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Blanchett R, Lau KH, Pfeifer GP. Homeobox and Polycomb target gene methylation in human solid tumors. Sci Rep 2024; 14:13912. [PMID: 38886487 PMCID: PMC11183203 DOI: 10.1038/s41598-024-64569-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
DNA methylation is an epigenetic mark that plays an important role in defining cancer phenotypes, with global hypomethylation and focal hypermethylation at CpG islands observed in tumors. These methylation marks can also be used to define tumor types and provide an avenue for biomarker identification. The homeobox gene class is one that has potential for this use, as well as other genes that are Polycomb Repressive Complex 2 targets. To begin to unravel this relationship, we performed a pan-cancer DNA methylation analysis using sixteen Illumina HM450k array datasets from TCGA, delving into cancer-specific qualities and commonalities between tumor types with a focus on homeobox genes. Our comparisons of tumor to normal samples suggest that homeobox genes commonly harbor significant hypermethylated differentially methylated regions. We identified two homeobox genes, HOXA3 and HOXD10, that are hypermethylated in all 16 cancer types. Furthermore, we identified several potential homeobox gene biomarkers from our analysis that are uniquely methylated in only one tumor type and that could be used as screening tools in the future. Overall, our study demonstrates unique patterns of DNA methylation in multiple tumor types and expands on the interplay between the homeobox gene class and oncogenesis.
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Affiliation(s)
- Reid Blanchett
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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Qu N, Chen D, Ma B, Zhang L, Wang Q, Wang Y, Wang H, Ni Z, Wang W, Liao T, Xiang J, Wang Y, Jin S, Xue D, Wu W, Wang Y, Ji Q, He H, Piao HL, Shi R. Integrated proteogenomic and metabolomic characterization of papillary thyroid cancer with different recurrence risks. Nat Commun 2024; 15:3175. [PMID: 38609408 PMCID: PMC11014849 DOI: 10.1038/s41467-024-47581-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Although papillary thyroid cancer (PTC) has a good prognosis, its recurrence rate is high and remains a core concern in the clinic. Molecular factors contributing to different recurrence risks (RRs) remain poorly defined. Here, we perform an integrative proteogenomic and metabolomic characterization of 102 Chinese PTC patients with different RRs. Genomic profiling reveals that mutations in MUC16 and TERT promoter as well as multiple gene fusions like NCOA4-RET are enriched by the high RR. Integrative multi-omics analyses further describe the multi-dimensional characteristics of PTC, especially in metabolism pathways, and delineate dominated molecular patterns of different RRs. Moreover, the PTC patients are clustered into four subtypes (CS1: low RR and BRAF-like; CS2: high RR and metabolism type, worst prognosis; CS3: high RR and immune type, better prognosis; CS4: high RR and BRAF-like) based on the omics data. Notably, the subtypes display significant differences considering BRAF and TERT promoter mutations, metabolism and immune pathway profiles, epithelial cell compositions, and various clinical factors (especially RRs and prognosis) as well as druggable targets. This study can provide insights into the complex molecular characteristics of PTC recurrences and help promote early diagnosis and precision treatment of recurrent PTC.
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Affiliation(s)
- Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Di Chen
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lijun Zhang
- Department of General Surgery, Ganmei Affiliated Hospital of Kunming Medical University (The First People's Hospital of Kunming), Kunming, Yunnan, China
- Department of Surgery, Kunming Medical University, Kunming, Yunnan, China
| | - Qiuping Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yuting Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongping Wang
- Department of Endocrinology, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhaoxian Ni
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Xiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yulong Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi Jin
- Department of Laparoscopic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dixin Xue
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weili Wu
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Hui He
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Department of Laparoscopic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Hai-Long Piao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- Department of Biochemistry & Molecular Biology, School of Life Sciences, China Medical University, Shenyang, China.
| | - Rongliang Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Liu W, Zhu J, Wu Z, Yin Y, Wu Q, Wu Y, Zheng J, Wang C, Chen H, Qazi TJ, Wu J, Zhang Y, Liu H, Yang J, Lu D, Zhang X, Ai Z. Insight of novel biomarkers for papillary thyroid carcinoma through multiomics. Front Oncol 2023; 13:1269751. [PMID: 37795451 PMCID: PMC10546062 DOI: 10.3389/fonc.2023.1269751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction The 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. Methods 6 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. Results The 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). Discussion Multiomics 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.
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Affiliation(s)
- 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
- 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
- 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
- Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- 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
- Department 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
- 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
| | - Daru Lu
- 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
| | - 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
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Wang J, Lei M, Xu Z. Aberrant expression of PROS1 correlates with human papillary thyroid cancer progression. PeerJ 2021; 9:e11813. [PMID: 34414029 PMCID: PMC8344691 DOI: 10.7717/peerj.11813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/28/2021] [Indexed: 02/05/2023] Open
Abstract
Background Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). Considering the important association between cellular immunity and PTC progression, it is worth exploring the biological significance of immune-related signaling in PTC. Methods Several bioinformatics tools, such as R software, WEB-based Gene SeT AnaLysis Toolkit (WebGestalt), Database for Annotation, Visualization and Integrated Discovery (DAVID), Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape were used to identify the immune-related hub genes in PTC. Furthermore, in vitro experiments were adopted to identify the proliferation and migration ability of PROS1 knockdown groups and control groups in PTC cells. Results The differentially expressed genes (DEGs) of five datasets from Gene Expression Omnibus (GEO) contained 154 upregulated genes and 193 downregulated genes, with Protein S (PROS1) being the only immune-related hub gene. Quantitative real-time polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) have been conducted to prove the high expression of PROS1 in PTC. Moreover, PROS1 expression was significantly correlated with lymph nodes classification. Furthermore, knockdown of PROS1 by shRNAs inhibited the cell proliferation and cell migration in PTC cells. Conclusions The findings unveiled the clinical relevance and significance of PROS1 in PTC and provided potential immune-related biomarkers for PTC development and prognosis.
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Affiliation(s)
- Jing Wang
- Department of Endocrinology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Department of Pathology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Minxiang Lei
- Department of Endocrinology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, Hunan, China
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