Head and Neck Cancer Omics/Integrated Precision Medicine (HOPE)

1. Background and Rationale 1.1 Need for Personalized Precision Medicine in Head and Neck Cancer Head and neck cancer (HNC) ranks as the sixth leading cause of cancer-related death, with over 650,000 new cases diagnosed worldwide each year. Approximately 60% of HNC patients present with locally advanced disease at diagnosis, and many experience recurrence or metastasis despite multimodal therapy . Major risk factors include tobacco and alcohol use, prior radiation therapy, and infection with human papillomavirus (HPV). Prognostic differences across racial groups are partly explained by the prevalence of HPV-associated disease and genetic factors. HPV infection is commonly observed in oropharyngeal cancers, particularly tonsillar cancers. Patients with HPV-positive oropharyngeal cancer generally respond better to treatment and have improved overall survival compared to HPV-negative patients. Conversely, epidermal growth factor receptor (EGFR) amplification is associated with poorer prognosis. HNC arises in diverse anatomical sites, including the oral cavity, pharynx, larynx, nasal cavity, nasopharynx, and salivary glands. Although squamous cell carcinoma is the most common subtype due to tobacco exposure, other histologies such as salivary gland carcinoma, adenoid cystic carcinoma, and others contribute to clinical heterogeneity. Although multimodal treatment-including surgery, radiation, and chemotherapy-is currently applied, outcomes for advanced laryngeal cancer remain limited, with 5-year overall survival (OS) around 40%. Moreover, HNC often affects the face and laryngeal region, significantly impairing quality of life by causing disfigurement, breathing difficulties, dysphagia, and voice disorders. Therapeutic efficacy is further limited by intra- and inter-tumoral heterogeneity and complex interactions within the tumor microenvironment (TME). Existing HNC research primarily reflects Western populations, whereas differences in subtype distribution, etiology, viral prevalence, and genetics in Asian populations necessitate localized data collection. Therefore, molecular and genetic analyses of domestic patient samples, along with TME research, are essential to implement personalized precision medicine in HNC. 1.2 Need for Longitudinal Follow-up Studies in Head and Neck Cancer Major causes of death in patients with advanced HNC include local recurrence, cervical lymph node metastasis, and resistance to systemic therapy. Even early-stage HNC has a reported local recurrence rate of 20-57%, and despite adjuvant chemoradiotherapy, the 5-year local recurrence rate remains approximately 30%. Recurrent or metastatic HNC carries a poor prognosis, with 5-year survival rates of only 20-30%. For squamous cell carcinoma of the head and neck (HNSCC), disease progression typically follows a stepwise sequence from precancerous leukoplakia in normal tissue, to primary carcinoma, and ultimately to lymph node metastasis. While studies have sought to identify markers predicting malignant transformation, molecular mechanisms remain unclear. HNSCC pathogenesis is multifactorial, involving tobacco, alcohol, and HPV infection. HPV is particularly influential in disease progression, and HPV-positive oropharyngeal cancer patients generally exhibit favorable outcomes. Genetic studies indicate that both innate and adaptive antiviral immune responses are suppressed in HPV-positive patients. Thus, continuous monitoring of clinical progression and tumor characteristics from early-stage disease to local recurrence or metastasis is critical to identify prognostic biomarkers and guide effective therapies. 1.3 Need for Tumor Microenvironment Research in Head and Neck Cancer Combination therapy with immune checkpoint inhibitors (ICIs) and chemotherapy has significantly improved overall survival. In the KEYNOTE-048 study, patients receiving pembrolizumab plus platinum-based chemotherapy achieved a median OS of 13.0 months, compared to 10.7 months for cetuximab plus chemotherapy (HR 0.71, 95% CI 0.59-0.85) over a median follow-up of 45 months. In patients with PD-L1 combined positive score (CPS) ≥20, HR was 0.62 (95% CI 0.46-0.84), and for CPS ≥1, HR was 0.64 (95% CI 0.53-0.78). Subgroup analysis showed that PD-L1 CPS correlated with OS in the pembrolizumab group, but not in the cetuximab group. Despite the introduction of ICIs, only 15-26% of patients respond well. Some patients with high PD-L1 do not respond, while a subset of low PD-L1 patients shows prolonged response. Biomarkers predicting ICI responders remain unclear. 1.4 Role of Samsung Medical Center in Head and Neck Cancer Research According to the 2021 cancer registry, approximately 3,000 cases of lip, oral cavity, and pharyngeal cancers were reported in Korea. In the same year, Samsung Medical Center recorded 550 cases, representing about one-fifth of national cases. The number of HNC cases at Samsung Medical Center continues to increase, with over half presenting as locally advanced disease. The 5-year survival rate for these patients is 78.5%, with localized tumors achieving 93.2% and distant metastases 37.8%. This is superior to national outcomes, highlighting the need for longitudinal follow-up and research using Samsung Medical Center patient data. ________________________________________
2. Study Objectives

The study aims to:

1. Collect clinical information from HNC patients visiting Samsung Medical Center.
2. Prospectively collect tissue and blood samples at initial diagnosis, before and during treatment, at disease progression, and upon suspected recurrence.
3. Identify biomarkers to support future personalized medicine approaches. ________________________________________
4. Study Design 3.1 Eligibility Criteria Inclusion Criteria
5. Age ≥20 years.
6. Histologically confirmed head and neck cancer, including tumors of the oral cavity, pharynx, larynx, nasal cavity, salivary glands, and other HNC sites. Patients diagnosed elsewhere are eligible if pathology is confirmed at Samsung Medical Center.
7. Histologic types include squamous cell carcinoma, undifferentiated carcinoma, poorly differentiated carcinoma, non-keratinizing carcinoma, adenocarcinoma, carcinoma of unknown primary in HNC, salivary gland cancer, malignant melanoma or sarcoma of the head and neck, and other relevant malignancies.
8. Patients scheduled for or having received appropriate HNC treatment (surgery, radiotherapy, cytotoxic chemotherapy, or immune checkpoint inhibitors).
9. Written informed consent obtained. Exclusion Criteria
10. Failure to meet inclusion criteria. 2. Other reasons deemed by the investigator to make the patient unsuitable for study participation.

Target Sample Size Approximately 350 patients per year are expected to undergo biopsy and blood sampling at Samsung Medical Center.

________________________________________ 3.2 Study Duration 60 months from IRB approval (~December 31, 2030).

________________________________________ 3.3 Study Procedures 3.3.1 Data Collection Clinical data and questionnaires will be collected from patients who provide informed consent. Tissue and blood samples will be collected prospectively at baseline, during treatment, at disease progression, and upon recurrence.

1. Clinical Data: Demographics, diagnosis (date, site, pathology, stage, HPV/P16 status), medical history, smoking/alcohol history, treatment details (surgery, radiation, chemotherapy), treatment response, progression, and survival will be collected. For patients not attending follow-up visits, survival and treatment information will be obtained via phone.
2. Tissue Collection: Fresh tissue will be collected when possible. Residual diagnostic or therapeutic samples stored in pathology may be used. During follow-up, tissue obtained for suspected recurrence will be stored, along with samples collected for treatment response assessment. Normal tissue distant from tumor, adjacent normal tissue, tumor tissue, and lymph nodes will be collected during surgery.
3. Blood Collection: Blood samples will be collected before treatment, during follow-up, at disease progression, and at imaging assessments. For patients receiving concurrent chemoradiotherapy (CCRT), blood will be collected before treatment, 3 weeks post-treatment (±1 week), 6 weeks post-treatment (±1 week), during imaging follow-up, and at progression. For patients receiving immune checkpoint inhibitors, blood will be collected at baseline, 3 weeks (±1), 6 weeks (±1), 12 weeks (±3), and at subsequent imaging assessments, with 20-30 mL per collection. Samples will be stored in secure, designated freezers.
4. Questionnaires: Administered at baseline, post-treatment, 3 months post-treatment, and every 6 months for 5 years. Items include demographics, lifestyle, medical history, pain, psychological status, quality of life (EORTC C30+HN35), PHQ-9, and social support.

3.3.2 Laboratory Analysis

• Tissue: WGS and WTS to characterize tumors; single-cell sequencing, spatial transcriptomics, or multiplex immunofluorescence for TME analysis. Immune cell populations (T cells, B cells, neutrophils, macrophages), immune gene signatures (IFN, IL family), T-cell subsets (CD4+, CD7+, CD8+, CD16, CD34+, CD38+, D56+), and PD-1/PD-L1 expression will be assessed pre- and post-treatment.
• Blood: WGS as normal reference, WTS for immune cell profiling, and ctDNA analysis for minimal residual disease (MRD).

3.3.3 Sample Management Samples will be stored with coded identifiers. De-identified samples may be sent to external laboratories; access to identifiers will be limited. Samples will be retained for 20 years or according to participant-specified duration. Post-study, external samples will be returned or destroyed. Samples with irreversibly anonymized identifiers will be handled per applicable regulations.

3.3.4 Future Research Use

• Sample Management: With participant consent, leftover samples may be stored for exploratory research without additional collection. External research may be performed by investigators not part of this study, using coded samples, which will be returned or destroyed after analysis.
• Data Management: With participant consent, de-identified clinical and genomic data (WES, WTS, WGS raw and analyzed data) may be used for future exploratory research. External institutions may receive coded data for analysis; identifiers will remain inaccessible.