1
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Zhang J, Xu S. High aggressiveness of papillary thyroid cancer: from clinical evidence to regulatory cellular networks. Cell Death Discov 2024; 10:378. [PMID: 39187514 PMCID: PMC11347646 DOI: 10.1038/s41420-024-02157-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 08/28/2024] Open
Abstract
The global incidence of thyroid cancer has increased over recent decades. Papillary thyroid cancer (PTC) is the most common type of thyroid cancer and accounts for nearly 90% of all cases. Typically, PTC has a good prognosis. However, some PTC variants exhibit more aggressive behaviour, which significantly increases the risk of postoperative recurrence. Over the past decade, the high metastatic potential of PTC has drawn the attention of many researchers and these studies have provided useful molecular markers for improved diagnosis, risk stratification and clinical approaches. The aim of this review is to discuss the progress in epidemiology, metastatic features, risk factors and molecular mechanisms associated with PTC aggressiveness. We present a detailed picture showing that epithelial-to-mesenchymal transition, cancer metabolic reprogramming, alterations in important signalling pathways, epigenetic aberrations and the tumour microenvironment are crucial drivers of PTC metastasis. Further research is needed to more fully elucidate the pathogenesis and biological behaviour underlying the aggressiveness of PTC.
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Affiliation(s)
- Junsi Zhang
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Sunwang Xu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
- Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
- Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Fuzhou, China.
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2
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Xu D, Lai Y, Liu H, Li H, Feng N, Liu Y, Gong C, Zhang Y, Zhou J, Shen Y. A diagnostic model based on DNA methylation haplotype block characteristics for identifying papillary thyroid carcinoma from thyroid adenoma. Transl Res 2024; 264:76-84. [PMID: 37863284 DOI: 10.1016/j.trsl.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Papillary thyroid carcinoma (PTC) is the most prevalent form of thyroid cancer. Methylation of some genes plays a crucial role in the tendency to malignancy as well as poor prognosis of thyroid cancer, suggesting that methylation features can serve as complementary markers for molecular diagnosis. In this study, we aimed to develop and validate a diagnostic model for PTC based on DNA methylation markers. A total of 142 thyroid nodule tissue samples containing 84 cases of PTC and 58 cases of thyroid adenoma (TA) were collected for reduced representation bisulfite sequencing (RRBS) and subsequent analysis. The diagnostic model was constructed by the logistic regression (LR) method followed by 5-cross validation and based on 94 tissue methylation haplotype block (MHB) markers. The model achieved an area under the receiver operating characteristic curve (AUROC) of 0.974 (95% CI, 0.964-0.981) on 108 training samples and 0.917 (95% CI, 0.864-0.973) on 27 independent testing samples. The diagnostic model scores showed significantly high in males (P = 0.0016), age ≤ 45 years (P = 0.026), high body mass index (BMI) (P = 0.040), lymph node metastasis (P = 0.00052) and larger nodules (P = 0.0017) in the PTC group, and the risk score of this diagnostic model showed significantly high in recurrent PTC group (P = 0.0005). These results suggest that the diagnostic model can be expected to be a powerful tool for PTC diagnosis and there are more potential clinical applications of methylation markers to be excavated.
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Affiliation(s)
- Dong Xu
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China
| | - Yi Lai
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China; Department of Traditional Chinese Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China
| | - Hongmei Liu
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - He Li
- Department of Traditional Chinese Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China
| | - Ningning Feng
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Yiying Liu
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Chengxiang Gong
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Yunzhi Zhang
- Singlera Genomics (Shanghai) Ltd., 8th Floor, Building 1, Lane 500, Furonghua Road, Pudong, Shanghai 201328, China
| | - Jiaqing Zhou
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China.
| | - Yuling Shen
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 160 Pujian Road, Shanghai, 200127, China.
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3
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Zhang X, Zhong Y, Liu L, Jia C, Cai H, Yang J, Wu B, Lv Z. Fasting regulates mitochondrial function through lncRNA PRKCQ-AS1-mediated IGF2BPs in papillary thyroid carcinoma. Cell Death Dis 2023; 14:827. [PMID: 38092752 PMCID: PMC10719255 DOI: 10.1038/s41419-023-06348-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 11/01/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Recurring evidence suggests that fasting has extensive antitumor effects in various cancers, including papillary thyroid carcinoma (PTC). However, the underlying mechanism of this relationship with PTC is unknown. In this study, we study the effect of fasting on glycolysis and mitochondrial function in PTC. We find that fasting impairs glycolysis and reduces mitochondrial dysfunction in vitro and in vivo and also fasting in vitro and fasting mimicking diets (FMD) in vivo significantly increase the expression of lncRNA-protein kinase C theta antisense RNA 1 (PRKCQ-AS1), during the inhibition of TPC cell glycolysis and mitochondrial function. Moreover, lncRNA PRKCQ-AS1 was significantly lower in PTC tissues and cells. In addition, PRKCQ-AS1 overexpression increased PTC cell glycolysis and mitochondrial function; PRKCQ-AS1 knockdown has the opposite effect. On further mechanistic analysis, we identified that PRKCQ-AS1 physically interacts with IGF2BPs and enhances protein arginine methyltransferases 7 (PRMT7) mRNA, which is the key player in regulating glycolysis and mitochondrial function in PTC. Hence, PRKCQ-AS1 inhibits tumor growth while regulating glycolysis and mitochondrial functions via IGF2BPs/PRMT7 signaling. These results indicate that lncRNA PRKCQ-AS1 is a key downstream target of fasting and is involved in PTC metabolic reprogramming. Further, the PRKCQ-AS1/IGF2BPs/PRMT7 axis is an ideal therapeutic target for PTC diagnosis and treatment.
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Affiliation(s)
- Xiaoping Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai hospital Affiliated with Jinan University, Jinan University, 519000, Guangdong, China.
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China.
| | - Yong Zhong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Lin Liu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Chengyou Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Haidong Cai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Jianshe Yang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Bo Wu
- Center of Thyroid, Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 200233, Shanghai, China.
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China.
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4
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Bhattacharya S, Mahato RK, Singh S, Bhatti GK, Mastana SS, Bhatti JS. Advances and challenges in thyroid cancer: The interplay of genetic modulators, targeted therapies, and AI-driven approaches. Life Sci 2023; 332:122110. [PMID: 37734434 DOI: 10.1016/j.lfs.2023.122110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Thyroid cancer continues to exhibit a rising incidence globally, predominantly affecting women. Despite stable mortality rates, the unique characteristics of thyroid carcinoma warrant a distinct approach. Differentiated thyroid cancer, comprising most cases, is effectively managed through standard treatments such as thyroidectomy and radioiodine therapy. However, rarer variants, including anaplastic thyroid carcinoma, necessitate specialized interventions, often employing targeted therapies. Although these drugs focus on symptom management, they are not curative. This review delves into the fundamental modulators of thyroid cancers, encompassing genetic, epigenetic, and non-coding RNA factors while exploring their intricate interplay and influence. Epigenetic modifications directly affect the expression of causal genes, while long non-coding RNAs impact the function and expression of micro-RNAs, culminating in tumorigenesis. Additionally, this article provides a concise overview of the advantages and disadvantages associated with pharmacological and non-pharmacological therapeutic interventions in thyroid cancer. Furthermore, with technological advancements, integrating modern software and computing into healthcare and medical practices has become increasingly prevalent. Artificial intelligence and machine learning techniques hold the potential to predict treatment outcomes, analyze data, and develop personalized therapeutic approaches catering to patient specificity. In thyroid cancer, cutting-edge machine learning and deep learning technologies analyze factors such as ultrasonography results for tumor textures and biopsy samples from fine needle aspirations, paving the way for a more accurate and effective therapeutic landscape in the near future.
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Affiliation(s)
- Srinjan Bhattacharya
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Rahul Kumar Mahato
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Satwinder Singh
- Department of Computer Science and Technology, Central University of Punjab, Bathinda 151401, Punjab, India.
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India
| | - Sarabjit Singh Mastana
- School of Sport, Exercise and Health Sciences, Loughborough University, Epinal Way, Leicestershire, Loughborough LE11 3TU, UK.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151401, Punjab, India.
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5
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Marczyk VR, Recamonde-Mendoza M, Maia AL, Goemann IM. Classification of Thyroid Tumors Based on DNA Methylation Patterns. Thyroid 2023; 33:1090-1099. [PMID: 37392021 DOI: 10.1089/thy.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Background: Alterations in DNA methylation are stable epigenetic events that can serve as clinical biomarkers. The aim of this study was to analyze methylation patterns among various follicular cell-derived thyroid neoplasms to identify disease subtypes and help understand and classify thyroid tumors. Methods: We employed an unsupervised machine learning method for class discovery to search for distinct methylation patterns among various thyroid neoplasms. Our algorithm was not provided with any clinical or pathological information, relying exclusively on DNA methylation data to classify samples. We analyzed 810 thyroid samples (n = 256 for discovery and n = 554 for validation), including benign and malignant tumors, as well as normal thyroid tissue. Results: Our unsupervised algorithm identified that samples could be classified into three subtypes based solely on their methylation profile. These methylation subtypes were strongly associated with histological diagnosis (p < 0.001) and were therefore named normal-like, follicular-like, and papillary thyroid carcinoma (PTC)-like. Follicular adenomas, follicular carcinomas, oncocytic adenomas, and oncocytic carcinomas clustered together forming the follicular-like methylation subtype. Conversely, classic papillary thyroid carcinomas (cPTC) and tall cell PTC clustered together forming the PTC-like subtype. These methylation subtypes were also strongly associated with genomic drivers: 98.7% BRAFV600E-driven cancers were PTC like, whereas 96.0% RAS-driven cancers had a follicular-like methylation pattern. Interestingly, unlike other diagnoses, follicular variant PTC (FVPTC) samples were split into two methylation clusters (follicular like and PTC like), indicating a heterogeneous group likely to be formed by two distinct diseases. FVPTC samples with a follicular-like methylation pattern were enriched for RAS mutations (36.4% vs. 8.0%; p < 0.001), whereas FVPTC- with PTC-like methylation patterns were enriched for BRAFV600E mutations (52.0% vs. 0%, Fisher exact p = 0.004) and RET fusions (16.0% vs. 0%, Fisher exact p = 0.003). Conclusions: Our data provide novel insights into the epigenetic alterations of thyroid tumors. Since our classification method relies on a fully unsupervised machine learning approach for subtype discovery, our results offer a robust background to support the classification of thyroid neoplasms based on methylation patterns.
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Affiliation(s)
- Vicente Rodrigues Marczyk
- Thyroid Unit, Endocrine Division, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Medical School, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Ana Luiza Maia
- Thyroid Unit, Endocrine Division, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Medical School, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Iuri Martin Goemann
- Thyroid Unit, Endocrine Division, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Medical School, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Medical School, Universidade do Vale do Rio dos Sinos (UNISINOS), Porto Alegre, Brazil
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6
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Zhao F, Zhu S, Fang J, Dong H, Zhu C. Correlation of DNA methylation and lymph node metastasis in papillary thyroid carcinoma. Head Neck 2023. [PMID: 37097909 DOI: 10.1002/hed.27377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/11/2023] [Accepted: 04/09/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer with a primarily good prognosis, and its 10-year survival rate is over 90%. However, PTC is prone to early lymph node metastasis. METHODS Thyroid cancer tissues from PTC patients with lymphatic metastasis and normal tissues were collected for DNA methylation analysis. Different methylation sites, different methylation regions, gene-enriched pathways, and protein-protein interactions (PPIs) were analyzed. RESULTS There were 1004 differentially methylated sites in the PTC group versus the control group; these involved 479 hypermethylated sites in 415 related genes, 525 hypomethylated sites in 482 related genes, 64 differentially methylated regions located in the CpG island region, 34 differentially methylated genes closely related to thyroid cancer, and 17 genes with differentially methylated genes in the DNA promoter region. CONCLUSION NDRG4 hypermethylation and FOXO3, ZEB2, and CDK6 hypomethylation were associated with PTC lymph node metastasis.
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Affiliation(s)
- Feng Zhao
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siyi Zhu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Fang
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huilei Dong
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Chenfang Zhu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Jasmine F, Aschebrook-Kilfoy B, Rahman MM, Zaagman G, Grogan RH, Kamal M, Ahsan H, Kibriya MG. Association of DNA Promoter Methylation and BRAF Mutation in Thyroid Cancer. Curr Oncol 2023; 30:2978-2996. [PMID: 36975440 PMCID: PMC10047424 DOI: 10.3390/curroncol30030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The BRAF V600E mutation and DNA promoter methylation play important roles in the pathogenesis of thyroid cancer (TC). However, the association of these genetic and epigenetic alterations is not clear. In this study, using paired tumor and surrounding normal tissue from the same patients, on a genome-wide scale we tried to identify (a) any association between BRAF mutation and DNA promoter methylation, and (b) if the molecular findings may provide a basis for therapeutic intervention. We included 40 patients with TC (female = 28, male = 12) without distant metastasis. BRAF mutation was present in 18 cases. We identified groups of differentially methylated loci (DML) that are found in (a) both BRAF mutant and wild type, (b) only in BRAF mutant tumors, and (c) only in BRAF wild type. BRAF mutation-specific promoter loci were more frequently hypomethylated, whereas BRAF wild-type-specific loci were more frequently hypermethylated. Common DML were enriched in cancer-related pathways, including the mismatch repair pathway and Wnt-signaling pathway. Wild-type-specific DML were enriched in RAS signaling. Methylation status of checkpoint signaling genes, as well as the T-cell inflamed genes, indicated an opportunity for the potential use of PDL1 inhibitors in BRAF mutant TC. Our study shows an association between BRAF mutation and methylation in TC that may have biological significance.
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Affiliation(s)
- Farzana Jasmine
- Institute for Population and Precision Health, Biological Sciences, University of Chicago, Chicago, IL 60637, USA
- Correspondence:
| | - Briseis Aschebrook-Kilfoy
- Institute for Population and Precision Health, Biological Sciences, University of Chicago, Chicago, IL 60637, USA
- Department of Public Health Science, University of Chicago, Chicago, IL 60637, USA
| | - Mohammad M. Rahman
- Department of Pathology, Bangabandhu Sheikh Mujib Medical University, Dhaka 1000, Bangladesh
| | - Garrett Zaagman
- Institute for Population and Precision Health, Biological Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Raymon H. Grogan
- Department of Surgery, Baylor St. Luke’s Medical Center, Houston, TX 77030, USA
| | - Mohammed Kamal
- Department of Pathology, The Laboratory, Dhaka 1205, Bangladesh
| | - Habibul Ahsan
- Institute for Population and Precision Health, Biological Sciences, University of Chicago, Chicago, IL 60637, USA
- Department of Public Health Science, University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G. Kibriya
- Institute for Population and Precision Health, Biological Sciences, University of Chicago, Chicago, IL 60637, USA
- Department of Public Health Science, University of Chicago, Chicago, IL 60637, USA
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8
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Acuña-Ruiz A, Carrasco-López C, Santisteban P. Genomic and epigenomic profile of thyroid cancer. Best Pract Res Clin Endocrinol Metab 2023; 37:101656. [PMID: 35461756 DOI: 10.1016/j.beem.2022.101656] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thyroid cancer is the most common malignancy of the endocrine system, and its incidence has been steadily increasing. Advances in sequencing have allowed analysis of the entire cancer genome, and has provided new information on the genetic lesions and modifications responsible for the onset, progression, dedifferentiation and metastasis of thyroid carcinomas. Moreover, integrated genomics has advanced our understanding of the development of cancer and its behavior, and has facilitated the identification of new genetic mutations and molecular pathways. The functional analysis of epigenetic modifications, such as DNA methylation, histone acetylation and non-coding RNAs, have contributed to define new regulatory mechanisms that control cell malignancy in thyroid cancer, especially aggressive forms. Here we review the most recent advances in genomics and epigenomics of thyroid cancer, which have resulted in a new classification and interpretation of the initiation and progression of thyroid tumors, providing new tools and opportunities for further investigation and for the clinical development of new treatment strategies.
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Affiliation(s)
- Adrián Acuña-Ruiz
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain.
| | - Carlos Carrasco-López
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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9
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Yi JW, Ha SY, Jee HG, Kim K, Kim SJ, Chai YJ, Choi JY, Lee KE. Induction of BRAF<sup>V600E</sup> Mutation in Thyroid Cells Leads to Frequent Hypermethylation. Clin Exp Otorhinolaryngol 2022; 15:273-282. [PMID: 35538718 PMCID: PMC9441509 DOI: 10.21053/ceo.2022.00206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
Objectives. The BRAFV600E mutation is a major driver mutation in papillary thyroid cancer. The aim of this study was to elucidate the correlation between DNA methylation and gene expression changes induced by the BRAFV600E mutation in thyroid cells. Methods. We used Nthy/BRAF cell lines generated by transfection of Nthy/ori cells with the wild-type BRAF gene (Nthy/WT cells) and the V600E mutant-type BRAF gene (Nthy/V600E cells). We performed gene expression microarray and DNA methylation array analyses for Nthy/WT and Nthy/V600E cells. Two types of array data were integrated to identify inverse correlations between methylation and gene expression. The results were verified in silico using data from The Cancer Genome Atlas (TCGA) and in vivo through pyrosequencing and quantitative real-time polymerase chain reaction (qRT-PCR). Results. In the Nthy/V600E cells, 199,821 probes were significantly hypermethylated, and 697 genes showed a “hypermethylation-downregulation” pattern in Nthy/V600E. Tumor suppressor genes and apoptosis-related genes were included. In total, 66,446 probes were significantly hypomethylated, and 227 genes showed a “hypomethylation-upregulation” pattern in Nthy/V600E cells. Protooncogenes and developmental protein-coding genes were included. In the TCGA analysis, 491/697 (70.44%) genes showed a hypermethylation-downregulation pattern, and 153/227 (67.40%) genes showed a hypomethylation-upregulation pattern. Ten selected genes showed a similar methylation-gene expression pattern in pyrosequencing and qRT-PCR. Conclusion. Induction of the BRAFV600E mutation in thyroid cells led to frequent hypermethylation. Anticancer genes, such as those involved in tumor suppression or apoptosis, were downregulated by upstream hypermethylation, whereas carcinogenic genes, such as protooncogenes, were upregulated by hypomethylation. Our results suggest that the BRAFV600E mutation in thyroid cells modulates DNA methylation and results in cancer-related gene expression.
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10
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Chen Z, Liu X, Liu F, Zhang G, Tu H, Lin W, Lin H. Identification of 4-methylation driven genes based prognostic signature in thyroid cancer: an integrative analysis based on the methylmix algorithm. Aging (Albany NY) 2021; 13:20164-20178. [PMID: 34456184 PMCID: PMC8436924 DOI: 10.18632/aging.203338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/01/2021] [Indexed: 12/09/2022]
Abstract
Thyroid cancer (TC) is known with a high rate of persistence and recurrence. We aimed to develop a prognostic signature to monitor and assess the survival of TC patients. mRNA expression and methylation data were downloaded from the TCGA database. Then, R package methylmix was applied to construct a mixed model was used to identify methylation-driven genes (MDGs) according to the methylation levels. Furthermore, an MDGs based prognostic signature and predictive nomogram were constructed according to the analysis of univariate and multivariate Cox regression. Totally 62 methylation-driven genes that were mainly enriched in substrate-dependent cell migration, cellular response to mechanical stimulus, et al. were found in TC tissues. aldolase C (AldoC), C14orf62, dishevelled 1 (DVL1), and protein tyrosine phosphatase receptor type C (PTPRC) were identified to be significantly related to patients' survival, and may serve as independent prognostic biomarkers for TC. Additionally, the prognostic methylation signature and a novel prognostic, predictive nomogram was established based on the methylation level of 4 MDGs. In this study, we developed a 4-MDGs based prognostic model, which might be the potential predictors for the survival rate of TC patients, and this findings might provide a novel sight for accurate monitoring and prognosis assessment.
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Affiliation(s)
- Zhiwei Chen
- Department of Pathology, The Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Xiaoli Liu
- Department of Pathology, The Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Fangfang Liu
- Department of Pathology, The Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Guolie Zhang
- Department of Thyroid Surgery, The Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Haijian Tu
- Clinical Laboratory, The Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Wei Lin
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Haifeng Lin
- Department of Gastroenterology, The Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
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11
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Thyroid Cancer Stem-Like Cells: From Microenvironmental Niches to Therapeutic Strategies. J Clin Med 2021; 10:jcm10071455. [PMID: 33916320 PMCID: PMC8037626 DOI: 10.3390/jcm10071455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/08/2023] Open
Abstract
Thyroid cancer (TC) is the most common endocrine malignancy. Recent progress in thyroid cancer biology revealed a certain degree of intratumoral heterogeneity, highlighting the coexistence of cellular subpopulations with distinct proliferative capacities and differentiation abilities. Among those subpopulations, cancer stem-like cells (CSCs) are hypothesized to drive TC heterogeneity, contributing to its metastatic potential and therapy resistance. CSCs principally exist in tumor areas with specific microenvironmental conditions, the so-called stem cell niches. In particular, in thyroid cancer, CSCs' survival is enhanced in the hypoxic niche, the immune niche, and some areas with specific extracellular matrix composition. In this review, we summarize the current knowledge about thyroid CSCs, the tumoral niches that allow their survival, and the implications for TC therapy.
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12
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Han R, Sun W, Huang J, Shao L, Zhang H. Sex-biased DNA methylation in papillary thyroid cancer. Biomark Med 2021; 15:109-120. [PMID: 33464123 DOI: 10.2217/bmm-2020-0215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Women have a higher risk of developing papillary thyroid cancer (PTC) than men. DNA methylation is known to differ between men and women. Materials & methods: Using the human methylation 450 BeadChip and RNA-sequence, we profiled the genome-wide DNA methylation patterns of papillary thyroid carcinoma patients and para-carcinoma tissue. Results: We first identified 398 different expression genes (DEGs) between males and females PTC. Then we analyzed the relationship between differentially methylated positions (DMPs) and DEGs at gene promoter regions and identified 39 genes and explored DMP-DEGs' correlation with immune cell infiltration and tumor purity. We also analyzed the relationship between genomic regions and enhancers. Conclusion: Our study identified 39 DMP-DEGs providing some new insights into the mechanisms of methylation-mediated gender differences in PTC.
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Affiliation(s)
- Rui Han
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China 110001
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China 110001
| | - Jiapeng Huang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China 110001
| | - Liang Shao
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China 110001
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, China 110001
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13
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Pitto L, Gorini F, Bianchi F, Guzzolino E. New Insights into Mechanisms of Endocrine-Disrupting Chemicals in Thyroid Diseases: The Epigenetic Way. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17217787. [PMID: 33114343 PMCID: PMC7662297 DOI: 10.3390/ijerph17217787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 12/26/2022]
Abstract
In recent years, the presence in the environment of chemical compounds with thyroid-disrupting effects is progressively increased. This phenomenon has risen concern for human health as the preservation of thyroid system homeostasis is essential for fetal development and for maintaining psychological and physiological wellbeing. An increasing number of studies explored the role of different classes of toxicants in the occurrence and severity of thyroid diseases, but large epidemiological studies are limited and only a few animal or in vitro studies have attempted to identify the mechanisms of chemical action. Recently, epigenetic changes such as alteration of methylation status or modification of non-coding RNAs have been suggested as correlated to possible deleterious effects leading to different thyroid disorders in susceptible individuals. This review aims to analyze the epigenetic alterations putatively induced by chemical exposures and involved in the onset of frequent thyroid diseases such as thyroid cancer, autoimmune thyroiditis and disruption of fetal thyroid homeostasis.
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Affiliation(s)
- Letizia Pitto
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (F.G.); (F.B.); (E.G.)
- Correspondence: ; Tel.: + 39-050-3153090
| | - Francesca Gorini
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (F.G.); (F.B.); (E.G.)
| | - Fabrizio Bianchi
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (F.G.); (F.B.); (E.G.)
| | - Elena Guzzolino
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy; (F.G.); (F.B.); (E.G.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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14
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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15
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Tan J, Liu L, Zuo Z, Song B, Cai T, Ding D, Lu Y, Ye X. Overexpression of novel long intergenic non‑coding RNA LINC02454 is associated with a poor prognosis in papillary thyroid cancer. Oncol Rep 2020; 44:1489-1501. [PMID: 32945494 PMCID: PMC7448410 DOI: 10.3892/or.2020.7712] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/04/2020] [Indexed: 12/16/2022] Open
Abstract
It has been revealed from microarray data analysis that long intergenic non-coding RNA 02454 (LINC02454) is highly expressed in papillary thyroid cancer (PTC). The aim of the present study was to explore the potential role of LINC02454 in the tumorigenesis of PTC. The mRNA expression levels of LINC02454 were assessed using data from The Cancer Genome Atlas (TCGA) and the GSE66783 cohort in thyroid cancer, and were validated using reverse transcription-quantitative PCR in 104 patients with PTC recruited in the present study. The association between the LINC02454 mRNA expression levels and the clinicopathological features of the 104 patients with PTC were also analyzed. Functional enrichment analyses were conducted on the differentially expressed genes in the high and low LINC02454 expression groups that were identified from the TCGA cohort. RNA interference, using short interfering (si)RNA against LINC02454, was used to investigate the role of LINC02454 in the biological functions of PTC cells in vitro. The expression level of LINC02454 was significantly increased in PTC tissues (P=0.0011) and was significantly associated with a larger tumor size, T stage, an advanced TNM stage and an increased lymph node metastasis (P<0.05), which was consistent with that in the TCGA and GSE66783 cohort. High expression levels of LINC02454 were observed in patients with PTC that also had BRAF mutations (P<0.001), and were significantly associated with a poorer disease-free survival in the TCGA cohort (P<0.05). Functional enrichment analysis indicated that LINC02454-related genes were significantly enriched in Gene Ontology terms, such as ‘positive regulation of cell proliferation’, ‘positive regulation of cell division’ and ‘cell adhesion’, and the following Kyoto Encyclopedia of Genes and Genomes pathways: ‘Pathways in cancer’ ‘proteoglycans in cancer’ and ‘ECM-receptor interaction’. In vitro, the knockdown of LINC02454 markedly arrested the cells in the G0/G1 phase of the cell cycle, and also led to an overall increase in apoptosis, as well as to an unexpected decrease in cell proliferation. LINC02454 may thus potentially function as an oncogene, which inhibits the apoptosis and enhances proliferation of PTC cells. Thus, as suggested by the findings of the present study, LINC02454 may be used as a diagnostic and prognostic biomarker for PTC in the future.
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Affiliation(s)
- Juan Tan
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, P.R. China
| | - Ling Liu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, P.R. China
| | - Zhihua Zuo
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, P.R. China
| | - Bin Song
- Department of Endocrinology, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Tingting Cai
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, P.R. China
| | - Dafa Ding
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, P.R. China
| | - Yibing Lu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, P.R. China
| | - Xiaolong Ye
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, P.R. China
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16
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Vos LD, Dietrich J, Strieth S, Bootz F, Dietrich D, Franzen A. PD-1, CTLA4, PD-L1 and PD-L2 DNA methylation in papillary thyroid carcinoma. Immunotherapy 2020; 12:903-920. [DOI: 10.2217/imt-2020-0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: We investigated DNA methylation patterns of immune checkpoint genes PD-1, PD-L1, PD-L2, CTLA4 and an adjacent long noncoding RNA in papillary thyroid carcinoma (PTC). Materials & methods: DNA methylation and mRNA expression were examined in PTCs. DNA methylation was correlated with mRNA expression, BRAF and RAS mutational status, and immune cell infiltration. Results: Inverse correlations between DNA methylation and mRNA expression were observed. Immune checkpoint expression correlated positively, and DNA methylation negatively, with immune cell infiltration. Higher DNA methylation levels accompanied by lower immune checkpoint expression were observed in RAS-mutated tumors. Conclusion: We suggest epigenetic regulation of immune checkpoints in PTC. Methylation was associated with BRAF and RAS mutation status. DNA methylation might be a promising biomarker candidate in the context of immunotherapies in PTC.
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Affiliation(s)
- Luka de Vos
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
- Department of Dermatology & Allergy, University Hospital Bonn, 53127 Bonn, Germany
| | - Jörn Dietrich
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Friedrich Bootz
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Dimo Dietrich
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Alina Franzen
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
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17
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Veschi V, Verona F, Lo Iacono M, D'Accardo C, Porcelli G, Turdo A, Gaggianesi M, Forte S, Giuffrida D, Memeo L, Todaro M. Cancer Stem Cells in Thyroid Tumors: From the Origin to Metastasis. Front Endocrinol (Lausanne) 2020; 11:566. [PMID: 32982967 PMCID: PMC7477072 DOI: 10.3389/fendo.2020.00566] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Thyroid tumors are extremely heterogeneous varying from almost benign tumors with good prognosis as papillary or follicular tumors, to the undifferentiated ones with severe prognosis. Recently, several models of thyroid carcinogenesis have been described, mostly hypothesizing a major role of the thyroid cancer stem cell (TCSC) population in both cancer initiation and metastasis formation. However, the cellular origin of TCSC is still incompletely understood. Here, we review the principal epigenetic mechanisms relevant to TCSC origin and maintenance in both well-differentiated and anaplastic thyroid tumors. Specifically, we describe the alterations in DNA methylation, histone modifiers, and microRNAs (miRNAs) involved in TCSC survival, focusing on the potential of targeting aberrant epigenetic modifications for developing novel therapeutic approaches. Moreover, we discuss the bidirectional relationship between TCSCs and immune cells. The cells of innate and adaptive response can promote the TCSC-driven tumorigenesis, and conversely, TCSCs may favor the expansion of immune cells with protumorigenic functions. Finally, we evaluate the role of the tumor microenvironment and the complex cross-talk of chemokines, hormones, and cytokines in regulating thyroid tumor initiation, progression, and therapy refractoriness. The re-education of the stromal cells can be an effective strategy to fight thyroid cancer. Dissecting the genetic and epigenetic landscape of TCSCs and their interactions with tumor microenvironment cells is urgently needed to select more appropriate treatment and improve the outcome of patients affected by advanced differentiated and undifferentiated thyroid cancers.
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Affiliation(s)
- Veronica Veschi
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Francesco Verona
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Melania Lo Iacono
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Caterina D'Accardo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Gaetana Porcelli
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Alice Turdo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Miriam Gaggianesi
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Stefano Forte
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | - Dario Giuffrida
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | - Matilde Todaro
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
- *Correspondence: Matilde Todaro
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18
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Boufraqech M, Nilubol N. Multi-omics Signatures and Translational Potential to Improve Thyroid Cancer Patient Outcome. Cancers (Basel) 2019; 11:E1988. [PMID: 31835496 PMCID: PMC6966476 DOI: 10.3390/cancers11121988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023] Open
Abstract
Recent advances in high-throughput molecular and multi-omics technologies have improved our understanding of the molecular changes associated with thyroid cancer initiation and progression. The translation into clinical use based on molecular profiling of thyroid tumors has allowed a significant improvement in patient risk stratification and in the identification of targeted therapies, and thereby better personalized disease management and outcome. This review compiles the following: (1) the major molecular alterations of the genome, epigenome, transcriptome, proteome, and metabolome found in all subtypes of thyroid cancer, thus demonstrating the complexity of these tumors and (2) the great translational potential of multi-omics studies to improve patient outcome.
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Affiliation(s)
| | - Naris Nilubol
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA;
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19
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Botezatu A, Iancu IV, Plesa A, Manda D, Popa O, Bostan M, Mihaila M, Albulescu A, Fudulu A, Vladoiu SV, Huica I, Dobrescu R, Anton G, Badiu C. Methylation of tumour suppressor genes associated with thyroid cancer. Cancer Biomark 2019; 25:53-65. [PMID: 31006665 DOI: 10.3233/cbm-182265] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Thyroid carcinoma is the most common endocrine malignancy worldwide. Changes in DNA methylation can cause silencing of normally active genes, especially tumour suppressor genes (TSG) or activation of normally silent genes. OBJECTIVE The aim of this study is to evaluate the degree of promoter methylation for a panel of markers for thyroid neoplasms and to establish their relationship with thyroid oncogenesis. METHODS To generate a comprehensive DNA methylation signature of TSGs involved in thyroid neoplasia, we use Human TSG EpiTect Methyl II Signature PCR Array-Qiagen for 24 samples (follicular adenomas and papillary thyroid carcinomas) compared with normal thyroid tissue. We extended the evaluation for three TSGs (TP73, WIF1, PDLIM4) using qMS-PCR. Statistical analysis was performed with GraphPad Prism. RESULTS We noted four important genes NEUROG1, ESR1, RUNX3, MLH1, which presented methylated promoter in tumour samples compared to normal. We found new characteristic of thyroid tumours: methylation of TP73, WIF1 and PDLIM4 TSGs, which can contribute to thyroid neoplasia. A significant correlation between BRAF V600E mutation and RET/PTC rearrangements with TIMP3 and CDH13, RARB methylation, respectively was observed. CONCLUSIONS TSGs promoter hypermethylation is a hallmark of cancer and a test that uses methylation quantification method is suitable for diagnosis and prognosis of thyroid cancer.
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Affiliation(s)
- Anca Botezatu
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Iulia V Iancu
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Adriana Plesa
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Dana Manda
- 'CI Parhon' National Institute of Endocrinology, Bucharest, Romania
| | - Oana Popa
- 'CI Parhon' National Institute of Endocrinology, Bucharest, Romania
| | - Marinela Bostan
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Mirela Mihaila
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Adrian Albulescu
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania.,National Institute for Chemical pharmaceutical Research and Development, Calea Vitan, Romania
| | - Alina Fudulu
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Susana V Vladoiu
- 'CI Parhon' National Institute of Endocrinology, Bucharest, Romania
| | - Irina Huica
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Ruxandra Dobrescu
- 'CI Parhon' National Institute of Endocrinology, Bucharest, Romania.,'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania
| | - Gabriela Anton
- 'Stefan S. Nicolau' Institute of Virology, Bucharest, Romania
| | - Corin Badiu
- 'CI Parhon' National Institute of Endocrinology, Bucharest, Romania.,'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania
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20
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Shakiba E, Movahedi M, Majd A, Hedayati M. Investigating the expression and promoter methylation of RET gene in patients with medullary thyroid cancer with unmutated RET. J Cell Physiol 2019; 234:16304-16311. [PMID: 30873628 DOI: 10.1002/jcp.28295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/02/2018] [Accepted: 12/07/2018] [Indexed: 01/24/2023]
Abstract
OBJECTIVE Thyroid cancer is one of the most common endocrine malignancies. Mutations in the rearranged during transfection (RET) gene, especially in exon 10, 11, and 16, as well as epigenetic modifications, constitute the major underlying molecular events leading to medullary thyroid cancer (MTC). There are few studies on the mutations and epigenetic changes of RET gene in Iranian patients with MTC. In the present study, we aimed to address this question and explore the clinical relevance of such genetic alternations in an Iranian population. METHODS Thirty-three patients with confirmed MTC who underwent thyroidectomy surgery in Imam Khomeini Hospital (Tehran, Iran) were enrolled. DNA extracted from cancerous tissues was amplified by polymerase chain reaction (PCR) and then was sequenced for identification of RET mutations. In patients with no identified mutations, the methylation status of RET promoter and its expression were further investigated using methylation-specific PCR and real-time PCR methods, respectively. RESULTS In MTC patients with no RET mutations, the promoter of the proto-oncogene was hypomethylated. Furthermore, RET gene expression was elevated in patients who revealed no mutations in neither of exon 10, 11, or 16 of the RET gene. CONCLUSION Hypomethylation of RET promoter may contribute to MTC pathogenesis. The methylation status of RET promoter could be a new potential prognostic, diagnostic and therapeutic marker in MTC.
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Affiliation(s)
- Elham Shakiba
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Monireh Movahedi
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ahmad Majd
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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21
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Wang M, Zhang K, Ngo V, Liu C, Fan S, Whitaker JW, Chen Y, Ai R, Chen Z, Wang J, Zheng L, Wang W. Identification of DNA motifs that regulate DNA methylation. Nucleic Acids Res 2019; 47:6753-6768. [PMID: 31334813 PMCID: PMC6649826 DOI: 10.1093/nar/gkz483] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/14/2019] [Accepted: 06/20/2019] [Indexed: 01/11/2023] Open
Abstract
DNA methylation is an important epigenetic mark but how its locus-specificity is decided in relation to DNA sequence is not fully understood. Here, we have analyzed 34 diverse whole-genome bisulfite sequencing datasets in human and identified 313 motifs, including 92 and 221 associated with methylation (methylation motifs, MMs) and unmethylation (unmethylation motifs, UMs), respectively. The functionality of these motifs is supported by multiple lines of evidence. First, the methylation levels at the MM and UM motifs are respectively higher and lower than the genomic background. Second, these motifs are enriched at the binding sites of methylation modifying enzymes including DNMT3A and TET1, indicating their possible roles of recruiting these enzymes. Third, these motifs significantly overlap with "somatic QTLs" (quantitative trait loci) of methylation and expression. Fourth, disruption of these motifs by mutation is associated with significantly altered methylation level of the CpGs in the neighbor regions. Furthermore, these motifs together with somatic mutations are predictive of cancer subtypes and patient survival. We revealed some of these motifs were also associated with histone modifications, suggesting a possible interplay between the two types of epigenetic modifications. We also found some motifs form feed forward loops to contribute to DNA methylation dynamics.
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Affiliation(s)
- Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Kai Zhang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Vu Ngo
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Chengyu Liu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Shicai Fan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - John W Whitaker
- Department of Genomics, Denovo Biopharma, 10240 Science Center Dr., San Diego, CA, USA
| | - Yue Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Rizi Ai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Zhao Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jun Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Lina Zheng
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Wei Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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22
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Gómez-Pérez AM, Cornejo Pareja IM, García Alemán J, Coín Aragüez L, Sebastián Ochoa A, Alcaide Torres J, Molina Vega M, Clu Fernández C, Mancha Doblas I, Tinahones FJ. New molecular biomarkers in differentiated thyroid carcinoma: Impact of miR-146, miR-221 and miR-222 levels in the evolution of the disease. Clin Endocrinol (Oxf) 2019; 91:187-194. [PMID: 30887564 DOI: 10.1111/cen.13972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/30/2023]
Abstract
OBJECTIVE MircroRNAs (miR) are small, noncoding RNA molecules of 18-25 nucleotides. Their dysregulation has been widely studied in many human tumours including differentiated thyroid cancer (DTC). miRs more frequently associated with these kinds of tumours are miR-146, miR-221 and miR-222. Our objective was to assess the relationship among circulating miR levels and the evolution and outcomes of disease. DESIGN We analysed a sample of 60 patients with DTC assigning them to one of three groups according to the dynamic scale of risk (excellent response, incomplete biochemical response and incomplete structural response). PATIENTS AND MEASUREMENTS At study inclusion, we determined thyroid-stimulating hormone, thyroxine, thyroglobulin, antithyroglobulin antibodies and plasma levels of miR-146, miR-221 and miR-222. RESULTS Male sex and advanced age at diagnosis were associated with the worst disease progression. miR-222 was twofold to threefold higher in tall cell papillary carcinomas (P = 0.038). miR-146 (P = 0.016) and miR-221 (P = 0.050) had a positive correlation with thyroglobulin at the time of sampling. In regression analysis, miR-146 (P = 0.006), miR-221 (P = 0.004) and miR-222 (P = 0.007) predicted more than 70% of the variation in thyroglobulin levels at the time of sampling. CONCLUSIONS Elevated miR-222 and miR-146 levels are associated with poorer outcomes of the disease and may have a prognostic value in the management and follow-up of DTC.
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Affiliation(s)
- Ana María Gómez-Pérez
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Isabel María Cornejo Pareja
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Jorge García Alemán
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Leticia Coín Aragüez
- Biomedical Research Institue (IBIMA), Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Arantzazu Sebastián Ochoa
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Juan Alcaide Torres
- Biomedical Research Institue (IBIMA), Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - María Molina Vega
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Carlos Clu Fernández
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Isabel Mancha Doblas
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
| | - Francisco J Tinahones
- Endocrinology and Nutrition Unit, Virgen de la Victoria University Hospital, Campus Universitario Teatinos SN, Málaga, Spain
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Zafon C, Gil J, Pérez-González B, Jordà M. DNA methylation in thyroid cancer. Endocr Relat Cancer 2019; 26:R415-R439. [PMID: 31035251 DOI: 10.1530/erc-19-0093] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
In recent years, cancer genomics has provided new insights into genetic alterations and signaling pathways involved in thyroid cancer. However, the picture of the molecular landscape is not yet complete. DNA methylation, the most widely studied epigenetic mechanism, is altered in thyroid cancer. Recent technological advances have allowed the identification of novel differentially methylated regions, methylation signatures and potential biomarkers. However, despite recent progress in cataloging methylation alterations in thyroid cancer, many questions remain unanswered. The aim of this review is to comprehensively examine the current knowledge on DNA methylation in thyroid cancer and discuss its potential clinical applications. After providing a general overview of DNA methylation and its dysregulation in cancer, we carefully describe the aberrant methylation changes in thyroid cancer and relate them to methylation patterns, global hypomethylation and gene-specific alterations. We hope this review helps to accelerate the use of the diagnostic, prognostic and therapeutic potential of DNA methylation for the benefit of thyroid cancer patients.
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Affiliation(s)
- Carles Zafon
- Diabetes and Metabolism Research Unit (VHIR) and Department of Endocrinology, University Hospital Vall d'Hebron and Autonomous University of Barcelona, Barcelona, Spain
- Consortium for the Study of Thyroid Cancer (CECaT), Catalonia, Spain
| | - Joan Gil
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
| | - Beatriz Pérez-González
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
| | - Mireia Jordà
- Consortium for the Study of Thyroid Cancer (CECaT), Catalonia, Spain
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
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24
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Affinito O, Salerno P, D'Alessio A, Cuomo M, Florio E, Carlomagno F, Proietti A, Giannini R, Basolo F, Chiariotti L, Cocozza S, Santoro M. Association between DNA methylation profile and malignancy in follicular-patterned thyroid neoplasms. Endocr Relat Cancer 2019; 26:451-462. [PMID: 30753136 DOI: 10.1530/erc-18-0308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/11/2019] [Indexed: 01/03/2023]
Abstract
Molecular differentiation between benign (follicular thyroid adenoma, FTA) and malignant (follicular thyroid carcinoma, FTC) thyroid neoplasms is challenging. Here, we explored the genome-wide DNA methylation profile of FTA (n.10) and FTC (n.11) compared to normal thyroid (NT) (n.7) tissues. FTC featured 3,564 differentially-methylated CpGs (DMCpG), most (84%) of them hypermethylated, with respect to normal controls. At the principal component analysis (PCA), the methylation profile of FTA occupied an intermediate position between FTC and normal tissue. A large fraction (n. 2,385) of FTC-associated DMCpG were related (intragenic or within 1500 bp from the transcription start site) to annotated genes (n. 1,786). FTC-hypermethylated genes were enriched for targets of the Polycomb transcriptional repressor complex and the specific histone H3 marks (H3K4me2/me3-H3K27me3) found in chromatin domains known as "bivalent". Transcriptome profiling by RNAseq showed that 7.9% of the DMCpGs-associated genes were differentially expressed in FTC compared to NT, suggesting that altered DNA methylation may contribute to their altered expression. Overall, this study suggests that perturbed DNA methylation, in particular hypermethylation, is a component of the molecular mechanisms leading to the formation of FTC and that DNA methylation profiling may help differentiating FTCs from their benign counterpart.
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Affiliation(s)
- Ornella Affinito
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
| | - Paolo Salerno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
| | - Alfonso D'Alessio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
| | - Mariella Cuomo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
| | - Ermanno Florio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale, Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Agnese Proietti
- Division of Anatomical Pathology, University Hospital of Pisa (AO-UP), Pisa, Italy
| | - Riccardo Giannini
- Department of Surgical, Medical, Molecular Pathology and Critical Area (Anatomical Pathology Section), University of Pisa, Pisa, Italy
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area (Anatomical Pathology Section), University of Pisa, Pisa, Italy
| | - Lorenzo Chiariotti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale, Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Sergio Cocozza
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy
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Valvo V, Nucera C. Coding Molecular Determinants of Thyroid Cancer Development and Progression. Endocrinol Metab Clin North Am 2019; 48:37-59. [PMID: 30717910 PMCID: PMC6366338 DOI: 10.1016/j.ecl.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Thyroid cancer is the most common endocrine malignancy. Its incidence and mortality rates have increased for patients with advanced-stage papillary thyroid cancer. The characterization of the molecular pathways essential in thyroid cancer initiation and progression has made huge progress, underlining the role of intracellular signaling to promote clonal evolution, dedifferentiation, metastasis, and drug resistance. The discovery of genetic alterations that include mutations (BRAF, hTERT), translocations, deletions (eg, 9p), and copy-number gain (eg, 1q) has provided new biological insights with clinical applications. Understanding how molecular pathways interplay is one of the key strategies to develop new therapeutic treatments and improve prognosis.
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Affiliation(s)
- Veronica Valvo
- Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Experimental Pathology, Department of Pathology, Cancer Research Institute (CRI), Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA; Department of Pathology, Center for Vascular Biology Research (CVBR), Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA
| | - Carmelo Nucera
- Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Experimental Pathology, Department of Pathology, Cancer Research Institute (CRI), Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA; Department of Pathology, Center for Vascular Biology Research (CVBR), Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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26
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Zhao Y, Zhong L, Yi H. A review on the mechanism of iodide metabolic dysfunction in differentiated thyroid cancer. Mol Cell Endocrinol 2019; 479:71-77. [PMID: 30287400 DOI: 10.1016/j.mce.2018.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/27/2022]
Abstract
The incidence of differentiated thyroid cancer (DTC) has been increasing rapidly worldwide, and the risk factors remain unclear. With the growing number of patients with DTC, the related issues have been gradually highlighted. 131Iodide (131I) is an important treatment for DTC and has the potential to reduce the risk of recurrence. 131I is also an effective treatment for distant metastases of thyroid carcinoma. However, iodide metabolism dysfunction in metastatic foci causes patients to lose the opportunity of 131I treatment. This article reviews the related mechanisms of iodide metabolism dysfunction in DTC cells and summarizes the clinical transformation progression.
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Affiliation(s)
- Yinlong Zhao
- Department of Nuclear Medicine, Second Hospital of Jilin University, Changchun, Jilin Province, 130041, PR China.
| | - Lili Zhong
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, Second Hospital of Jilin University, Changchun, 130041, PR China.
| | - Heqing Yi
- Department of Nuclear Medicine, Zhejiang Cancer Hospital, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang, 310021, PR China.
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27
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Zarkesh M, Zadeh-Vakili A, Azizi F, Foroughi F, Akhavan MM, Hedayati M. Altered Epigenetic Mechanisms in Thyroid Cancer Subtypes. Mol Diagn Ther 2018; 22:41-56. [PMID: 28986854 DOI: 10.1007/s40291-017-0303-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Thyroid carcinoma (TC) is the most frequent malignant neoplasm of the endocrine system. Molecular methods for diagnosis of invasive thyroid disease can be effectively adopted. Epigenetic factors play an important role in the diversity patterns of gene expression and the phenotypic and biological characteristics of TC subtypes. We aimed to review epigenetic changes in the main subtypes of TC, along with a presentation of the methods that have examined these changes, and active clinical trials for the treatment of advanced TCs targeting epigenetic changes. A literature analysis was performed in MEDLINE using PubMed, Elsevier, and Google Scholar for studies published up to 2016, using the keywords: "Epigenetic alterations" OR "Epigenetic changes", "thyroid cancers", "papillary thyroid cancer", "medullary thyroid cancer", "follicular thyroid cancer", and "anaplastic thyroid cancer", which resulted in 310 articles in English. All related abstracts were reviewed and studies were included that were published in English, had available full text, and determined the details of the methods and materials associated with the epigenetic patterns of TC and its subtypes (100 articles). Analysis of epigenetic alterations in TC subtypes helps to identify pathogenesis and can play an important role in the classification and diagnosis of tumors. Epigenetic mechanisms, especially aberrant methylation of DNA and microRNAs (miRs), are likely to play an important role in thyroid tumorigenesis. Further studies are required to elucidate the role of histone modification mechanisms in TC development.
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Affiliation(s)
- Maryam Zarkesh
- Cellular and Molecular Endocrine Research Center (CMERC), Research Institute for Endocrine Sciences of Shahid Beheshti University of Medical Sciences, 19395-4763, Tehran, Iran
| | - Azita Zadeh-Vakili
- Cellular and Molecular Endocrine Research Center (CMERC), Research Institute for Endocrine Sciences of Shahid Beheshti University of Medical Sciences, 19395-4763, Tehran, Iran.
| | - Fereidoun Azizi
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Forough Foroughi
- Department of Pathology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maziar Mohammad Akhavan
- Skin Research Center School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center (CMERC), Research Institute for Endocrine Sciences of Shahid Beheshti University of Medical Sciences, 19395-4763, Tehran, Iran.
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28
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Yim JH, Choi AH, Li AX, Qin H, Chang S, Tong SWT, Chu P, Kim BW, Schmolze D, Lew R, Ibrahim Y, Poroyko VA, Salvatierra S, Baker A, Wang J, Wu X, Pfeifer GP, Fong Y, Hahn MA. Identification of Tissue-Specific DNA Methylation Signatures for Thyroid Nodule Diagnostics. Clin Cancer Res 2018; 25:544-551. [PMID: 30093451 DOI: 10.1158/1078-0432.ccr-18-0841] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/01/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022]
Abstract
PURPOSE Thyroid cancer is frequently difficult to diagnose due to an overlap of cytologic features between malignant and benign nodules. This overlap leads to unnecessary removal of the thyroid in patients without cancer. While providing some improvement over cytopathologic diagnostics, molecular methods frequently fail to provide a correct diagnosis for thyroid nodules. These approaches are based on the difference between cancer and adjacent thyroid tissue and assume that adjacent tissues are the same as benign nodules. However, in contrast to adjacent tissues, benign thyroid nodules can contain genetic alterations that can be found in cancer.Experimental Design: For the development of a new molecular diagnostic test for thyroid cancer, we evaluated DNA methylation in 109 thyroid tissues by using genome-wide single-base resolution DNA methylation analysis. The test was validated in a retrospective cohort containing 65 thyroid nodules. RESULTS By conducting reduced representation bisulfite sequencing in 109 thyroid specimens, we found significant differences between adjacent tissue, benign nodules, and cancer. These tissue-specific signatures are strongly linked to active enhancers and cancer-associated genes. Based on these signatures, we developed a new epigenetic approach for thyroid diagnostics. According to the validation cohort, our test has an estimated specificity of 97% [95% confidence interval (CI), 81-100], sensitivity of 100% (95% CI, 87-100), positive predictive value of 97% (95% CI, 83-100), and negative predictive value of 100% (95% CI, 86-100). CONCLUSIONS These data show that epigenetic testing can provide outstanding diagnostic accuracy for thyroid nodules.See related commentary by Mitmaker et al., p. 457.
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Affiliation(s)
- John H Yim
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California.
| | - Audrey H Choi
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Arthur X Li
- Department of Information Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Hanjun Qin
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| | - Sue Chang
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Sun-Wing T Tong
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Peiguo Chu
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Byung-Wook Kim
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Ryan Lew
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Yasmine Ibrahim
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Valeriy A Poroyko
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Sylvana Salvatierra
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Alysha Baker
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Jinhui Wang
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan
| | - Yuman Fong
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Maria A Hahn
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California.
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Tan J, Qian X, Song B, An X, Cai T, Zuo Z, Ding D, Lu Y, Li H. Integrated bioinformatics analysis reveals that the expression of cathepsin S is associated with lymph node metastasis and poor prognosis in papillary thyroid cancer. Oncol Rep 2018; 40:111-122. [PMID: 29749483 PMCID: PMC6059735 DOI: 10.3892/or.2018.6428] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/26/2018] [Indexed: 12/20/2022] Open
Abstract
The prognosis of the majority of patients with papillary thyroid cancer (PTC) is excellent, although there are patients who experience disease recurrence and progression. The aim of the present study was to identify potential prognostic risk markers in PTC. Differentially expressed genes (DEGs), identified from four Genome Expression Omnibus cohorts were subjected to functional enrichment analyses with Gene Ontology terms and the Kyoto Encyclopedia of Genes and Genome pathways. Hub genes, filtered from cytoHubba, were validated using the The Cancer Genome Atlas (TCGA) cohort, and their associations with clinicopathological features and prognosis were analyzed. A total of 277 DEGs were identified following data preprocessing. DEGs were primarily enriched in 'small cell lung cancer', 'ECM-receptor interaction', 'pathways in cancer'and 'tyrosine metabolism'. Hub genes [APOE, cathepsin S (CTSS), insulin receptor substrate 1 (IRS1), KIT, LGALS3, RUNX2 and TGFBR1] were extracted from cytoHubba. Their expression in the TCGA cohort was consistent with that in the GEO cohorts. CTSS (P=0.006) and IRS1 (P=0.005) were associated with disease‑free survival, as determined using the Kaplan-Meier analysis. CTSS was an independent risk factor for poor disease‑free survival (HR, 2.649; 95% CI, 1.095-6.409; P=0.031). Patients with high expression of CTSS exhibited different histological types (increased tall-cell subtype and reduced follicular subtype; P<0.001), more frequent lymph node metastasis (P<0.001) and advanced tumor-node-metastasis stages (P=0.049) compared with the low-expression group. High expression of CTSS was independently associated with lymph node metastasis (OR, 2.015; 95% CI, 1.225-3.315; P=0.006). Therefore, CTSS may serve as a predictive risk marker for the progression and prognosis of PTC.
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Affiliation(s)
- Juan Tan
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
- Department of Gerontology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, P.R. China
| | - Xiaoxiao Qian
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Bin Song
- Department of Endocrinology, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Xiumin An
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Tingting Cai
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Zhihua Zuo
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Dafa Ding
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Yibing Lu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Hong Li
- Medical Examination Center, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, P.R. China
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NKX2.5 is expressed in papillary thyroid carcinomas and regulates differentiation in thyroid cells. BMC Cancer 2018; 18:498. [PMID: 29716526 PMCID: PMC5930850 DOI: 10.1186/s12885-018-4399-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND NKX2.5 is a transcription factor transiently expressed during thyroid organogenesis. Recently, several works have pointed out the oncogenic role of NKX2.5 in a variety of tumors. We therefore hypothesized that NKX2.5 could also play a role in thyroid cancer. METHODS The validation of NKX2.5 expression was assessed by immunohistochemistry analysis in a Brazilian case series of 10 papillary thyroid carcinoma (PTC) patients. Then, the long-term prognostic value of NKX2.5 and its correlation with clinicopathologic features of 51 PTC patients was evaluated in a cohort with 10-years follow-up (1990-1999). Besides, the effect of NKX2.5 overexpression on thyroid differentiation markers and function was also investigated in a non-tumor thyroid cell line (PCCL3). RESULTS NKX2.5 was shown to be expressed in most PTC samples (8/10, case series; 27/51, cohort). Patients who had tumors expressing NKX2.5 showed lower rates of persistence/recurrence (p = 0.013). Overexpression of NKX2.5 in PCCL3 cells led to: 1) downregulation of thyroid differentiation markers (thyrotropin receptor, thyroperoxidase and sodium-iodide symporter); 2) reduced iodide uptake; 3) increased extracellular H2O2 generation, dual oxidase 1 mRNA levels and activity of DuOx1 promoter. CONCLUSIONS In summary, NKX2.5 is expressed in most PTC samples analyzed and its presence correlates to better prognosis of PTC. In vitro, NKX2.5 overexpression reduces the expression of thyroid differentiation markers and increases ROS production. Thus, our data suggests that NKX2.5 could play a role in thyroid carcinogenesis.
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31
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Buj R, Mallona I, Díez-Villanueva A, Zafon C, Mate JL, Roca M, Puig-Domingo M, Reverter JL, Mauricio D, Peinado MA, Jordà M. Kallikreins Stepwise Scoring Reveals Three Subtypes of Papillary Thyroid Cancer with Prognostic Implications. Thyroid 2018; 28:601-612. [PMID: 29635968 DOI: 10.1089/thy.2017.0501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most common type of thyroid cancer. Unlike most cancers, its incidence has dramatically increased in the last decades mainly due to increased diagnosis of indolent PTCs. Adequate risk stratification is crucial to avoid the over-treatment of low-risk patients, as well as the under-treatment of high-risk patients, but the currently available markers are still insufficient. Kallikreins (KLKs) are emergent biomarkers in cancer, but their involvement in PTC is unknown. METHODS This study analyzed DNA methylation (HumanMethylation arrays) and gene expression (RNA-Seq) of KLKs, BRAF and RAS mutations, and clinical data from four published thyroid cancer data sets including normal and tumor tissues (n = 73, n = 475, n = 20, and n = 82) as discovery, training, and validation series. The C4.5 classification algorithm was used to generate a decision tree. Disease-free survival was estimated using Kaplan-Meier and Cox approaches. Specific analyses were performed using real-time polymerase chain reaction and immunohistochemistry. RESULTS The entire KLK family was deregulated in PTC, displaying a specific epigenetic and transcriptional profile strongly associated with BRAFV600E or RAS mutations. Thus, a decision-tree algorithm was developed based on three KLKs with >80% sensitivity and >95% specificity, identifying BRAF- and RAS-mutated tumors. Notably, tumors lacking these mutations were classified as BRAF- or RAS-like. Most importantly, the KLK algorithm uncovered a novel PTC subtype showing favorable prognostic features. CONCLUSIONS The KLK algorithm could lead to a new clinically applicable strategy with important implications for the risk stratification of PTC and the management of patients.
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Affiliation(s)
- Raquel Buj
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
| | - Izaskun Mallona
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
| | - Anna Díez-Villanueva
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
| | - Carles Zafon
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 3 Diabetes and Metabolism Research Unit (VHIR) and Department of Endocrinology, University Hospital Vall d'Hebron and Autonomous University of Barcelona , Barcelona, Spain
- 4 Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases (CIBERDEM), Institute of Health Carlos III (ISCIII) , Madrid, Spain
| | - José L Mate
- 5 Department of Pathology, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
| | - Mireia Roca
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
| | - Manel Puig-Domingo
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 4 Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases (CIBERDEM), Institute of Health Carlos III (ISCIII) , Madrid, Spain
- 6 Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
- 7 Biomedical Research Networking Center in Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII) , Madrid, Spain
| | - Jordi L Reverter
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 6 Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
| | - Dídac Mauricio
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 4 Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases (CIBERDEM), Institute of Health Carlos III (ISCIII) , Madrid, Spain
- 6 Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
| | - Miguel A Peinado
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
| | - Mireia Jordà
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 7 Biomedical Research Networking Center in Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII) , Madrid, Spain
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32
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Klein Hesselink EN, Zafon C, Villalmanzo N, Iglesias C, van Hemel BM, Klein Hesselink MS, Montero-Conde C, Buj R, Mauricio D, Peinado MA, Puig-Domingo M, Riesco-Eizaguirre G, Reverter JL, Robledo M, Links TP, Jordà M. Increased Global DNA Hypomethylation in Distant Metastatic and Dedifferentiated Thyroid Cancer. J Clin Endocrinol Metab 2018; 103:397-406. [PMID: 29165662 DOI: 10.1210/jc.2017-01613] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022]
Abstract
CONTEXT Global DNA hypomethylation is a major event for the development and progression of cancer, although the significance in thyroid cancer remains unclear. Therefore, we aimed to investigate its role in thyroid cancer progression and its potential as a prognostic marker. METHODS Global hypomethylation of Alu repeats was used as a surrogate marker for DNA global hypomethylation, and was assessed using the Quantification of Unmethylated Alu technique. Mutations in BRAF and RAS were determined by Sanger sequencing. RESULTS Ninety primary thyroid tumors were included [28 low-risk differentiated thyroid cancer (DTC), 13 pediatric DTC, 33 distant metastatic DTC, 7 poorly differentiated thyroid cancer (PDTC), and 9 anaplastic thyroid cancer (ATC)], as well as 24 distant metastases and 20 normal thyroid tissues. An increasing hypomethylation was found for distant metastatic DTC [median, 4.0; interquartile range (IQR), 3.1 to 6.2] and PDTC/ATC (median, 9.3; IQR, 7.0 to 12.1) as compared with normal thyroid tissue (median, 2.75; IQR, 2.30 to 3.15), whereas low-risk and pediatric DTC were not affected by hypomethylation. Alu hypomethylation was similar between distant metastases and matched primary tumors. Within distant metastatic DTC, Alu hypomethylation was increased in BRAF vs RAS mutated tumors. Kaplan-Meier and Cox regression analyses showed that thyroid cancer-related and all-cause mortality were associated with tumor hypomethylation, but this association was lost after adjustment for thyroid cancer risk category. CONCLUSION Distant metastatic DTC, PDTC, and ATC were increasingly affected by global Alu hypomethylation, suggesting that this epigenetic entity may be involved in thyroid cancer progression and dedifferentiation.
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Affiliation(s)
- Esther N Klein Hesselink
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Carles Zafon
- Diabetes and Metabolism Research Unit, Vall d'Hebron University Hospital, Barcelona, Spain
- Department of Endocrinology, Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
- Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
| | - Núria Villalmanzo
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
| | - Carmela Iglesias
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Pathology, Vall D'Hebron University Hospital, Barcelona, Spain
| | - Bettien M van Hemel
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mariëlle S Klein Hesselink
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Raquel Buj
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
| | - Dídac Mauricio
- Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital, Badalona, Spain
| | - Miguel A Peinado
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
| | - Manel Puig-Domingo
- Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital, Badalona, Spain
- Biomedical Research Networking Center in Rare Diseases, CIBERER, Institute of Health Carlos III, Madrid, Spain
| | - Garcilaso Riesco-Eizaguirre
- Department of Endocrinology and Nutrition, Hospital Universitario de Móstoles, Madrid, Spain
- Biomedical Research Networking Center in Oncology, CIBERONC, Institute of Health Carlos III, Madrid, Spain
| | - Jordi L Reverter
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital, Badalona, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center, Madrid, Spain
- Biomedical Research Networking Center in Rare Diseases, CIBERER, Institute of Health Carlos III, Madrid, Spain
| | - Thera P Links
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mireia Jordà
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
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Niu H, Yang J, Yang K, Huang Y. The relationship between RASSF1A promoter methylation and thyroid carcinoma: A meta-analysis of 14 articles and a bioinformatics of 2 databases (PRISMA). Medicine (Baltimore) 2017; 96:e8630. [PMID: 29145283 PMCID: PMC5704828 DOI: 10.1097/md.0000000000008630] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA promoter methylation can suppresses gene expression and shows an important role in the biological functions of Ras association domain family 1A (RASSF1A). Many studies have performed to elucidate the role of RASSF1A promoter methylation in thyroid carcinoma, while the results were conflicting and heterogeneous. Here, we analyzed the data of databases to determine the relationship between RASSF1A promoter methylation and thyroid carcinoma. METHODS We used the data from 14 cancer-normal studies and Gene Expression Omnibus (GEO) database to analyze RASSF1A promoter methylation in thyroid carcinoma susceptibility. The data from the Cancer Genome Atlas project (TCGA) database was used to analyze the relationship between RASSF1A promoter methylation and thyroid carcinoma susceptibility, clinical characteristics, prognosis. Odds ratios were estimated for thyroid carcinoma susceptibility and hazard ratios were estimated for thyroid carcinoma prognosis. The heterogeneity between studies of meta-analysis was explored using H, I values, and meta-regression. We adopted quality criteria to classify the studies of meta-analysis. Subgroup analyses were done for thyroid carcinoma susceptibility according to ethnicity, methods, and primers. RESULTS Result of meta-analysis indicated that RASSF1A promoter methylation is associated with higher susceptibility to thyroid carcinoma with small heterogeneity. Similarly, the result from GEO database also showed that a significant association between RASSF1A gene promoter methylation and thyroid carcinoma susceptibility. For the results of TCGA database, we found that RASSF1A promoter methylation is associated with susceptibility and poor disease-free survival (DFS) of thyroid carcinoma. In addition, we also found a close association between RASSF1A promoter methylation and patient tumor stage and age, but not in patients of different genders. CONCLUSIONS The methylation status of RASSF1A promoter is strongly associated with thyroid carcinoma susceptibility and DFS. The RASSF1A promoter methylation test can be applied in the clinical diagnosis of thyroid carcinoma.
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Affiliation(s)
- Heng Niu
- Chest Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan
| | - Jingyu Yang
- Chest Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan
| | - Kunxian Yang
- Chest Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan
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Bisarro dos Reis M, Barros-Filho MC, Marchi FA, Beltrami CM, Kuasne H, Pinto CAL, Ambatipudi S, Herceg Z, Kowalski LP, Rogatto SR. Prognostic Classifier Based on Genome-Wide DNA Methylation Profiling in Well-Differentiated Thyroid Tumors. J Clin Endocrinol Metab 2017; 102:4089-4099. [PMID: 28938489 PMCID: PMC5673278 DOI: 10.1210/jc.2017-00881] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/11/2017] [Indexed: 12/15/2022]
Abstract
Context Even though the majority of well-differentiated thyroid carcinoma (WDTC) is indolent, a number of cases display an aggressive behavior. Cumulative evidence suggests that the deregulation of DNA methylation has the potential to point out molecular markers associated with worse prognosis. Objective To identify a prognostic epigenetic signature in thyroid cancer. Design Genome-wide DNA methylation assays (450k platform, Illumina) were performed in a cohort of 50 nonneoplastic thyroid tissues (NTs), 17 benign thyroid lesions (BTLs), and 74 thyroid carcinomas (60 papillary, 8 follicular, 2 Hürthle cell, 1 poorly differentiated, and 3 anaplastic). A prognostic classifier for WDTC was developed via diagonal linear discriminant analysis. The results were compared with The Cancer Genome Atlas (TCGA) database. Results A specific epigenetic profile was detected according to each histological subtype. BTLs and follicular carcinomas showed a greater number of methylated CpG in comparison with NTs, whereas hypomethylation was predominant in papillary and undifferentiated carcinomas. A prognostic classifier based on 21 DNA methylation probes was able to predict poor outcome in patients with WDTC (sensitivity 63%, specificity 92% for internal data; sensitivity 64%, specificity 88% for TCGA data). High-risk score based on the classifier was considered an independent factor of poor outcome (Cox regression, P < 0.001). Conclusions The methylation profile of thyroid lesions exhibited a specific signature according to the histological subtype. A meaningful algorithm composed of 21 probes was capable of predicting the recurrence in WDTC.
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Affiliation(s)
- Mariana Bisarro dos Reis
- International Research Center, CIPE, A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics, São Paulo 01509-010, SP, Brazil
- Department of Urology, Faculty of Medicine, UNESP, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Mateus Camargo Barros-Filho
- International Research Center, CIPE, A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics, São Paulo 01509-010, SP, Brazil
| | - Fábio Albuquerque Marchi
- International Research Center, CIPE, A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics, São Paulo 01509-010, SP, Brazil
| | - Caroline Moraes Beltrami
- International Research Center, CIPE, A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics, São Paulo 01509-010, SP, Brazil
| | - Hellen Kuasne
- International Research Center, CIPE, A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics, São Paulo 01509-010, SP, Brazil
| | | | - Srikant Ambatipudi
- Epigenetics Group; International Agency for Research on Cancer (IARC), Lyon 69372, France
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, United Kingdom
| | - Zdenko Herceg
- Epigenetics Group; International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C. Camargo Cancer Center, São Paulo 01509-010, SP, Brazil
| | - Silvia Regina Rogatto
- Department of Urology, Faculty of Medicine, UNESP, São Paulo State University, Botucatu 18618-970, SP, Brazil
- Department of Clinical Genetics, Vejle Hospital and Institute of Regional Health Research, University of Southern Denmark, Vejle, 7100, Denmark
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Jin Y, Jin W, Zheng Z, Chen E, Wang Q, Wang Y, Wang O, Zhang X. GABRB2 plays an important role in the lymph node metastasis of papillary thyroid cancer. Biochem Biophys Res Commun 2017; 492:323-330. [PMID: 28859983 DOI: 10.1016/j.bbrc.2017.08.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 08/27/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Thyroid cancer is a common malignant tumor of the endocrine system. Its incidence has increased continuously worldwide for the past three decades. With advanced sequencing technology, we discovered that GABRB2 gene is overexpressed in tumor tissues and closely associated with vertebrate nervous systems. However, its role in cancer remains unclear. METHODS We conducted a massively parallel whole transcriptome resequencing and a comprehensive analysis of matched papillary thyroid carcinoma (PTC) tumors and normal tissues in 19 patients. Results showed that GABRB2 expression was significantly upregulated in thyroid cancer. Forty-five pairs of tumors and normal tissues were subjected to reverse transcription polymerase chain reaction to validate previous findings. The specific functions of GABRB2 in PTC cell lines (BCPAP, TPC1, and KTC-1) transfected with small interfering RNA were determined through cell colony formation, Cell Counting Kit-8, Transwell migration, Transwell invasion, and apoptosis assays. The effect of DNA demethylation on this gene was also examined. RESULTS GABRB2 was remarkably overexpressed in primarily sequenced PTC tumors and validation cohort (T: N = 4.94 ± 3.43:0.83 ± 1.71, P < 0.001), and this observation was consistent with that in the TCGA cohort (T: N = 38.92 ± 35.53:0.30 ± 0.55, P < 0.001). GABRB2 overexpression was correlated with lymph node metastasis in both cohorts (P < 0.01). In vitro experiments revealed that GABRB2 downregulation significantly inhibited the colony formation, migration, and invasion of the three PTC cell lines. CONCLUSION GABRB2 plays important tumorigenic functions and acts as a novel oncogene in PTC.
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Affiliation(s)
- Yixiang Jin
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Wenxu Jin
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhouci Zheng
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Endong Chen
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qingxuan Wang
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yinghao Wang
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ouchen Wang
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaohua Zhang
- Departments of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Neary JL, Perez SM, Peterson K, Lodge DJ, Carless MA. Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia. Genomics 2017; 109:204-213. [PMID: 28365388 PMCID: PMC5526217 DOI: 10.1016/j.ygeno.2017.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/14/2017] [Accepted: 03/26/2017] [Indexed: 12/11/2022]
Abstract
We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene expression changes using a pooled sample approach. MBD-seq and MeDIP-seq identified 769 and 1771 differentially methylated regions (DMRs) between F2 offspring of MAM-exposed rats and saline control rats, respectively. The assays showed good concordance, with ~56% of MBD-seq-detected DMRs being identified by or proximal to MeDIP-seq DMRs. There was no significant overlap between DMRs and differentially expressed genes, suggesting that DNA methylation regulatory effects may act upon more distal genes, or are too subtle to detect using our approach. Methylation and gene expression gene ontology enrichment analyses identified biological processes important to schizophrenia pathophysiology, including neuron differentiation, prepulse inhibition, amphetamine response, and glutamatergic synaptic transmission regulation, reinforcing the utility of the MAM rodent model for schizophrenia research.
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Affiliation(s)
- Jennifer L Neary
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
| | - Stephanie M Perez
- Department of Pharmacology, Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Kara Peterson
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
| | - Daniel J Lodge
- Department of Pharmacology, Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Melanie A Carless
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
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Kotian S, Zhang L, Boufraqech M, Gaskins K, Gara SK, Quezado M, Nilubol N, Kebebew E. Dual Inhibition of HDAC and Tyrosine Kinase Signaling Pathways with CUDC-907 Inhibits Thyroid Cancer Growth and Metastases. Clin Cancer Res 2017; 23:5044-5054. [PMID: 28600475 DOI: 10.1158/1078-0432.ccr-17-1043] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/08/2017] [Accepted: 06/05/2017] [Indexed: 12/18/2022]
Abstract
Purpose: There is currently no standard therapy for anaplastic thyroid cancer (ATC) and poorly differentiated thyroid cancer (PDTC), which account for two-thirds of thyroid cancer-related deaths. Driver mutations in the PI3K/AKT and RAF/RAS/MEK/ERK pathways are common in ATC and PDTC. Histone deacetylases (HDAC) regulate cancer initiation and progression. Our aim was to determine the therapeutic efficacy of simultaneously targeting these pathways in thyroid cancer with a single agent and to evaluate biomarkers of treatment response.Experimental Design: CUDC-907 is a first-in-class compound, functioning as a dual inhibitor of HDACs and the PI3K/AKT pathway. We investigated its antiproliferative effect in vitro and in vivoResults: CUDC-907 significantly inhibited cellular proliferation in thyroid cancer cell lines, induced G2-M arrest with decreased levels of the checkpoint regulators cyclin B1, AURKA, AURKB, PLK1, and increased p21 and p27. Treatment induced apoptosis with increased caspase-3/7 activity and decreased survivin levels and decreased cellular migration and invasion. CUDC-907 treatment caused H3 hyperacetylation and decreased HDAC2 expression. HDAC2 was upregulated in ATC and other thyroid cancer histologic subtypes. CUDC-907 treatment reduced both p-AKT and p-ERK1/2 levels. Finally, CUDC-907 treatment, in a metastatic mouse model of thyroid cancer, showed significant inhibition of growth and metastases, and tumors from treated mice had decreased HDAC2 expression, suggesting that this may be a useful biomarker of response.Conclusions: Dual inhibition of HDAC and the tyrosine kinase signaling pathways with CUDC-907 is a promising treatment strategy for advanced, metastatic thyroid cancer. Clin Cancer Res; 23(17); 5044-54. ©2017 AACR.
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Affiliation(s)
- Shweta Kotian
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Lisa Zhang
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Myriem Boufraqech
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Kelli Gaskins
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sudheer Kumar Gara
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Naris Nilubol
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Electron Kebebew
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland. .,Department of Surgery, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia
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Penha RCC, Lima SCS, Boroni M, Ramalho-Oliveira R, Viola JP, de Carvalho DP, Fusco A, Pinto LFR. Intrinsic LINE-1 Hypomethylation and Decreased Brca1 Expression are Associated with DNA Repair Delay in Irradiated Thyroid Cells. Radiat Res 2017; 188:144-155. [PMID: 28574327 DOI: 10.1667/rr14532.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Exposure to ionizing radiation greatly increases the risk of developing papillary thyroid carcinoma (PTC), especially during childhood, mainly due to gradual inactivation of DNA repair genes and DNA damages. Recent molecular characterization of PTC revealed DNA methylation deregulation of several promoters of DNA repair genes. Thus, epigenetic silencing might be a plausible mechanism for the activity loss of tumor suppressor genes in radiation-induced thyroid tumors. Herein, we investigated the impact of ionizing radiation on global methylation and CpG islands within promoter regions of homologous recombination (HR) and non-homologous end joining (NHEJ) genes, as well as its effects on gene expression, using two well-established normal differentiated thyroid cell lines (FRTL5 and PCCL3). Our data reveal that X-ray exposure promoted G2/M arrest in normal thyroid cell lines. The FRTL5 cells displayed a slower kinetics of double-strand breaks (DSB) repair and a lower long interspersed nuclear element-1 (LINE-1) methylation than the PCCL3 cells. Nevertheless, acute X-ray exposure does not alter the expression of genes involved in HR and NHEJ pathways, apart from the downregulation of Brca1 in thyroid cells. On the other hand, HR and NHEJ gene expressions were upregulated in radiation-induced senescent thyroid cells. Taken together, these data suggest that FRTL5 cells intrinsically have less efficient DNA DSB repair machinery than PCCL3 cells, as well as genomic instability, which could predispose the FRTL5 cells to unrepaired DSB lesions and, therefore, gene mutations.
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Affiliation(s)
| | | | - Mariana Boroni
- a Instituto Nacional de Câncer - INCA, Rio de Janeiro, Brazil
| | | | - João P Viola
- a Instituto Nacional de Câncer - INCA, Rio de Janeiro, Brazil
| | - Denise Pires de Carvalho
- c Instituto de Biofisica Carlos Chagas Filho - CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alfredo Fusco
- a Instituto Nacional de Câncer - INCA, Rio de Janeiro, Brazil.,b Istituto di Endocrinologia ed Oncologia Sperimentale - CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
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Beltrami CM, dos Reis MB, Barros-Filho MC, Marchi FA, Kuasne H, Pinto CAL, Ambatipudi S, Herceg Z, Kowalski LP, Rogatto SR. Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas. Clin Epigenetics 2017; 9:45. [PMID: 28469731 PMCID: PMC5414166 DOI: 10.1186/s13148-017-0346-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/14/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is a common endocrine neoplasm with a recent increase in incidence in many countries. Although PTC has been explored by gene expression and DNA methylation studies, the regulatory mechanisms of the methylation on the gene expression was poorly clarified. In this study, DNA methylation profile (Illumina HumanMethylation 450K) of 41 PTC paired with non-neoplastic adjacent tissues (NT) was carried out to identify and contribute to the elucidation of the role of novel genic and intergenic regions beyond those described in the promoter and CpG islands (CGI). An integrative and cross-validation analysis were performed aiming to identify molecular drivers and pathways that are PTC-related. RESULTS The comparisons between PTC and NT revealed 4995 methylated probes (88% hypomethylated in PTC) and 1446 differentially expressed transcripts cross-validated by the The Cancer Genome Atlas data. The majority of these probes was found in non-promoters regions, distant from CGI and enriched by enhancers. The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes (mainly in the promoter and body regions, respectively) with negative and positive correlation, respectively. Genes showing negative correlation underlined FGF and retinoic acid signaling as critical canonical pathways disrupted by DNA methylation in PTC. BRAF mutation was detected in 68% (28 of 41) of the tumors, which presented a higher level of demethylation (95% hypomethylated probes) compared with BRAF wild-type tumors. A similar integrative analysis uncovered 40 of 254 differentially expressed genes, which are potentially regulated by DNA methylation in BRAFV600E-positive tumors. The methylation and expression pattern of six selected genes (ERBB3, FGF1, FGFR2, GABRB2, HMGA2, and RDH5) were confirmed as altered by pyrosequencing and RT-qPCR. CONCLUSIONS DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC, especially in tumors harboring BRAFV600E. In addition to the promoter region, gene body and 3'UTR methylation have also the potential to influence the gene expression levels (both, repressing and inducing). The integrative analysis revealed genes potentially regulated by DNA methylation pointing out potential drivers and biomarkers related to PTC development.
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Affiliation(s)
- Caroline Moraes Beltrami
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
| | - Mariana Bisarro dos Reis
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
- Department of Urology, Faculty of Medicine, UNESP, Sao Paulo State University, Botucatu, São Paulo Brazil
| | - Mateus Camargo Barros-Filho
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
| | - Fabio Albuquerque Marchi
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
| | - Hellen Kuasne
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
- Department of Urology, Faculty of Medicine, UNESP, Sao Paulo State University, Botucatu, São Paulo Brazil
| | | | - Srikant Ambatipudi
- Epigenetics Group; International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group; International Agency for Research on Cancer (IARC), Lyon, France
| | - Luiz Paulo Kowalski
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
- Department of Head and Neck Surgery and Otorhinolaryngology, A. C. Camargo Cancer Center, São Paulo, SP Brazil
| | - Silvia Regina Rogatto
- Department of Urology, Faculty of Medicine, UNESP, Sao Paulo State University, Botucatu, São Paulo Brazil
- Department of Clinical Genetics, Vejle Hospital and Institute of Regional Health Research, University of Southern Denmark, Kabbeltoft 25, Vejle, 7100 Denmark
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40
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CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma. Sci Rep 2017; 7:44033. [PMID: 28272462 PMCID: PMC5356381 DOI: 10.1038/srep44033] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/31/2017] [Indexed: 01/13/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer, and its incidence rate is rapidly growing. It is necessary to understand the pathogenesis of PTC to develop effective diagnosis methods. Promoter methylation has been recognized to contribute to the alterations in gene expression observed in tumorigenesis. Our RNA-seq data identified 1191 differentially expressed mRNAs and 147 differentially expressed lncRNAs in PTC. Next, promoter methylation of these genes was detected by reduced representation bisulfite sequencing (RRBS) technology and comprehensively analyzed to identify differential methylation. In total, 14 genes (13 mRNAs and 1 lncRNA), in which methylation was intimately involved in regulating gene expression, were proposed as novel diagnostic biomarkers. To gain insights into the relationships among these 14 genes, a core co-function network was constructed based on co-expression, co-function and co-methylation data. Notably, CXCL12 was identified as an essential gene in the network that was closely connected with the other genes. These data suggested that CXCL12 down-regulation in PTC may be caused by promoter hypermethylation. Our study was the first to perform an RRBS analysis for PTC and suggested that CXCL12 may contribute to PTC development by methylation-mediated epigenetic regulation of gene expression.
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Sorrenti S, Baldini E, Tartaglia F, Catania A, Arcieri S, Pironi D, Calò PG, Filippini A, Ulisse S. Nodular thyroid disease in the elderly: novel molecular approaches for the diagnosis of malignancy. Aging Clin Exp Res 2017; 29:7-13. [PMID: 27832468 DOI: 10.1007/s40520-016-0654-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/12/2016] [Indexed: 12/14/2022]
Abstract
Epithelial thyroid cancers (TC) comprise two differentiated histotypes (DTC), the papillary (PTC) and the follicular (FTC) thyroid carcinomas which, following dedifferentiation, are assumed to give rise to the poorly differentiated thyroid carcinomas and the rare, but highly aggressive and invariably fatal, anaplastic thyroid carcinomas. Although thyroid cancer mortality has not been changed, its annual incidence has increased over the last two decades, mainly because of the improved ability to diagnose malignant transformation in small non-palpable thyroid nodules. Despite DTC patients have a favorable prognosis, aggressive disease is more frequently observed in the elderly showing a higher disease-specific mortality. Of relevance is the high prevalence of nodular thyroid disease in aged patients being higher than 90%, in women older than 60 year, and 60% in men older than 80 year. This implies a careful evaluation of thyroid nodules in this group of patients in order to exclude malignancy. In fact, despite the tremendous progress in the comprehension of the underlying molecular mechanisms deregulated in DTC progression, several aspects of their clinical management remain to be solved and novel diagnostic strategies are sorely needed. Here, we will attempt to review new molecular approaches, which are currently being exploited in order to ameliorate the diagnosis of thyroid nodules.
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Rodríguez-Rodero S, Delgado-Álvarez E, Díaz-Naya L, Martín Nieto A, Menéndez Torre E. Epigenetic modulators of thyroid cancer. ACTA ACUST UNITED AC 2017; 64:44-56. [PMID: 28440770 DOI: 10.1016/j.endinu.2016.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 09/14/2016] [Accepted: 09/20/2016] [Indexed: 12/14/2022]
Abstract
There are some well known factors involved in the etiology of thyroid cancer, including iodine deficiency, radiation exposure at early ages, or some genetic changes. However, epigenetic modulators that may contribute to development of these tumors and be helpful to for both their diagnosis and treatment have recently been discovered. The currently known changes in DNA methylation, histone modifications, and non-coding RNAs in each type of thyroid carcinoma are reviewed here.
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Affiliation(s)
- Sandra Rodríguez-Rodero
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain; Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Elías Delgado-Álvarez
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Lucía Díaz-Naya
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Alicia Martín Nieto
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Edelmiro Menéndez Torre
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain.
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Shou F, Xu F, Li G, Zhao Z, Mao Y, Yang F, Wang H, Guo H. RASSF1A promoter methylation is associated with increased risk of thyroid cancer: a meta-analysis. Onco Targets Ther 2017; 10:247-257. [PMID: 28123306 PMCID: PMC5234557 DOI: 10.2147/ott.s124417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Objective Previous studies have reported that Ras-associated domain family 1A (RASSF1A), the most commonly silenced tumor suppressor via promoter methylation, played vital roles in the development of carcinogenesis. The purpose of this meta-analysis was to determine whether RASSF1A promoter methylation increased the risk of thyroid cancer. Methods PubMed, Embase, ISI Web of Knowledge, and Chinese National Knowledge Infrastructure databases were searched to obtain eligible studies. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the strength of the associations, using Stata 12.0 software. The methodological quality of included studies was evaluated using Newcastle–Ottawa scale table. Egger’s test and Begg’s test were applied to detect publication biases. TSA 0.9 software was used to calculate the required information size and whether the result was conclusive. Results A total of 10 articles with 12 studies that included 422 thyroid cancer patients, identifying the association of RASSF1A promoter methylation with thyroid cancer risk, were collected in this meta-analysis. Overall, RASSF1A promoter methylation significantly increased the risk of thyroid cancer (total, OR=8.27, CI=4.38–15.62, P<0.05; Caucasian, OR=9.25, CI=3.97–21.56, P<0.05; Asian, OR=7.01, CI=2.68–18.38, P<0.05). In the subgroup analysis based on sample type, a significant association between thyroid cancer group and control group was found (normal tissue, OR=9.55, CI=4.21–21.67, P<0.05; adjacent tissue, OR=6.80, CI=2.49–18.56, P<0.05). The frequency of RASSF1A promoter methylation in follicular thyroid carcinoma was higher than in control group (OR=11.88, CI=5.80–24.32, P<0.05). In addition, the results indicated that the RASSF1A promoter methylation was correlated with papillary thyroid carcinoma in Caucasians and Asians (total, OR=8.07, CI=3.54–18.41, P<0.05; Caucasian, OR=11.35, CI=2.39–53.98, P<0.05; Asian, OR=6.67, CI=2.53–17.64, P<0.05). On the basis of the trial sequential analysis, the significant association of RASSF1A promoter methylation with thyroid cancer risk was found, and there was no need to perform further studies. Conclusion This meta-analysis confirms that RASSF1A promoter methylation is a risk factor for thyroid tumor.
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Affiliation(s)
| | - Feng Xu
- Department of Breast and Thyroid Surgery
| | - Gang Li
- Department of General Practice
| | | | - Ying Mao
- Department of Special Inspection Section
| | | | - Hongming Wang
- Department of Acupuncture and Moxibustion, Shaoxing People's Hospital, Shaoxing, People's Republic of China
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White MG, Nagar S, Aschebrook-Kilfoy B, Jasmine F, Kibriya MG, Ahsan H, Angelos P, Kaplan EL, Grogan RH. Epigenetic Alterations and Canonical Pathway Disruption in Papillary Thyroid Cancer: A Genome-wide Methylation Analysis. Ann Surg Oncol 2016; 23:2302-9. [PMID: 26979305 DOI: 10.1245/s10434-016-5185-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 01/22/2023]
Abstract
BACKGROUND Alterations in DNA methylation have been demonstrated in a variety of malignancies, including papillary thyroid cancer (PTC). The full extent of dysregulation in PTC and the downstream affected pathways remains unclear. Here we report a genome-wide analysis of PTC methylation, the dysregulation of various canonical pathways, and assess its potential as a diagnostic test. METHODS A discovery set utilized 49 PTCs and matched normal controls from The Cancer Genome Atlas. Another set of 16 PTCs and 13 normal controls were used as a replication set. Genome-wide methylation analysis was done using Illumina 450 K methylation chips. Differentially methylated loci (DML) were identified by comparing PTC and matched normal tissues. DML were defined as false-discovery rate p < 0.05 and absolute Δβ ≥ 0.2. DML were then analyzed for pathway and disease commonalities using Qiagen Ingenuity Pathway Analysis. RESULTS Of 485,577 CpG sites analyzed, 1226 DML were identified in our discovery and replication sets, and 1061 (86.5 %) DML showed hypomethylation when comparing tumor with normal tissue. Support vector machine classification was able to differentiate benign from malignant tissue in 107 (94.7 %) of 113 tested samples, including 15 (83.3 %) of 18 samples lacking a clearly deleterious mutation. Statistically significant associations with multiple canonical pathways, diseases, and biofunctions were observed including PI3K, PTEN, wnt/β-catenin, and p53. CONCLUSIONS Epigenetic dysregulation of multiple canonical pathways are associated with the development of PTC. This methylation signature shows promise as a future adjunctive screening test for thyroid nodules.
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Affiliation(s)
- Michael G White
- Endocrine Surgery Research Program, Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Sapna Nagar
- Endocrine Surgery Research Program, Department of Surgery, The University of Chicago, Chicago, IL, USA
| | | | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Peter Angelos
- Endocrine Surgery Research Program, Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Edwin L Kaplan
- Endocrine Surgery Research Program, Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Raymon H Grogan
- Endocrine Surgery Research Program, Department of Surgery, The University of Chicago, Chicago, IL, USA.
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Sun W, Chatterjee B, Wang Y, Stevenson HS, Edelman DC, Meltzer PS, Barr FG. Distinct methylation profiles characterize fusion-positive and fusion-negative rhabdomyosarcoma. Mod Pathol 2015; 28:1214-24. [PMID: 26226845 PMCID: PMC6345526 DOI: 10.1038/modpathol.2015.82] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/26/2015] [Indexed: 01/19/2023]
Abstract
Rhabdomyosarcoma comprises two major subtypes, fusion positive (PAX3-FOXO1 or PAX7-FOXO1) and fusion negative. To investigate the significance of DNA methylation in these subtypes, we analyzed methylation profiles of 37 rhabdomyosarcoma tumors and 10 rhabdomyosarcoma cell lines, as well as 8 normal tissues. Unsupervised clustering of DNA methylation clearly distinguished the fusion-positive and fusion-negative subsets. The fusion-positive tumors showed substantially lower overall levels of methylation compared with fusion-negative tumors. Comparison with the methylation pattern of normal skeletal muscle and bone marrow indicates that fusion-negative rhabdomyosarcoma is more similar to these normal tissues compared with fusion-positive rhabdomyosarcoma, and suggests that many of the methylation differences between these subtypes arise from 'aberrant' hyper- and hypomethylation events in fusion-positive rhabdomyosarcoma. Integrative methylation and gene expression analysis revealed that methylation differences between fusion-positive and fusion-negative tumors could either be positively or negatively associated with mRNA expression. There was no significant difference in the distribution of PAX3-FOXO1-binding sites between genes with and without differential methylation. However, the finding that PAX3-FOXO1-binding sites were enriched among genes that were both differentially methylated and differentially expressed suggests that the fusion protein interacts with DNA methylation to regulate target gene expression. An 11-gene DNA methylation signature, classifying the rhabdomyosarcoma tumors into fusion-positive and fusion-negative subsets, was established and validated by pyrosequencing assays. Notably, EMILIN1 (part of the 11-gene signature) showed higher methylation and lower mRNA expression in fusion-positive compared with fusion-negative tumors, and demonstrated demethylation and re-expression in multiple fusion-positive cell lines after treatment with 5-aza-2'-deoxycytidine. In conclusion, our study demonstrates that fusion-positive and fusion-negative rhabdomyosarcoma tumors possess characteristic methylation profiles that contribute to the expression differences between these fusion subtypes. These findings indicate an important relationship between fusion status and epigenetic changes in rhabdomyosarcoma, present a novel approach for ascertaining fusion status, and may identify new therapeutic targets in rhabdomyosarcoma.
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Affiliation(s)
- Wenyue Sun
- Cancer Molecular Pathology Section, Laboratory of Pathology
| | | | - Yonghong Wang
- Clinical Molecular Profiling Core, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Holly S. Stevenson
- Clinical Molecular Profiling Core, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Daniel C. Edelman
- Clinical Molecular Profiling Core, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Paul S. Meltzer
- Clinical Molecular Profiling Core, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
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Keelawat S, Thorner PS, Shuangshoti S, Bychkov A, Kitkumthorn N, Rattanatanyong P, Boonyayothin W, Poumsuk U, Ruangvejvorachai P, Mutirangura A. Detection of global hypermethylation in well-differentiated thyroid neoplasms by immunohistochemical (5-methylcytidine) analysis. J Endocrinol Invest 2015; 38:725-32. [PMID: 25740063 DOI: 10.1007/s40618-015-0246-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/20/2015] [Indexed: 12/13/2022]
Abstract
PURPOSE While global hypomethylation of DNA has been found in several malignancies, studies on thyroid tumours have shown controversial results using different techniques. To help resolve this issue, we assessed methylation status using two different techniques in papillary thyroid carcinomas (PTC) and follicular adenomas (FA) and carcinomas (FTC), comparing adjacent non-neoplastic thyroid tissue. METHODS A series of 15 FA, 18 FTC and 17 PTC were assessed by: (1) measurement of methylation levels of long interspersed nuclear elements (LINE-1) using a combined bisulfite restriction analysis polymerase chain reaction protocol and (2) immunostaining with an anti-5-methylcytidine antibody that detects methylated DNA regardless of the DNA sequence. Immunostaining was scored by image analysis. RESULTS Methylation levels of LINE-1 in FA, FTC and PTC were not significantly different from adjacent normal tissue. There was no significant difference in methylation levels of LINE-1 between FA, FTC and PTC (p = 0.44). By immunohistochemical staining for methylation, the 5-methylcytidine score was significantly higher in tumours than in normal tissue counterparts, for FA (p < 0.001), FTC (p = 0.04) and PTC (p = 0.02). PTC showed the highest 5-methylcytidine expression amongst all tumours which was significantly different from FTC (p = 0.015), but not FA (p = 0.09). There was no correlation in methylation level between LINE-1 and 5-methylcytidine scores for each group and overall. CONCLUSIONS Well-differentiated thyroid neoplasms (FA, FTC and PTC) were not found by two independent methods to undergo global hypomethylation as part of an oncogenic sequence from normal tissue to carcinoma. Instead, hypermethylation was detected in all types of tumours, implying that this epigenetic event may contribute to oncogenic development of thyroid neoplasms (both benign and malignant).
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Affiliation(s)
- S Keelawat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
| | - P S Thorner
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
- Division of Pathology, Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - S Shuangshoti
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - A Bychkov
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - N Kitkumthorn
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - P Rattanatanyong
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - W Boonyayothin
- Department of Pathology, Chonburi Hospital, 69 Moo 2, Tambon Baan Seaun, Ampur Mueung, Chonburi, Thailand
| | - U Poumsuk
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - P Ruangvejvorachai
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - A Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Ma WY, Hsiung LC, Wang CH, Chiang CL, Lin CH, Huang CS, Wo AM. A novel 96well-formatted micro-gap plate enabling drug response profiling on primary tumour samples. Sci Rep 2015; 5:9656. [PMID: 25866290 PMCID: PMC4394194 DOI: 10.1038/srep09656] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 03/03/2015] [Indexed: 12/04/2022] Open
Abstract
Drug-based treatments are the most widely used interventions for cancer management. Personalized drug response profiling remains inherently challenging with low cell count harvested from tumour sample. We present a 96well-formatted microfluidic plate with built-in micro-gap that preserves up to 99.2% of cells during multiple assay/wash operation and only 9,000 cells needed for a single reagent test (i.e. 1,000 cells per test spot x 3 selected concentration x triplication), enabling drug screening and compatibility with conventional automated workstations. Results with MCF7 and MDA-MB-231 cell lines showed that no statistical significance was found in dose-response between the device and conventional 96-well plate control. Primary tumour samples from breast cancer patients tested in the device also showed good IC50 prediction. With drug screening of primary cancer cells must consider a wide range of scenarios, e.g. suspended/attached cell types and rare/abundant cell availability, the device enables high throughput screening even for suspended cells with low cell count since the signature microfluidic cell-trapping feature ensures cell preservation in a multiple solution exchange protocol.
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Affiliation(s)
- Wei-Yuan Ma
- Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
| | - Lo-Chang Hsiung
- Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
| | - Chen-Ho Wang
- Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
| | - Chi-Ling Chiang
- Institute of Zoology, National Taiwan University, Taipei, Taiwan
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Andrew M Wo
- Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
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Cao S, Yan B, Lu Y, Zhang G, Li J, Zhai W, Guo W, Zhang S. Methylation of promoter and expression silencing of GPX3 gene in hepatocellular carcinoma tissue. Clin Res Hepatol Gastroenterol 2015; 39:198-204. [PMID: 25445749 DOI: 10.1016/j.clinre.2014.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 02/04/2023]
Abstract
BACKGROUND/AIMS Accumulating evidence has identified transcriptional silencing by aberrant methylation of CpG islands as a potential mechanism for the inactivation of tumor suppressor genes. The role of aberrant methylation of the GPX3 promoter in hepatocellular carcinoma (HCC) is not yet clear. We investigated the association of the status of GPX3 promoter methylation and GPX3 protein expression with the clinicopathological progression of HCC. METHODOLOGY Sixty HCC tumor and matched non-cancerous tissues were included in this study, and methylation was examined using MSP. GPX3 mRNA and protein levels were evaluated using RT-PCR and western blot analysis, respectively. Clinicopathological data were compiled for correlation analyses. RESULTS Among the 60 HCC cases, 76.7% (46/60) showed at elevated DNA methylation and displayed significantly lower levels of GPX3 mRNA and protein expression. Low or undetectable GPX3 protein expression was observed in 10 of 60 tumors. GPX3 promoter methylation was detected in 46 of 60 (76.7%) tumors, while no GPX3 gene promoter methylation was observed in the matched non-cancerous specimens. There was a negative correlation between promoter methylation and GPX3 mRNA levels (P<0.05). Analysis of clinicopathological data revealed that both mRNA and protein were significantly associated with portal tumor thrombosis, metastasis and differentiation. In additional, GPX3 methylation showed a relationship with portal tumor thrombosis, metastasis and differentiation. CONCLUSIONS Our results suggest that promoter methylation may be a mechanism for inactivation of GPX3, possibly leading to subsequent carcinogenesis and progression of HCC.
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Affiliation(s)
- Shengli Cao
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Hepatobiliary and Pancreatic Surgery & Digestive Organ Transplantation of Henan Province, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Bing Yan
- Key Laboratory of Hepatobiliary and Pancreatic Surgery & Digestive Organ Transplantation of Henan Province, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Yantao Lu
- Key Laboratory of Hepatobiliary and Pancreatic Surgery & Digestive Organ Transplantation of Henan Province, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Gong Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Jie Li
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Wenlong Zhai
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Hepatobiliary and Pancreatic Surgery & Digestive Organ Transplantation of Henan Province, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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49
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Integrated genomic characterization of papillary thyroid carcinoma. Cell 2015; 159:676-90. [PMID: 25417114 DOI: 10.1016/j.cell.2014.09.050] [Citation(s) in RCA: 2013] [Impact Index Per Article: 223.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 09/16/2014] [Accepted: 09/23/2014] [Indexed: 02/07/2023]
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Here, we describe the genomic landscape of 496 PTCs. We observed a low frequency of somatic alterations (relative to other carcinomas) and extended the set of known PTC driver alterations to include EIF1AX, PPM1D, and CHEK2 and diverse gene fusions. These discoveries reduced the fraction of PTC cases with unknown oncogenic driver from 25% to 3.5%. Combined analyses of genomic variants, gene expression, and methylation demonstrated that different driver groups lead to different pathologies with distinct signaling and differentiation characteristics. Similarly, we identified distinct molecular subgroups of BRAF-mutant tumors, and multidimensional analyses highlighted a potential involvement of oncomiRs in less-differentiated subgroups. Our results propose a reclassification of thyroid cancers into molecular subtypes that better reflect their underlying signaling and differentiation properties, which has the potential to improve their pathological classification and better inform the management of the disease.
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Affiliation(s)
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- Cancer Genome Atlas Program Office, National Cancer Institute at NIH, 31 Center Drive, Bldg. 31, Suite 3A20, Bethesda MD 20892, USA.
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50
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Prescott JD, Zeiger MA. TheREToncogene in papillary thyroid carcinoma. Cancer 2015; 121:2137-46. [DOI: 10.1002/cncr.29044] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Jason D. Prescott
- Endocrine Surgery, Department of Surgery; The Johns Hopkins University School of Medicine; Baltimore Maryland
| | - Martha A. Zeiger
- Endocrine Surgery, Department of Surgery; The Johns Hopkins University School of Medicine; Baltimore Maryland
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