and epigenetic profiling methods (ChIP, CUT&RUN, chromatin tracing) in LUAD cells and mouse models to define how the chromatin-modifying enzyme Rnf2 regulates the cancer 3D genome through a non-canonical function in promoting an active chromatin state. Finally, the experiments in Aim 3 leverage analogous autochthonous mouse models of EGFR-driven LUAD and Kras-driven pancreatic ductal adenocarcinoma to determine how oncogenic driver (Kras vs. EGFR) and tissue of origin (lung vs. pancreas) impact the 3D genome and resultant effects on tumor biology. Together, these experiments will establish how alterations in the 3D genome – as assessed by in situ chromatin tracing – drive context-dependent cancer development, the underlying mechanisms that promote their pro-tumorigenic effects, and their capacity to serve as novel predictive biomarkers for cancer therapy.





None