HPV genomic structure in cervical cancer radiation response and recurrence detection

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PROJECT SUMMARY/ABSTRACT Cervical cancer is one of the most common cancer diagnoses among women, and treatment failure of standard of care (SOC) chemoradiation therapy (CRT) for locally advanced cervical cancer (LACC) is as high as 30-50%. Since recurrent and metastatic diseases are not curable or detected too late to be treatable, there is a pressing need for pre-treatment biomarkers to identify patients at risk of CRT treatment failure and post-treatment biomarkers to detect LACC recurrence and metastasis early. TCGA’s effort to establish pre-treatment biomarkers for cervical cancer by molecular stratification using human genes failed to associate to patient outcomes. On the other hand, we recently demonstrated that HPV genotypes and HPV alternative splicing affect LACC recurrence and survival after CRT. In our preliminary data, we additionally identified a diversity of HPV genomic structures (HPV-GS), including HPV-human gene fusions involving alternative spliced HPV exons, that affect human oncogene expression. We hypothesize that the variance of HPV genomic structural features among LACC patients may represent a valuable clinical sequencing application to develop LACC SOC CRT biomarkers. For post-treatment markers, we currently use F-fluorodeoxyglucose PET/CT (FDG-PET) images at 3–6 months to define metabolic response, which was shown in our previous publications to predict patterns of failure after radiotherapy for cervical cancer. We hypothesize that HPV genomic features can serve as post-treatment biomarkers for LACC recurrence and metastasis detection that are both more accurate and detectable at earlier timepoints. To achieve these goals, we will first test whether variance in HPV-GS can be utilized to develop a clinical pre-treatment biomarker by developing a series of novel HPV-GS analysis tools based on our expertise in both HPV genomics and human structural variants. HPV features will be extracted from matched DNA and RNA sequencing data, and their prognostic values will be tested using samples from our cervical tumor bank of LACC patients uniformly treated with curative-intent CRT. Second, we will examine whether CRT-induced LACC clonal evolution can be used to identify treatment-resistant HPV-GS as on-treatment biomarkers. A novel deep targeted sequencing approach will be used on single-nucleotide variants (SNV) and HPV-GS to identify LACC subclones and fit HPV-GS in the context of clonal evolution. We will also examine the mechanisms of HPV- human gene fusions using clonogenic survival assays and other standard assays. Last, we will use our proven highly-sensitive and flexible CAPP-Seq technology to evaluate whether circulating tumor DNA (ctDNA) can be used to develop HPV-GS tests for early diagnosis and post-CRT recurrence detection. We expect combining both SNVs and HPV-GS will result in an optimized application superior to using single types of features alone. Taken together, we expect our genomic and mechanistic research on HPV-GS biomarkers in the context of CRT- induced LACC evolution will create a series of optimized pre-treatment and recurrence biomarkers that can be applied in the clinic for personalized alternative treatment regimens.