Enlisting HPV integration events to illuminate drivers and target treatment in invasive cervical cancer

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PROJECT SUMMARY Invasive cervical cancer (ICC) kills nearly 311,000 women each year worldwide with an estimated 50% increase in deaths by 2040. In the U.S., ICC ranks third for average years of life lost and disproportionately affects minority groups and women of low socioeconomic status. Women with advanced or recurrent ICC soon develop resistance to current chemotherapy options, and about 90% die within 2 years. Our intent is to define clinically relevant and targetable ICC genes and pathways to improve patients’ treatments and outcomes. Our central hypothesis is that HPV integration events—and the changes they exert on the host genome and epigenome—confer a selective advantage to disease progression and provide opportunities to pinpoint genes and pathways relevant to treating ICC. Using The Cancer Genome Atlas (TCGA) ICC cohort (CESC), we developed a pipeline to identify integration detected genes (IDGs) altered by HPV integration in some ICCs and by genomic and/or epigenomic modifications in other ICCs. Elements of our pipeline focus on proximity to the integration site, clonal representation of the integration event, patient- and disease-specific gene expression, association with ICC survival, and frequency of alteration in ICC. For this proposal, we will expand our discovery pipeline to a newly completed multi-omics ICC cohort, the HTMCP (HIV+ Tumor Molecular Characterization Project), incorporating new technology and testing the functional contribution of IDGs to ICC and chemoresponse. This in-depth characterization of a plethora of IDGs will help us identify novel targets/pathways which is a critical step towards better therapy for women with ICC. To this end, we will pursue the following Specific Aims: Identify and filter IDGs from HPV integration sites in HTMCP samples using our established pipeline, long-read DNA and cDNA sequencing, and other genomic studies (Aim 1), determine the functional contribution of IDGs to ICC and their therapeutic targeting potential using siRNA-mediated KD and/or CRISPR-based gene editing in cervical cancer cell lines and orthotopic xenograft models, (Aim 2), and determine the clinical relevance and biomarker potential of IDGs (Aim 3).