RNA Oncoimmune Phenotyping of HPV-Positive p16-Positive Oropharyngeal Squamous Cell Carcinomas by Nodal Status

Abstract

Many HPV-16 and p16-positive tumors are treated as "lower-risk," but they do not have similar genetic compositions at the biological level. The identification of subgroups with unique expression patterns, such as those with nodal metastases, may guide physicians toward alternative or more aggressive therapies. In our study, unguided clustering suggested that that the larger biological characteristics of a tumor could be a better prognostic biomarker.

Artificial Intelligence for the Otolaryngologist: A State of the Art Review

“…Using machine learning, the authors developed a 40-gene profile that accurately predicted the presence of nodal disease based on gene expression in the primary tumor. 40 Similarly, Carnielli et al used machine learning to develop a proteomic signature to predict the presence of lymph node metastasis in oral cancer. In the future, such profiles may be used to guide treatment decisions by intensifying treatment for patients with high-risk patterns of gene expression and reducing treatment-related morbidity for patients with low-risk profiles.…”

“…Stepp and colleagues compared gene expression profiles between node‐negative and node‐positive HPV‐related oropharyngeal squamous cell carcinomas. Using machine learning, the authors developed a 40‐gene profile that accurately predicted the presence of nodal disease based on gene expression in the primary tumor 40 . Similarly, Carnielli et al used machine learning to develop a proteomic signature to predict the presence of lymph node metastasis in oral cancer.…”

High‐Throughput NanoString Analysis of Oncogenic Human Papillomavirus and Tumor Microenvironment Transcription in Head and Neck Squamous Cell Carcinoma

“…Utilization of an RNA multiplex assay such as the NanoString nCounter allows a researcher to obtain tumor‐specific information such as the likelihood of nodal metastasis as well as direct identification of HPV transcription simultaneously (Figs. 2 and 3 and Stepp et al., 2018).…”

Development of a Novel Molecular Test for Determining HPV Integration Status in HPV-Positive Oropharynx Cancers

“…Methods | Under approval of The University of North Carolina at Chapel Hill's institutional review board, RNA from formalin-fixed, paraffin-embedded tissues from 123 known OPSCC tumors described previously, 4 with an additional 8 HPV genes, were included in the target NanoString code set following the manufacturer's protocol. Total RNA input was adjusted to 100 ng based on DV300 values from the 4200 TapeStation (Agilent) profiles: (100/percent of sample >300 nt) × 100 ng.…”