Friday, May 16, 2025
5/16/2025
SOX2 acts in the 3D genome of squamous cancer - PROJECT SUMMARY As one of the most common and deadly cancer types worldwide, squamous cancer can occur to diverse organ sites including lung, esophagus, upper digestive tracts, cervix, and skin. Current treatments of squamous cancer are mainly limited to aggressive surgeries or unspecific chemotherapies and radiotherapies, while biomarker- guided targeted therapies are largely missing. The majority of squamous cancers are associated with overexpression of the SOX2 gene, encoding an SRY-box transcription factor. SOX2 plays important roles in specifying squamous lineages, but drives squamous cancer formation when hyperactivated. Despite the importance of SOX2 in squamous cancer, SOX2 as a transcription factor is a difficult target for small molecules. Identification of alternative therapeutic targets is hindered by our limited knowledge of mechanisms of the SOX2 oncogene. In particular, two key questions remain largely unknown: 1) how the SOX2 oncogene is transcriptionally activated, and 2) how the SOX2 transcription factor regulates its target genes in squamous cancer. We will address these questions in the 3D genome context that is essential for promoter-enhancer interactions and gene regulation, but has been largely missed from traditional linear genomics approaches. Based on our preliminary data, we hypothesize that the SOX2 oncogene is transcriptionally activated by regulators bound at a distal enhancer through a long-range chromatin loop, and that the encoded SOX2 transcription factor in turn binds to enhancers, cooperating with the cohesin complex and other co- factors, to regulate the 3D genome architecture and oncogenic transcriptional programs. We will combine functional 3D genomics with myriad CRISPR technologies to test this hypothesis. In Aim 1, we will determine the regulatory mechanism underlying overexpression of the SOX2 oncogene in squamous cancer. Focusing on a squamous-cancer specific enhancer that we identified as a principal driver of SOX2 overexpression, we will utilize motif analysis and dCas9-APEX-mediated proteomics to identify transcription factors and chromatin regulators responsible for SOX2 overexpression. In addition, we will use epigenome editing approaches to interfere the chromatin loop connecting the enhancer to the SOX2 promoter and determine its role in SOX2 transcriptional activation. In Aim 2, we will determine how the SOX2 transcription factor regulates oncogenic transcriptional programs in squamous cancer. We will apply 3D genomics to identify chromatin loops connecting SOX2 binding sites to their direct target genes. We will then prioritize and functionally characterize 10 SOX2- target genes. We will also determine the role of SOX2 in cohesin recruitment and chromatin looping. Furthermore, we will identify additional SOX2 co-factors that cooperate with SOX2 in transcriptional regulation. The successful completion of this proposal will reveal novel mechanisms of the SOX2 oncogene in squamous cancer. The findings will uncover alternative therapeutic targets for SOX2-driven squamous cancers from diverse organ sites.
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