Insight of novel biomarkers for papillary thyroid carcinoma through multiomics

Frontiers in Oncology

Oncology

Jun Wu¹  Yuqing Zhang¹  Talal Jamil Qazi²  Houbao Liu³  Yongxiang Yin⁴  Wei Liu⁵  Jiaojiao Zheng⁵  Zhilong Ai⁵  Cong Wang⁶  Junkan Zhu⁷  Qiao Wu⁸  Yiming Wu⁹  Xumin Zhang^1,10  Zhen Wu^1,10  Hongyan Chen^1,10  Daru Lu^1,11  Jingmin Yang^1,12 

[1] Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Cell Bank, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China;Department of Biomedical Engineering, Balochistan University of Engineering and Technology, Khuzdar, Pakistan;Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China;Department of Pathology, Wuxi Maternal and Child Health Care Hospital, Womens Hospital of Jiangnan University, Jiangnan University, Jiangsu, China;Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China;Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China;Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China;Xiamen Clinical Research Center for Cancer Therapy, Xiamen, China;Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China;School of Basic Medical Sciences, Fudan University, Shanghai, China;Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China;State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China;Shanghai WeHealth BioMedical Technology Co., Ltd., Shanghai, China;State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China;State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China;National Health Commission Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China;State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China;Shanghai WeHealth BioMedical Technology Co., Ltd., Shanghai, China;National Health Commission Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China;

关键词: papillary thyroid carcinoma;    landscape;    multiomics;    biomarkers;    prediction;    diagnosis;    prognosis;   

DOI  :  10.3389/fonc.2023.1269751

 received in 2023-07-30, accepted in 2023-09-05,  发布年份 2023

来源: Frontiers

【 摘 要 】

IntroductionThe overdiagnosing of papillary thyroid carcinoma (PTC) in China necessitates the development of an evidence-based diagnosis and prognosis strategy in line with precision medicine. A landscape of PTC in Chinese cohorts is needed to provide comprehensiveness.Methods6 paired PTC samples were employed for whole-exome sequencing, RNA sequencing, and data-dependent acquisition mass spectrum analysis. Weighted gene co-expression network analysis and protein-protein interactions networks were used to screen for hub genes. Moreover, we verified the hub genes' diagnostic and prognostic potential using online databases. Logistic regression was employed to construct a diagnostic model, and we evaluated its efficacy and specificity based on TCGA-THCA and GEO datasets.ResultsThe basic multiomics landscape of PTC among local patients were drawn. The similarities and differences were compared between the Chinese cohort and TCGA-THCA cohorts, including the identification of PNPLA5 as a driver gene in addition to BRAF mutation. Besides, we found 572 differentially expressed genes and 79 differentially expressed proteins. Through integrative analysis, we identified 17 hub genes for prognosis and diagnosis of PTC. Four of these genes, ABR, AHNAK2, GPX1, and TPO, were used to construct a diagnostic model with high accuracy, explicitly targeting PTC (AUC=0.969/0.959 in training/test sets).DiscussionMultiomics analysis of the Chinese cohort demonstrated significant distinctions compared to TCGA-THCA cohorts, highlighting the unique genetic characteristics of Chinese individuals with PTC. The novel biomarkers, holding potential for diagnosis and prognosis of PTC, were identified. Furthermore, these biomarkers provide a valuable tool for precise medicine, especially for immunotherapeutic or nanomedicine based cancer therapy.

【 授权许可】

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Copyright © 2023 Liu, Zhu, Wu, Yin, Wu, Wu, Zheng, Wang, Chen, Qazi, Wu, Zhang, Liu, Yang, Lu, Zhang and Ai