Genome Editing Research Center; Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
Personalized Genomic Medicine Research Center; Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
Thyroid. 2020 Feb;30(2):192-203. doi: 10.1089/thy.2019.0011. Epub 2020 Jan 9.
There are no reliable biomarkers to accurately differentiate indolent thyroid tumors from more aggressive thyroid cancers. This study aimed to develop new DNA methylation markers for diagnosis and recurrence risk stratification of papillary thyroid carcinoma (PTC). Thyroid tumor-specific DNA methylation profiling was investigated in 34 fresh frozen tissues, which included nontumor ( = 7), noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP, = 6) and PTC ( = 21), using the Illumina HumanMethylation EPIC array. We performed a genome-wide assessment of thyroid tumor-specific differentially methylated CpG sites in the discovery set, then validated the top candidate markers in an independent set of 293 paraffin tissue samples comprised of follicular adenoma (FA, = 61), Hürthle cell adenoma (HA, = 24), NIFTP ( = 56), PTC ( = 120), follicular thyroid carcinoma ( = 27), and Hürthle cell carcinoma ( = 5), by pyrosequencing. Three selected markers (cg10705422, cg17707274, and cg26849382) differentiated nonmalignant (FA, HA, and NIFTP) tumors from differentiated thyroid cancers with area under the receiver operating characteristic curve of 0.83, 0.83, and 0.80, respectively. Low DNA methylation levels for three markers were significantly associated with recurrent or persistent disease (odds ratio (OR) = 3.860 [95% confidence interval (CI) 1.194-12.475]) and distant metastasis (OR = 4.009 [CI 1.098-14.632]) in patients with differentiated thyroid cancer. A subgroup analysis for the validation set showed that PTC patients with low DNA methylation levels more frequently had aggressive histology, extrathyroidal extension, lymph node metastasis, mutations, and recurrent or persistent disease than those with high levels of methylation markers. All PTC patients who developed disease recurrence had low DNA methylation levels for three markers. DNA methylation levels of three markers can be useful for differentiating differentiated thyroid cancer from nonmalignant follicular thyroid lesions, and may serve as prognostic biomarkers for predicting recurrent or persistent disease after surgery for differentiated thyroid cancer.
目前尚无可靠的生物标志物能准确地区分惰性甲状腺肿瘤和侵袭性甲状腺癌。本研究旨在寻找新的 DNA 甲基化标志物，用于诊断和复发风险分层。
我们使用 Illumina HumanMethylation EPIC 芯片对 34 例新鲜冷冻组织（包括非肿瘤组织（n=7）、具有滤泡状肿瘤特征的非侵袭性滤泡甲状腺肿瘤（n=6）和甲状腺乳头状癌（n=21））进行甲状腺肿瘤特异性 DNA 甲基化谱分析。在发现集中，我们对甲状腺肿瘤特异性差异甲基化 CpG 位点进行了全基因组评估，然后在由滤泡性腺瘤（n=61）、嗜酸细胞瘤（n=24）、非侵袭性滤泡状肿瘤（n=56）、甲状腺乳头状癌（n=120）、滤泡状甲状腺癌（n=27）和嗜酸细胞瘤（n=5）组成的 293 例石蜡组织样本独立集中，通过焦磷酸测序验证了候选标志物的 top 标记物。
三个标记物（cg10705422、cg17707274 和 cg26849382）可将非恶性肿瘤（FA、HA 和 NIFTP）与分化型甲状腺癌区分开来，ROC 曲线下面积分别为 0.83、0.83 和 0.80。三个标记物的低甲基化水平与分化型甲状腺癌患者的疾病复发或持续存在（比值比（OR）=3.860 [95%置信区间（CI）1.194-12.475]）和远处转移（OR=4.009 [CI 1.098-14.632]）显著相关。验证集中的亚组分析显示，与高甲基化标记物相比，DNA 低甲基化水平的 PTC 患者更常具有侵袭性组织学特征、甲状腺外侵犯、淋巴结转移、基因突变和疾病复发或持续存在。所有发生疾病复发的 PTC 患者均存在三个标记物的 DNA 低甲基化水平。
这三个标记物的甲基化水平可用于区分分化型甲状腺癌和非恶性滤泡性甲状腺病变，并且可能作为预测分化型甲状腺癌手术后复发或持续存在的预后生物标志物。
