Background: Differentiating potentially malignant thyroid nodules among those undetermined by cytology avoid unnecessary surgical procedures. Aberrant DNA methylation is ubiquitous in human cancers, including thyroid tumors. Biomarkers based on methylation profiles have been successfully used to diagnose early stage malignancy in many human cancers.
Objective and hypotheses: To determine the genome-wide promoter methylation status of cytologically indeterminate thyroid nodules.
Methods: We obtained genomic DNA from frozen samples of three classical (CVPTC) and three follicular variant papillary (FVPTC), two follicular adenomas (FA) and three adenomatous goiter (AG) removed from 11 unrelated patients. The DNA methylation fraction was enriched using methyl-DNA immunoprecipitation and interrogated on Affymetrix human promoter 1.0 array. For control, DNA from normal thyroid tissue patients were also extracted and pooled in a single reaction. All array data analysis were performed using pre-defined tiling workflow in Partek® Genomics Suite Software 6.4. In general, P values <0.05 were considered statistically significant.
Results: We identified genes that are differentially hypermethylated in each thyroid tumor subtypes compared to normal tissue: 189 in CVPTC, 192 in FVPTC, 313 in FA, and 288 in AG. We also categorized thyroid tumors samples in two broad groups: benign (FA and AG) or malignant (CVPTC and FVPTC); 139 and 138 hypermethylated loci were exclusively observed in benign and malign tumors respectively. In addition, we further found that the tumor suppressor RPS6 (ribosomal protein S6) and the SLC5A4 (solute sarrier family 5 member 4) genes were among selectively hypermethylated loci in malignant group. Subsequent analysis with large numbers of patients with thyroid cancer will be required to assess the usefulness of RPS6 and SLC5A4 promoter methylation as biomarkers of malignancy.
Conclusion: Our findings confirmed previous results which demonstrated that DNA methylation signatures were only distinguished between well differentiated and non-differentiated thyroid cancers.
18 Sep 2014 - 20 Sep 2014