Evgeny Izumchenko

Sinonasal squamous cell carcinoma (SNSCC) is a rare malignancy arising de novo or from inverted papilloma (IP), a benign neoplasm with malignant potential. The molecular drivers of IP-associated SNSCC (IP-SNSCC) remain poorly defined, and no effective therapies are available. Progress is hindered by limited preclinical studies and prospective clinical investigations. We performed multi-omic profiling, including whole-exome, RNA, and mitochondrial DNA sequencing (mtDNA-Seq), of matched normal sinonasal epithelium, IP, and SNSCC samples from 11 patients. Analyses revealed a stepwise transcriptional continuum across histological stages, marked by progressive activation of the cell cycle, extracellular matrix remodeling, and metabolic pathways, with suppression of immune and apoptotic signaling. Shared genomic aberrations were detected in only a subset of paired IP and SNSCC specimens, whereas mtDNA-Seq revealed no overlapping mutations, indicating divergent mitochondrial evolution even in clonally related lesions. Given the need for targeted therapies, we applied PandaOmics, an AI-driven target discovery platform, to genes progressively upregulated during IP-SNSCC development. We first prioritized targets with FDA-approved inhibitors, identifying CDK6, EGFR, HDAC, and SRC/YES1 as repurposing candidates, and nominated AURKA, PLK4, TTK, and CDK1/7 as druggable preclinical targets. Together, this study defines the molecular basis of IP-SNSCC and provides a foundation for future translational investigation.

Supplementary Table 1. Representativeness of Study Participants.

Supplementary Figure 1. Progression free survival Kaplan-meier estimates for patients that rapidly clear ctHPV-DNA (≥95% ctHPV-DNA reduction) after cycles 1 and 2 (red) versus patients that do not achieve rapid ctHPV-DNA clearance after cycles 1 and 2 (blue).

Supplemental Table 3. Discordance between deep radiographic response (>50% tumor shrinkage per RECIST v1.1) and rapid ctHPV-DNA clearance (≥95% reduction) after 1 cycle.

Supplemental Table 2. Correlation coefficients (p-values) for ctHPV-DNA kinetics and radiographic response following neoadjuvant chemotherapy.

Purpose:Human papillomavirus–associated (HPV+) oropharyngeal carcinoma is associated with excellent survival, yet treatment drives substantial toxicity. Improved biomarkers are needed to select patients for de-escalated treatment. Circulating tumor HPV DNA (ctHPV-DNA) represents a promising noninvasive biomarker to gauge treatment response and surveil for disease recurrence.Patients and Methods: A prospective biomarker clinical trial of response-stratified de-escalation was conducted. Eligible patients with non-metastatic HPV+ oropharyngeal carcinoma received neoadjuvant chemotherapy, followed by risk/response-stratified de-escalation with transoral robotic surgery, de-escalated radiation with or without chemotherapy to 50 Gy, or standard chemoradiation to 70 Gy. Deep response (≥50% tumor shrinkage per RECIST v1.1) qualified patients for de-escalation. ctHPV-DNA was measured using HPV-SEQ in plasma at baseline, during neoadjuvant chemotherapy, radiation, and following treatment. The primary endpoint was the correlation of ctHPV-DNA kinetics and radiographic response.Results:Forty-six eligible patients were enrolled, and 488 ctHPV-DNA samples were analyzed (median 11 per patient). The median follow-up was 30 months, and five recurrences were observed (10.9%). Baseline ctHPV-DNA was detected in 95% of evaluable patients. Rapid early ctHPV-DNA clearance after one cycle of neoadjuvant therapy (≥95% reduction) predicted radiographic deep response (P = 0.04). Detection of ctHPV-DNA 3 months or later after treatment was associated with worse progression-free and overall survival (P < 0.001). Sensitivity, specificity, and positive and negative predictive values of longitudinal ctHPV-DNA were 100%. The longest lead time from positive ctHPV-DNA to detection of recurrent disease was 25 months.Conclusions:Rapid early clearance of ctHPV-DNA during neoadjuvant therapy demonstrates utility in predicting response to treatment. Detectable ctHPV-DNA following treatment is predictive of both disease recurrence and worse survival.

Supplemental Table 4. Per-patient sensitivity and specificity of detectable ctHPV-DNA at 12 weeks or later following treatment.

Purpose: Human papillomavirus–associated (HPV+) oropharyngeal carcinoma is associated with excellent survival, yet treatment drives substantial toxicity. Improved biomarkers are needed to select patients for de-escalated treatment. Circulating tumor HPV DNA (ctHPV-DNA) represents a promising noninvasive biomarker to gauge treatment response and surveil for disease recurrence. Patients and Methods: A prospective biomarker clinical trial of response-stratified de-escalation was conducted. Eligible patients with non-metastatic HPV+ oropharyngeal carcinoma received neoadjuvant chemotherapy, followed by risk/response-stratified de-escalation with transoral robotic surgery, de-escalated radiation with or without chemotherapy to 50 Gy, or standard chemoradiation to 70 Gy. Deep response (≥50% tumor shrinkage per RECIST v1.1) qualified patients for de-escalation. ctHPV-DNA was measured using HPV-SEQ in plasma at baseline, during neoadjuvant chemotherapy, radiation, and following treatment. The primary endpoint was the correlation of ctHPV-DNA kinetics and radiographic response. Results: Forty-six eligible patients were enrolled, and 488 ctHPV-DNA samples were analyzed (median 11 per patient). The median follow-up was 30 months, and five recurrences were observed (10.9%). Baseline ctHPV-DNA was detected in 95% of evaluable patients. Rapid early ctHPV-DNA clearance after one cycle of neoadjuvant therapy (≥95% reduction) predicted radiographic deep response (P = 0.04). Detection of ctHPV-DNA 3 months or later after treatment was associated with worse progression-free and overall survival (P < 0.001). Sensitivity, specificity, and positive and negative predictive values of longitudinal ctHPV-DNA were 100%. The longest lead time from positive ctHPV-DNA to detection of recurrent disease was 25 months. Conclusions: Rapid early clearance of ctHPV-DNA during neoadjuvant therapy demonstrates utility in predicting response to treatment. Detectable ctHPV-DNA following treatment is predictive of both disease recurrence and worse survival.