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Chen H, Liu Y, Wang F, Sun J, Gong C, Zhu M, Xu M, He Q, Liu R, Su Z, Zhong D, Liu L. MeIS: DNA methylation-based immune response signatures for thyroid nodule diagnostics. J Clin Endocrinol Metab 2024:dgae141. [PMID: 38450587 DOI: 10.1210/clinem/dgae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
CONTEXT Accurately distinguishing between benign thyroid nodules (BTNs) and papillary thyroid cancers (PTCs) with current conventional methods poses a significant challenge. OBJECTIVE We identify DNA methylation markers of immune response-related genes for distinguishing BTNs and PTCs. METHODS In this study, we analyzed a public reduced representative bisulfite sequencing (RRBS) dataset and revealed distinct methylation patterns associated with immune signals in PTCs and BTNs. Based on these findings, we developed a diagnostic classifier named as the Methylation-based Immune Response Signature (MeIS), which was composed of fifteen DNA methylation markers associated with immune response-related genes. We validated the MeIS's performance in two independent cohorts: ZS's retrospective cohort (50 PTC and 18 BTN surgery-leftover samples) and ZS's preoperative cohort (31 PTC and 30 BTN fine-needle aspiration (FNA) samples). RESULTS The MeIS classifier demonstrated significant clinical promise, achieving AUCs of 0.96, 0.98, 0.89 and 0.90 in the training set, validation set, ZS's retrospective cohort, and ZS's preoperative cohort, respectively. For the cytologically indeterminate thyroid nodules, in the ZS's retrospective cohort, MeIS exhibited a sensitivity of 91% and a specificity of 82%; in the ZS's preoperative cohort, MeIS achieved a sensitivity of 84% and a specificity of 74%. Additionally, combining MeIS and BRAFV600E detection improved the detecting performance of cytologically indeterminate thyroid nodules, yielding sensitivities of 98% and 87%, and specificities of 82% and 74% in the ZS's retrospective cohort and ZS's preoperative cohort, respectively. CONCLUSIONS The fifteen markers we identified can be employed to improve the diagnostic of cytologically indeterminate thyroid nodules.
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Affiliation(s)
- Huang Chen
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Yiying Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Feihang Wang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
| | - Jin Sun
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | | | - Min Zhu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Minjie Xu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Dingrong Zhong
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Lingxiao Liu
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
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