Insight of novel biomarkers for papillary thyroid carcinoma through multiomics

Wei Liu; Junkan Zhu; Junkan Zhu; Zhen Wu; Yongxiang Yin; Qiao Wu; Qiao Wu; Yiming Wu; Jiaojiao Zheng; Cong Wang; Cong Wang; Cong Wang; Hongyan Chen; Talal Jamil Qazi; Jun Wu; Yuqing Zhang; Houbao Liu; Jingmin Yang; Jingmin Yang; Jingmin Yang; Daru Lu; Daru Lu; Xumin Zhang; Zhilong Ai

doi:10.3389/fonc.2023.1269751

Frontiers in Oncology (Sep 2023)

Insight of novel biomarkers for papillary thyroid carcinoma through multiomics

Wei Liu,
Junkan Zhu,
Junkan Zhu,
Zhen Wu,
Yongxiang Yin,
Qiao Wu,
Qiao Wu,
Yiming Wu,
Jiaojiao Zheng,
Cong Wang,
Cong Wang,
Cong Wang,
Hongyan Chen,
Talal Jamil Qazi,
Jun Wu,
Yuqing Zhang,
Houbao Liu,
Jingmin Yang,
Jingmin Yang,
Jingmin Yang,
Daru Lu,
Daru Lu,
Xumin Zhang,
Zhilong Ai

Affiliations

Wei Liu: Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
Junkan Zhu: Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
Junkan Zhu: School of Basic Medical Sciences, Fudan University, Shanghai, China
Zhen Wu: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
Yongxiang Yin: Department of Pathology, Wuxi Maternal and Child Health Care Hospital, Womens Hospital of Jiangnan University, Jiangnan University, Jiangsu, China
Qiao Wu: Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
Qiao Wu: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
Yiming Wu: Shanghai WeHealth BioMedical Technology Co., Ltd., Shanghai, China
Jiaojiao Zheng: Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
Cong Wang: Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
Cong Wang: Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
Cong Wang: Xiamen Clinical Research Center for Cancer Therapy, Xiamen, China
Hongyan Chen: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
Talal Jamil Qazi: Department of Biomedical Engineering, Balochistan University of Engineering and Technology, Khuzdar, Pakistan
Jun Wu: 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
Yuqing Zhang: 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
Houbao Liu: 0Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
Jingmin Yang: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
Jingmin Yang: Shanghai WeHealth BioMedical Technology Co., Ltd., Shanghai, China
Jingmin Yang: 1National Health Commission Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China
Daru Lu: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
Daru Lu: 1National Health Commission Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China
Xumin Zhang: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
Zhilong Ai: Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China

DOI: https://doi.org/10.3389/fonc.2023.1269751
Journal volume & issue: Vol. 13

Abstract

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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.

Published in Frontiers in Oncology

ISSN: 2234-943X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Medicine: Internal medicine: Neoplasms. Tumors. Oncology. Including cancer and carcinogens
Website: https://www.frontiersin.org/journals/oncology/

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