Development of a First-in-class High Throughput Screening Assay Based on Chromatin Accessibility

Authors

• D Williams
• A McFadden
• T Sanchez
• AJ Hepperla
• M Henderson
• G Stott
• I Davis
• S Pattenden

Abstract

Chromatin dysregulation has been implicated in the development of a wide range of diseases, including cancer, where genetic alterations in chromatin regulatory factors and aberrant activity of transcriptional regulators alters chromatin states. Mutations in many chromatin-associated proteins have been recognized as driver mutations across multiple diverse tumors. As appreciation of the importance of chromatin dysregulation in cancers has grown, chromatin regulatory proteins have emerged as promising targets for therapeutic discovery. To identify small-molecule regulators that can reverse chromatin alterations in cancer, we are developing a target agnostic small molecule screening technology that exploits tumor-specific chromatin accessibility states as a relevant and direct functional readout for identifying novel therapeutics.
Towards this goal, we have developed a high-throughput version of the Assay for Transpose-Accessible Chromatin with sequencing (ATAC-seq), termed HT-ATAC-seq (high-throughput ATAC-seq). As a proof-of-concept, we are assaying chromatin accessibility in models of Ewing sarcoma, a highly aggressive pediatric cancer with ~50% mortality. Using this cancer model, we have developed a nuclei preparation method that can reproducibly isolate nuclei from cells from each well across an entire 384-well plate for subsequent ATAC-seq. From a small-molecule library pilot screen of 331 annotated modulators of the epigenome, we identified several previously established regulators of chromatin structure in Ewing sarcoma, including the HDAC inhibitor Panobinostat, as well as several novel chromatin regulators. This assay not only shows promise for identifying modulators of chromatin state in Ewing sarcoma, but we anticipate the assay platform could be implemented in other cancers or diseases with altered chromatin states.

Scientific Focus Area: Molecular Pharmacology

This page was last updated on Monday, September 25, 2023