Identification of Tissue-Specific DNA Methylation Signatures for Thyroid Nodule Diagnostics

Abstract

Thyroid cancer is frequently difficult to diagnose due to an overlap of cytologic features between malignant and benign nodules. This overlap leads to unnecessary removal of the thyroid in patients without cancer. While providing some improvement over cytopathologic diagnostics, molecular methods frequently fail to provide a correct diagnosis for thyroid nodules. These approaches are based on the difference between cancer and adjacent thyroid tissue and assume that adjacent tissues are the same as benign nodules. However, in contrast to adjacent tissues, benign thyroid nodules can contain genetic alterations that can be found in cancer. For the development of a new molecular diagnostic test for thyroid cancer, we evaluated DNA methylation in 109 thyroid tissues by using genome-wide single-base resolution DNA methylation analysis. The test was validated in a retrospective cohort containing 65 thyroid nodules. By conducting reduced representation bisulfite sequencing in 109 thyroid specimens, we found significant differences between adjacent tissue, benign nodules, and cancer. These tissue-specific signatures are strongly linked to active enhancers and cancer-associated genes. Based on these signatures, we developed a new epigenetic approach for thyroid diagnostics. According to the validation cohort, our test has an estimated specificity of 97% [95% confidence interval (CI), 81-100], sensitivity of 100% (95% CI, 87-100), positive predictive value of 97% (95% CI, 83-100), and negative predictive value of 100% (95% CI, 86-100). These data show that epigenetic testing can provide outstanding diagnostic accuracy for thyroid nodules.

Association between DNA methylation profile and malignancy in follicular-patterned thyroid neoplasms

“…The reduced Δβ value combined with the small sample size probably accounted for the lack of significance of the FTA-NT comparison ( Supplementary Table 1). Similarly, Yim et al (2019) also noted that benign thyroid nodules frequently feature an epigenetic pattern intermediate between normal thyroids and malignant nodules.…”

“…Importantly, the same study also suggested prognostic implications of the DNA methylation profile, with massive hypomethylation in aggressive (PDTC/ATC) thyroid cancer subtypes (Bisarro Dos Reis et al 2017). Recently, Yim et al (2019) showed that a DNA methylation-based molecular method, named Diagnostic DNA Methylation Signature approach (DDMS), features high sensitivity/specificity in the identification of malignant and benign thyroid nodules.…”

DNA methylation in thyroid cancer

“…These findings, which are consistent with results from Mancikova et al andAffinito et al (Mancikova et al 2014, Affinito et al 2019), suggested that DNA methylation in promoters does not have a widespread role in controlling gene expression in PTC. On the other hand, by using RRBS, Yim et al identified a unique DNA methylation signature of 4,575 CpGs specific to benign nodules, most of which were hypermethylated compared to adjacent normal tissues and malignant nodules, that may have important diagnostic applications (Yim et al 2019).They also analyzed specimens with lymphocytic thyroiditis and, in accordance with the results from Bisarro dos Reis et al, suggested that the presence of immune-infiltrating cells in tumors may affect DNA methylation patterns (Bisarro dos .…”

“…However, the series of samples used contained a low number of recurrent cases; thus, further analyses are required to validate its potential for prognostic use. Finally, Yim et al, who profiled PTC DNA methylation by RRBS, developed a new diagnostic method, the so-called diagnostic DNA methylation signature (DDMS) approach, which is based on 373 differentially methylated regions with tissue-specific DNA methylation patterns in benign and malignant nodules (Yim et al 2019). A notable proportion of these markers were associated with active enhancers and cancer-related genes.…”

Identification of hub genes in papillary thyroid carcinoma: robust rank aggregation and weighted gene co-expression network analysis

“…With these therapeutic approaches, most patients with PTC have a good prognosis, but there were some challenges for both patients and clinicians. The consequence of surgical excision that is one of the important treatments for thyroid cancer may be the increased incidence of hypothyroidism [5]; PTC is often difficult to diagnose because of similarities between malignant and benign nodules, which results in some benign patients having their thyroid removed [6]; treatment of refractory radioiodine differentiated thyroid cancer still faces challenges and some slowmoving tumors were overdiagnosed and overtreated. In terms of molecular therapy, the combined use of immune checkpoint inhibitors and BRAF (especially BRAFV600E) inhibitors is aussichtsreich in the treatment of thyroid cancer and some progress has been made [7].…”