Abstract A054 A genome-derived cell state reporter permits dissection and control of intratumoral heterogeneity and chemoresistance
Authors: Shendy Noha AM , Zhang Yang , Lee Ha-Won , Nance Stephanie , Khashana Yousef , Nezhady Mohammad AM , Ritter Elaine , Singh Shivendra , Liu Qi , Fan Yiping , Yang Jun , Patel Anand G. , Qi Jun , Chen Taosheng , Abraham Brian J. , Durbin Adam D. 
Published: September 2024

Sequential changes in epigenomically specified transcriptional cell states are essential for normal developmental progression. These normal processes are co-opted in cancers, allowing genetically identical cells in different states to cooperatively form heterogeneous tumors. Specific cell states may display distinct malignant properties, including variability in sensitivity to conventional therapies, resulting in heterogeneous responses to therapy and a potential mechanism of patient relapse. As a result, deriving mechanistic approaches to control cell state transitions for therapeutic benefit has been limited by the lack of tractable live-cell tools able to reflect complex and multifaceted cell states. To address this problem, here we demonstrate the design, conception, synthesis and interrogation of a new method termed “Transcriptional Reporter Elements of Cell State” (TRECS). TRECS integrates epigenomics and transcriptomics to identify endogenous genomic elements that can label and separate cell states within heterogenous populations. Using integrative three-dimentional chromatin conformation data and CRISPR deletion studies, we link the mechanism of TRECS reporter activity to control by master transcriptional regulators of distinct cell states. Implementing this system in the high-risk pediatric solid tumor neuroblastoma, we quantitate intratumoral transcriptional and epigenetic heterogeneity and observe real-time cell state plasticity. We demonstrate that neuroblastoma cell line models generally contain plastic cell populations, including one cell state with intrinsic broad chemoresistance. Capitalizing on this intrinsic cell state plasticity, we perform a high-throughput imaging-based small molecule screen to identify chemical controllers of cell state. We identify the coactivator proteins EP300/CBP as primary regulators of the neuroblastoma chemoresistant cell state. Transient disruption of EP300/CBP activity induces sustained epigenetic and transcriptional reprogramming, which fundamentally alters the chemoresistant neuroblastoma cell state, resulting in enhanced chemosensitivity. These findings demonstrate a new, scalable approach to visualize and dissect high-risk cell states with distinct malignant properties in heterogenous tumors. This platform also guides chemical-genetic strategies to control especially challenging cell states, for example, by targeting EP300/CBP maintenance of chemoresistance.

Citation Format: Noha AM Shendy, Yang Zhang, Ha-Won Lee, Stephanie Nance, Yousef Khashana, Mohammad AM Nezhady, Elaine Ritter, Shivendra Singh, Qi Liu, Yiping Fan, Jun Yang, Anand G. Patel, Jun Qi, Taosheng Chen, Brian J. Abraham, Adam D. Durbin. A genome-derived cell state reporter permits dissection and control of intratumoral heterogeneity and chemoresistance [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr A054.