DNA methylation-based method to differentiate malignant from benign thyroid lesions

Mateus Camargo Barros-Filho, Mariana Bisarro Dos Reis, Caroline Moraes Beltrami, Julia Bette Homem de Mello, Fábio Albuquerque Marchi, Hellen Kuasne, Sandra Aparecida Drigo, Victor Piana de Andrade, Mauro Ajaj Saieg, Clóvis Antonio Lopes Pinto, Luiz Paulo Kowalski, Silvia Regina Rogatto*

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Resumé

Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3% sensitivity and 82.4% specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4% sensitivity and 87.5% specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7% sensitivity and 75.4% specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7% sensitivity and 89.5% specificity in confirmed malignant tumors, and 100% sensitivity and 89% specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.

OriginalsprogEngelsk
TidsskriftThyroid
Vol/bind29
Udgave nummer9
Sider (fra-til)1244-1254
ISSN1050-7256
DOI
StatusUdgivet - sep. 2019

Fingeraftryk

DNA Methylation
Cell Biology
Thyroid Nodule
Neoplasms
Databases
Unnecessary Procedures
ROC Curve
Differential Diagnosis

Citer dette

Barros-Filho, M. C., Dos Reis, M. B., Beltrami, C. M., de Mello, J. B. H., Marchi, F. A., Kuasne, H., ... Rogatto, S. R. (2019). DNA methylation-based method to differentiate malignant from benign thyroid lesions. Thyroid, 29(9), 1244-1254. https://doi.org/10.1089/thy.2018.0458
Barros-Filho, Mateus Camargo ; Dos Reis, Mariana Bisarro ; Beltrami, Caroline Moraes ; de Mello, Julia Bette Homem ; Marchi, Fábio Albuquerque ; Kuasne, Hellen ; Drigo, Sandra Aparecida ; de Andrade, Victor Piana ; Saieg, Mauro Ajaj ; Pinto, Clóvis Antonio Lopes ; Kowalski, Luiz Paulo ; Rogatto, Silvia Regina. / DNA methylation-based method to differentiate malignant from benign thyroid lesions. I: Thyroid. 2019 ; Bind 29, Nr. 9. s. 1244-1254.
@article{7c0434d8b33a41d293a5986b585a2f51,
title = "DNA methylation-based method to differentiate malignant from benign thyroid lesions",
abstract = "Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3{\%} sensitivity and 82.4{\%} specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4{\%} sensitivity and 87.5{\%} specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7{\%} sensitivity and 75.4{\%} specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7{\%} sensitivity and 89.5{\%} specificity in confirmed malignant tumors, and 100{\%} sensitivity and 89{\%} specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.",
author = "Barros-Filho, {Mateus Camargo} and {Dos Reis}, {Mariana Bisarro} and Beltrami, {Caroline Moraes} and {de Mello}, {Julia Bette Homem} and Marchi, {F{\'a}bio Albuquerque} and Hellen Kuasne and Drigo, {Sandra Aparecida} and {de Andrade}, {Victor Piana} and Saieg, {Mauro Ajaj} and Pinto, {Cl{\'o}vis Antonio Lopes} and Kowalski, {Luiz Paulo} and Rogatto, {Silvia Regina}",
year = "2019",
month = "9",
doi = "10.1089/thy.2018.0458",
language = "English",
volume = "29",
pages = "1244--1254",
journal = "Thyroid",
issn = "1050-7256",
publisher = "Mary Ann Liebert Incorporated",
number = "9",

}

Barros-Filho, MC, Dos Reis, MB, Beltrami, CM, de Mello, JBH, Marchi, FA, Kuasne, H, Drigo, SA, de Andrade, VP, Saieg, MA, Pinto, CAL, Kowalski, LP & Rogatto, SR 2019, 'DNA methylation-based method to differentiate malignant from benign thyroid lesions', Thyroid, bind 29, nr. 9, s. 1244-1254. https://doi.org/10.1089/thy.2018.0458

DNA methylation-based method to differentiate malignant from benign thyroid lesions. / Barros-Filho, Mateus Camargo; Dos Reis, Mariana Bisarro; Beltrami, Caroline Moraes; de Mello, Julia Bette Homem; Marchi, Fábio Albuquerque; Kuasne, Hellen; Drigo, Sandra Aparecida; de Andrade, Victor Piana; Saieg, Mauro Ajaj; Pinto, Clóvis Antonio Lopes; Kowalski, Luiz Paulo; Rogatto, Silvia Regina.

I: Thyroid, Bind 29, Nr. 9, 09.2019, s. 1244-1254.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - DNA methylation-based method to differentiate malignant from benign thyroid lesions

AU - Barros-Filho, Mateus Camargo

AU - Dos Reis, Mariana Bisarro

AU - Beltrami, Caroline Moraes

AU - de Mello, Julia Bette Homem

AU - Marchi, Fábio Albuquerque

AU - Kuasne, Hellen

AU - Drigo, Sandra Aparecida

AU - de Andrade, Victor Piana

AU - Saieg, Mauro Ajaj

AU - Pinto, Clóvis Antonio Lopes

AU - Kowalski, Luiz Paulo

AU - Rogatto, Silvia Regina

PY - 2019/9

Y1 - 2019/9

N2 - Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3% sensitivity and 82.4% specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4% sensitivity and 87.5% specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7% sensitivity and 75.4% specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7% sensitivity and 89.5% specificity in confirmed malignant tumors, and 100% sensitivity and 89% specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.

AB - Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3% sensitivity and 82.4% specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4% sensitivity and 87.5% specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7% sensitivity and 75.4% specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7% sensitivity and 89.5% specificity in confirmed malignant tumors, and 100% sensitivity and 89% specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.

U2 - 10.1089/thy.2018.0458

DO - 10.1089/thy.2018.0458

M3 - Journal article

C2 - 31328658

VL - 29

SP - 1244

EP - 1254

JO - Thyroid

JF - Thyroid

SN - 1050-7256

IS - 9

ER -

Barros-Filho MC, Dos Reis MB, Beltrami CM, de Mello JBH, Marchi FA, Kuasne H et al. DNA methylation-based method to differentiate malignant from benign thyroid lesions. Thyroid. 2019 sep;29(9):1244-1254. https://doi.org/10.1089/thy.2018.0458