LAMPS

PROJECT SUMMARY- CORE 3 Condensates formed by macromolecular assemblies play a crucial role in chromatin regulation; however, the fundamental principles governing how functional partners interact within condensates to regulate gene expression remain elusive. A key limiting step is the lack of experimental means for the inducible formation and purification of condensates from native chromatin in disease-relevant cells. Due to this limitation, it remains unclear whether the formation of nuclear condensates is the causal mechanism of fusion oncoprotein (FO)- mediated gene activation or simply the consequence of activated gene expression. The Advanced Technology and Genomics (ATG) core at St. Jude Children’s Research Hospital serves as Core 3 for the FusOnc Program Project by providing new technology platforms, namely Light-Activated Macromolecular Phase Separation (LAMPS), for studying the causal relationships between FO-mediated condensate formation, chromatin dysregulation, and oncogenic gene transcription in multiple pediatric cancers. LAMPS incorporates CRISPR-based chromatin purification, optogenetics, and multi-omic approaches to 1) determine whether and how FO-mediated condensation reprograms chromatin regulation, 2) identify the macromolecular components of FO condensates in native chromatin, and 3) elucidate the mechanism(s) of condensate-mediated chromatin dysregulation for oncogenic function. Leveraging the extensive expertise of the ATG core in innovating technologies for studying genome regulation (see later in this section and biosketches), Core 3 will provide technical support, consultation, and services to all Projects for the application of LAMPS to a diverse set of FOs, including study design, experimentation, and statistically rigorous analysis and interpretation of multi-omics datasets. Together with other project leaders, our Core team has the potential to capitalize on the collective expertise and interdisciplinary approaches, producing novel insights into understanding the molecular underpinnings of FO-mediated oncogenic functions.