Ultrasensitive detection of circulating DNA methylation for head and neck cancer prognosis - PROJECT SUMMARY/ ABSTRACT Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent aggressive cancers worldwide. Despite advances in diagnostics and treatments, the 5-year survival of HNSCC remains low (~50%). Patients with HPV-negative tumors exhibited an even worse prognosis. There is a pressing and unmet need to identify reliable molecular biomarkers for prognostic prediction in HNSCC, crucial for personalized patient care. This enables the selection of more aggressive or novel treatments like immunotherapy for high-risk patients, while also guiding treatment deintensification for those at low risk. DNA methylation (DNAme) is a key player in all major cancer hallmarks, encompassing a range of processes from tumorigenesis and cancer progression to its pivotal role in shaping the tumor-immune microenvironment and influencing drug/treatment resistance. DNAme is also known to be responsive to both genetic variations and environmental exposures, both of which are driving factors underlying the etiology and pathogenesis of HNSCC. Building upon extensive preliminary data, we hypothesize that the incorporation of non-invasive and ultrasensitive detection of circulating DNA methylation, including analysis of circulating cell-free DNA and immune cells from peripheral blood, will markedly enhance the precision of prognostic predictions in patients with HNSCC. In this R01 project, we propose to establish a dedicated clinical cohort of HNSCC named PHENEX, along with novel analytical methodologies (Aim 1) to validate, discover and optimize noninvasive liquid biopsy tests for HNSCC based on cell-free DNA methylome of plasma samples (circulating tumor panel); (Aim 2) to uncover novel DNAme biomarkers in the matched peripheral immune cells to further improve the liquid biopsy test for the prognostic biomarker discovery (circulating immune panel); and finally (Aim 3) to investigate the potential of integrating cancer-specific and immune-specific biomarkers for immunotherapy outcome prediction (PHENEX-IO). We will utilize an ultrasensitive technology developed by our team, known as cfMBD-seq, for ultra-low-input DNA methylome analysis of HNSCC plasma samples. As an integral part of our biomarker discovery process, the matched tumor tissues will also be profiled for DNAme, providing a holistic understanding of the epigenetic landscape in HNSCC. The PHENEX cohort will leverage both existing tissue samples collected from Moffitt Total Cancer Care (TCC) and established biospecimen collection workflows for prospective sample collection, aiming to create an effective and sustainable resource. This project will be undertaken by a team of investigators who have proven track record and extensive experience in head and neck oncology and epigenomic biomarker discovery. Collectively, our results are set to deliver an immediate translational impact by informing more precise therapeutic strategies and clinical management of HNSCC, ultimately improving the overall outcome for patients battling this dismal disease.
