Identification of chromatin regulators required for enhancer hijacking in cancer genomes

Genomic instability is a hallmark of cancer, and many human cancers display structural variants such as translocations, inversions, deletions, and duplications. These structural variants can promote cancer development through various mechanisms, including "enhancer hijacking," where non-cognate enhancers aberrantly activate oncogenes. This phenomenon has recently been identified in a broad range of cancers, suggesting that enhancer hijacking is an underappreciated mechanism of oncogene dysregulation across many cancer types. Enhancer hijacking is characterized by the regulation of genes by ectopic enhancers, suggesting that the genes that are subject to enhancer hijacking are capable of being regulated promiscuously by enhancers they have never otherwise seen before in evolution. However, whether there are mechanisms that facilitate such promiscuous gene regulation events is unclear. As enhancer hijacking is a cancer specific phenomenon, understanding the mechanisms that drive enhancer hijacking may help identify potential future therapeutic targets that would be effective in diverse cancers. Therefore, there is an urgent need to better understand the processes that contribute to enhancer hijacking in cancer genomes. In preliminary data supporting this proposal, CRISPR/Cas9 genome wide knock-out screens using engineered enhancer hijacking reporters identified two paralogs, STAG1 and STAG2, as have opposing effects in regulating enhancer hijacking. STAG1 and STAG2 are mutually exclusive components of the cohesin complex, and in the CRISPR/Cas9 screens, STAG1 is critical for promoting enhancer hijacking, while STAG2 represses it. Given that STAG2 is frequently inactivated in cancers, our overarching hypothesis is that the balance of STAG1 and STAG2 containing cohesin complexes regulates ectopic gene expression in enhancer hijacking. This proposal aims to investigate the mechanisms of STAG1 and STAG2 regulation of enhancer hijacking and to identify general and lineage-specific regulators of enhancer hijacking. Specific Aim 1 will determine how STAG1 and STAG2 influence the stability of 3D chromatin interactions between hijacked enhancers and oncogenes. Specific Aim 2 will explore the impact of STAG1 and STAG2 on enhancer hijacking of different genes across diverse lineages in cell lines and patient-derived organoids. Specific Aim 3 will develop scalable genome-wide methods to identify additional regulators of enhancer hijacking, employing Perturb-seq-based approaches. The successful completion of these aims will enhance our understanding of enhancer hijacking in cancer genomes, offering insights into potential therapeutic strategies for cancers driven by these events. Project Number: 1R01CA304705-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Jesse Dixon | Institution: SALK INSTITUTE FOR BIOLOGICAL STUDIES, La Jolla, CA | Award Amount: $795,143 | Activity Code: R01 | Study Section: Cancer Genetics Study Section[CG] View on NIH RePORTER: https://reporter.nih.gov/project-details/11368273