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.