Fig. 6: Methylation and expression profiling and diagnostic potential of candidate biomarkers through PTC tissues. | npj Precision Oncology

Fig. 6: Methylation and expression profiling and diagnostic potential of candidate biomarkers through PTC tissues.

From: Epigenomic profiling of papillary thyroid carcinoma reveals distinct subtypes with clinical implications

Fig. 6

A Quantification of methylation signals using methylation control DNA with each qMSP primer set. Each qMSP was performed with three technical replicates. B Quantification of DNA methylation signal with BCPAP genomic DNA following 5-Aza treatment using each qMSP primer set. Three independent experiments were conducted. C DNA methylation signal quantification across genomic DNA from PTC subgroups using surgical thyroid specimens. The average diagnostic score of each subgroup was calculated. D Validation of gene expression via quantitative PCR in the discovery cohort, using surgical thyroid specimens. PTC tissues were categorized according to the methylation status of 329 DMRs. E Assessment of biomarker methylation levels in 30 FNAB samples from patients with PTC using real-time MSP. F Assessment of biomarker expression levels in 30 FNAB samples from patients with PTC using real-time PCR. G PCA plot of 30 patients’ qMSP scores (PC1, representing methylation levels) and qRT-PCR scores (PC2, representing gene expression levels). (A, C, D) Two-sided t-tests were used for comparisons. (B) One-sided t-test was applied due to the anticipated decrease in methylation signal following 5-Aza treatment. (E, F) Unpaired Student’s t test was used to compare groups. ***P < 0.001; **P < 0.01; *P < 0.05.

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