MicroRNA-Based Liquid Biopsy Assay for Early Diagnosis of Head and Neck Cancer

A microRNA-based liquid biopsy assay has been developed that enables early diagnosis of oropharyngeal squamous cell carcinoma, a disease causing hundreds of thousands of fatalities each year.

Oropharyngeal squamous cell carcinoma (OPSCC), also known as tonsil cancer or head and neck cancer, is a disease in which abnormal cells with the potential to both grow locally and metastasize to other parts of the body are found in the tissue of the part of the throat (oropharynx) that includes the base of the tongue, the tonsils, the soft palate, and the walls of the pharynx. The two types of oropharyngeal cancers are HPV-positive oropharyngeal cancer, which is caused by an oral human papillomavirus (HPV) infection; and HPV-negative oropharyngeal cancer, which is linked to use of alcohol, tobacco, or both. OPSCC is frequently diagnosed at an advanced stage, since the disease often causes minimal symptoms other than metastasis to neck lymph nodes.


Tumor cells release microRNA (miRNA)-containing small extracellular vesicles into their extracellular environment and these vesicles are present in circulating blood. Thus, the miRNA content of circulating small extracellular vesicles has the potential to provide a unique molecular signature for multiple possibilities such as diagnosis, prognosis and surveillance of cancers.

Extracellular vesicles (EVs), which include exosomes, microvesicles, and apoptotic bodies, are cell-derived lipid-bilayer-enclosed structures, with sizes ranging from 30 to 5,000 nanometers. The vesicles, which contain RNA, proteins, lipids, and metabolites that are reflective of the cell type of origin, are either released from the cell when multivesicular bodies (MVBs) fuse with the plasma membrane, or they are released directly from the plasma membrane.

Previous studies have suggested that MiRNAs are potential biomarkers for early head and neck squamous cell cancer diagnosis, prognosis, recurrence, and presence of metastatic disease. However, there is no widespread agreement on a panel of miRNAs with clinically meaningful utility for head and neck squamous cell cancers. This could be due to variations in the collection, storage, pre-processing, and isolation of RNA, but several reports have indicated that the selection and reproducibility of biomarkers has been widely affected by the methods used for data analysis. The primary analysis issues appear to be model overfitting and the incorrect application of statistical techniques.

Seeking better tools for diagnosis of head and neck cancer, investigators at Flinders University (Adelaide, Australia) developed a robust statistical approach to identify a miRNA signature that can distinguish controls and patients with inflammatory disease from patients with human papilloma virus positive (HPV+) OPSCC.

For this study, the investigators harvested small extracellular vesicles from the serum of 20 control patients, 20 patients with gastroesophageal reflux disease (GORD), and 40 patients with locally advanced HPV+ OPSCC. MicroRNAs were purified, and expression profiled using ThermoFisher Scientific (Waltham, MA, USA) OpenArray technology. A novel cross validation method, using lasso regression, was developed to stabilize selection of miRNAs for inclusion in a prediction model. The method, named StaVarSel (for Stable Variable Selection), was used to derive a diagnostic biomarker signature.

Results revealed that a standard cross validation approach was unable to produce a biomarker signature with good cross validated predictive capacity. In contrast, StaVarSel produced a regression model containing 11 miRNA ratios with potential clinical utility.

Senior author Dr. Damian Hussey, a researcher in medicine and public health at Flinders University, said, "MicroRNAs are potential biomarkers for early head and neck squamous cell cancer diagnosis, prognosis, recurrence, and presence of metastatic disease. However, there is no widespread agreement on a panel of miRNAs with clinically meaningful utility for head and neck squamous cell cancers."

The liquid biopsy diagnostic assay for head and neck cancer was described in the July 10, 2020, online edition of the Journal of Translational Medicine.

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Flinders University
ThermoFisher Scientific