Using Saliva Epigenetic Data to Develop and Validate a Multivariable Predictor of Esophageal Cancer Status

Abstract

Background: Salivary epigenetic biomarkers may detect esophageal cancer. Methods: A total of 256 saliva samples from esophageal adenocarcinoma patients and matched volunteers were analyzed with Illumina EPIC methylation arrays. Three datasets were created, using 64% for discovery, 16% for testing and 20% for validation. Modules of gene-based methylation probes were created using weighted gene coexpression network analysis. Module significance to disease and gene importance to module were determined and a random forest classifier generated using best-scoring gene-related epigenetic probes. A cost-sensitive wrapper algorithm maximized cancer diagnosis. Results: Using age, sex and seven probes, esophageal adenocarcinoma was detected with area under the curve of 0.72 in discovery, 0.73 in testing and 0.75 in validation datasets. Cancer sensitivity was 88% with specificity of 31%. Conclusion: We have demonstrated a potentially clinically viable classifier of esophageal cancer based on saliva methylation.

Keywords::

• biomarker panel
• diagnosis
• epigenetics
• esophageal adenocarcinoma
• saliva

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.futuremedicine.com/doi/suppl/10.2217/epi-2023-0248

Author contributions

T Stone: study conception, collection, data analysis, data interpretation, manuscript preparation. V Ward, A Hogan, KMA Ho, A Wilson, H McBain, M Duku, P Wolfson, S Cheung: project administration, data collection. SPIT Study Group Collaborators: data collection. A Rosenfeld: study conception, data interpretation, manuscript preparation, supervisory oversight. L Lovat: study conception, data analysis, data interpretation, manuscript preparation, supervisory oversight.

Financial disclosure

The SPIT study is funded by Guts UK Charity, the Charles Wolfson Foundation and the Rosetrees Trust (A1338). This research was funded in whole, or in part, by the Wellcome Trust (203145Z/16/Z). L Lovat is also funded by the National Institute for Health Research (NIHR) UCLH Biomedical Research Centre. The funders had no role in the design or reporting of the study. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Competing interests disclosure

The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Writing disclosure

No writing assistance was utilized in the production of this manuscript.

Clinical trial data disclosure

The authors certify that this manuscript reports original clinical trial data. Deidentified, individual data that underlie the results reported in this article (text, tables, figures and appendices) will be available indefinitely for anyone who wants access to them.

Ethical conduct of research

Ethical approval for the study was obtained from the Coventry & Warwick Research Ethics Committee (Ref: 17/WM/0079) and registered with the ISRCTN Registry (ISRCTN11921553). The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Data sharing statement

Raw data, processed data and accompanying metadata have been deposited to the Gene Expression Omnibus (GEO) database under the accession code GSE232332.

Additional information

Funding

The SPIT study is funded by Guts UK Charity, the Charles Wolfson Foundation and the Rosetrees Trust (A1338). This research was funded in whole, or in part, by the Wellcome Trust (203145Z/16/Z). L Lovat is also funded by the National Institute for Health Research (NIHR) UCLH Biomedical Research Centre. The funders had no role in the design or reporting of the study. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.