Abstract PR08: Leveraging single-cell epigenomics to uncover regulatory programs in lung adenocarcinoma
Authors: LaFave Lindsay M. , Kartha Vinay , Ma Sai , Meli Kevin , Priore Isabella Del , Lareau Caleb , Sanker Venkat , Naranjo Santiago , Westcott Peter , Chiang Zachary , Brack Alison , Law Travis , Regev Aviv , Buenrostro Jason D , Jacks Tyler 
Published: June 2020

Abstract
A hallmark of cancer development is the loss of cellular identity due to the dysregulation of regulatory networks that maintain functional, differentiated states. Chromatin state has been linked to this control of cellular identity and developmental processes; however, the mechanisms by which these regulatory landscapes are disrupted during cancer progression are not well understood. To this end, we leveraged an optimized single-cell ATAC-sequencing (scATAC-seq) strategy using a combinatorial indexing-based technology to assess chromatin state changes that occur in a mouse model of lung adenocarcinoma (LUAD). We utilized a well-established LUAD mouse model in which mice conditionally express the KrasG12D mutation and lose p53 expression in alveolar type II cells following Cre-mediated recombination, termed the KP model. In this model, KP tumors progress from early-stage hyperplasias to metastatic, advanced adenocarcinomas without acquiring additional somatic mutations, suggesting that these phenotypic transitions may be driven in part by epigenetic mechanisms. Using scATAC-seq, we profiled 16,044 normal lung, primary KP tumor, and metastatic cells to assess chromatin state changes across LUAD progression. We found that LUAD tumor evolution was characterized by a heterogeneous epigenomic continuum that was associated with loss of alveolar identity and progression to metastasis. Interestingly, we identified a reproducible metastatic state that was homogeneous, suggesting that cancer cells funnel towards a stable epigenetic state. In addition, we utilized novel computational tools to assess combinatorial transcription factor (TF)-driven programs that delineate stages of cancer progression in the KP model. From these analyses, we identified a clear transition point that corresponded to progressive gain of RUNX2 transcription factor activity. Using CRISPR activation and knockout strategies, we found that RUNX2 regulated the chromatin accessibility of several regulatory programs involved in extracellular matrix remodeling, suggesting that RUNX2 signaling is a critical event in LUAD progression and metastasis. In addition, gene signatures derived from this RUNX-activated state were highly predictive of survival in human LUAD. Together, these results demonstrated the power of single-cell epigenomics to identify TF-driven regulatory programs as key biomarkers of tumor progression.
This abstract is also being presented as Poster A40.
Citation Format: Lindsay M. LaFave, Vinay Kartha, Sai Ma, Kevin Meli, Isabella Del Priore, Caleb Lareau, Venkat Sanker, Santiago Naranjo, Peter Westcott, Zachary Chiang, Alison Brack, Travis Law, Aviv Regev, Jason D Buenrostro, Tyler Jacks. Leveraging single-cell epigenomics to uncover regulatory programs in lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR08.