A rapid increase in incidence of thyroid cancer has been reported in recent years. However, ambiguities between benign and malignant nodules in cytological features have led to unnecessary thyroidectomy or over-treatment. We aimed to identify DNA methylation markers to accurately classify thyroid nodules, which may be developed into non-invasive screening diagnostics for thyroid cancer to reduce unnecessary thyroid removals.
Genome-wide DNA methylation profiles of papillary thyroid cancer nodules (tissue, N = 37; plasma, N = 55), benign nodules (tissue, N = 37; plasma, N = 55) and healthy samples (buffy coat, N = 20; plasma, N = 123) were generated by a modified RRBS method. An independent RRBS dataset including 89 malignant and 72 benign nodules was derived from Yim et al. 2019. We adopted Singlera’s MONOD+ assay to interrogate the methylation state of over 4,000,000 CpG sites across more than 200,000 methylation haplotype blocks (MHBs). We identified discriminatory DNA methylation MHBs by Wilcox rank sum test. Using our dataset as a training set, we built several diagnostic models to classify thyroid nodules using machine learning methods. We validated the model by classifying public methylation datasets of thyroid tissues.
We generated an initial list of top 1000 DNA methylation markers and built a classification model by the random forest method. We classified DNA methylation profiles of thyroid nodules published by Yim et al. 2019. Results show that this model achieved a sensitivity of 82%, a specificity of 94.4% and AUC of 0.94 (95% CI, 0.91-0.98). We randomly selected the 2/3 plasma samples as training data to build a prediction model. The model yielded an accuracy of 72% in the validation cohort. We also identified 2392 deferentially methylated regions by comparing benign tissues with malignant tissues. DMR associated genes are highly enriched in many cancer related pathways and MSigDB immunologic signatures, indicating the development of thyroid cancer is closely associated with immune dysfunction.
Our study demonstrates that DNA methylation markers can robustly differentiate thyroid nodules. They are thus promising candidates to develop non-invasive diagnostics for thyroid cancer screening.
Clinical trial identification
Legal entity responsible for the study
The First Affiliated Hospital of Sun Yat-sen University.
National Natural Science Foundation of China (81772850).
All authors have declared no conflicts of interest.