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Amjad E, Asnaashari S, Jahanban-Esfahlan A, Sokouti B. The role of MAPK, notch and Wnt signaling pathways in papillary thyroid cancer: Evidence from a systematic review and meta-analyzing microarray datasets employing bioinformatics knowledge and literature. Biochem Biophys Rep 2024; 37:101606. [PMID: 38371530 PMCID: PMC10873880 DOI: 10.1016/j.bbrep.2023.101606] [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: 09/15/2023] [Revised: 11/19/2023] [Accepted: 12/07/2023] [Indexed: 02/20/2024] Open
Abstract
Papillary thyroid cancer (PTC) is a prevalent kind of thyroid cancer (TC), with the risk of metastasis increasing faster than any other malignancy. So, understanding the role of PTC in pathogenesis requires studying the various gene expressions to find out which particular molecular biomarkers will be helpful. The authors conducted a comprehensive search on the PubMed microarray database and a meta-analysis approach on the remaining ones to determine the differentially expressed genes between PTC and normal tissues, along with the analyses of overall survival (OS) and recurrence-free survival (RFS) rates in patients with PTC. We considered the associated genes with MAPK, Wnt, and Notch signaling pathways. Two GEO datasets have been included in this research, considering inclusion and exclusion criteria. Nineteen genes were found to have higher differences through the meta-analysis procedure. Among them, ten genes were upregulated, and nine genes were downregulated. The expression of 19 genes was examined using the GEPIA2 database, and the Kaplan-Meier plot statistics were used to analyze RFS and the OS rates. We discovered seven significant genes with the validation: PRICKLE1, KIT, RPS6KA5, GADD45B, FGFR2, FGF7, and DTX4. To further explain these findings, it was discovered that the mRNA expression levels of these seven genes and the remaining 12 genes were shown to be substantially linked with the results of the experimental literature investigations on the PTC. Our research found nineteen panels of genes that could be involved in the PTC progression and metastasis and the immune system infiltration of these cancers.
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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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Wortinger LA, Stavrum AK, Shadrin AA, Szabo A, Rukke SH, Nerland S, Smelror RE, Jørgensen KN, Barth C, Andreou D, Weibell MA, Djurovic S, Andreassen OA, Thoresen M, Ursini G, Agartz I, Le Hellard S. Divergent epigenetic responses to perinatal asphyxia in severe mental disorders. Transl Psychiatry 2024; 14:16. [PMID: 38191519 PMCID: PMC10774425 DOI: 10.1038/s41398-023-02709-7] [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: 01/17/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
Epigenetic modifications influenced by environmental exposures are molecular sources of phenotypic heterogeneity found in schizophrenia and bipolar disorder and may contribute to shared etiopathogenetic mechanisms of these two disorders. Newborns who experienced perinatal asphyxia have suffered reduced oxygen delivery to the brain around the time of birth, which increases the risk of later psychiatric diagnosis. This study aimed to investigate DNA methylation in blood cells for associations with a history of perinatal asphyxia, a neurologically harmful condition occurring within the biological environment of birth. We utilized prospective data from the Medical Birth Registry of Norway to identify incidents of perinatal asphyxia in 643 individuals with schizophrenia or bipolar disorder and 676 healthy controls. We performed an epigenome wide association study to distinguish differentially methylated positions associated with perinatal asphyxia. We found an interaction between methylation and exposure to perinatal asphyxia on case-control status, wherein having a history of perinatal asphyxia was associated with an increase of methylation in healthy controls and a decrease of methylation in patients on 4 regions of DNA important for brain development and function. The differentially methylated regions were observed in genes involved in oligodendrocyte survival and axonal myelination and functional recovery (LINGO3); assembly, maturation and maintenance of the brain (BLCAP;NNAT and NANOS2) and axonal transport processes and neural plasticity (SLC2A14). These findings are consistent with the notion that an opposite epigenetic response to perinatal asphyxia, in patients compared with controls, may contribute to molecular mechanisms of risk for schizophrenia and bipolar disorder.
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Affiliation(s)
- Laura A Wortinger
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway.
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Anne-Kristin Stavrum
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Alexey A Shadrin
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Attila Szabo
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | | | - Stener Nerland
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Runar Elle Smelror
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kjetil Nordbø Jørgensen
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychiatry, Telemark Hospital, Skien, Norway
| | - Claudia Barth
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dimitrios Andreou
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Melissa A Weibell
- TIPS-Network for Clinical Research in Psychosis, Department of Psychiatry, Stavanger University Hospital, Stavanger, Norway
- Faculty of Health, Network for Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Srdjan Djurovic
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Marianne Thoresen
- Department of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Neonatal Neuroscience, Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingrid Agartz
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Stephanie Le Hellard
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
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Bukowski A, Hoyo C, Vielot NA, Graff M, Kosorok MR, Brewster WR, Maguire RL, Murphy SK, Nedjai B, Ladoukakis E, North KE, Smith JS. Epigenome-wide methylation and progression to high-grade cervical intraepithelial neoplasia (CIN2+): a prospective cohort study in the United States. BMC Cancer 2023; 23:1072. [PMID: 37932662 PMCID: PMC10629205 DOI: 10.1186/s12885-023-11518-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Methylation levels may be associated with and serve as markers to predict risk of progression of precancerous cervical lesions. We conducted an epigenome-wide association study (EWAS) of CpG methylation and progression to high-grade cervical intraepithelial neoplasia (CIN2 +) following an abnormal screening test. METHODS A prospective US cohort of 289 colposcopy patients with normal or CIN1 enrollment histology was assessed. Baseline cervical sample DNA was analyzed using Illumina HumanMethylation 450K (n = 76) or EPIC 850K (n = 213) arrays. Participants returned at provider-recommended intervals and were followed up to 5 years via medical records. We assessed continuous CpG M values for 9 cervical cancer-associated genes and time-to-progression to CIN2+. We estimated CpG-specific time-to-event ratios (TTER) and hazard ratios using adjusted, interval-censored Weibull accelerated failure time models. We also conducted an exploratory EWAS to identify novel CpGs with false discovery rate (FDR) < 0.05. RESULTS At enrollment, median age was 29.2 years; 64.0% were high-risk HPV-positive, and 54.3% were non-white. During follow-up (median 24.4 months), 15 participants progressed to CIN2+. Greater methylation levels were associated with a shorter time-to-CIN2+ for CADM1 cg03505501 (TTER = 0.28; 95%CI 0.12, 0.63; FDR = 0.03) and RARB Cluster 1 (TTER = 0.46; 95% CI 0.29, 0.71; FDR = 0.01). There was evidence of similar trends for DAPK1 cg14286732, PAX1 cg07213060, and PAX1 Cluster 1. The EWAS detected 336 novel progression-associated CpGs, including those located in CpG islands associated with genes FGF22, TOX, COL18A1, GPM6A, XAB2, TIMP2, GSPT1, NR4A2, and APBB1IP. CONCLUSIONS Using prospective time-to-event data, we detected associations between CADM1-, DAPK1-, PAX1-, and RARB-related CpGs and cervical disease progression, and we identified novel progression-associated CpGs. IMPACT Methylation levels at novel CpG sites may help identify individuals with ≤CIN1 histology at higher risk of progression to CIN2+ and inform risk-based cervical cancer screening guidelines.
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Affiliation(s)
- Alexandra Bukowski
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA.
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
| | - Nadja A Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
| | - Michael R Kosorok
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wendy R Brewster
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rachel L Maguire
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Belinda Nedjai
- Centre for Prevention, Detection and Diagnosis, Wolfson Institute of Population Health, Queen Mary University London, London, UK
| | - Efthymios Ladoukakis
- Centre for Prevention, Detection and Diagnosis, Wolfson Institute of Population Health, Queen Mary University London, London, UK
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
| | - Jennifer S Smith
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, 27599, USA
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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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Petrini I, Cecchini RL, Mascaró M, Ponzoni I, Carballido JA. Papillary Thyroid Carcinoma: A thorough Bioinformatic Analysis of Gene Expression and Clinical Data. Genes (Basel) 2023; 14:1250. [PMID: 37372430 DOI: 10.3390/genes14061250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The likelihood of being diagnosed with thyroid cancer has increased in recent years; it is the fastest-expanding cancer in the United States and it has tripled in the last three decades. In particular, Papillary Thyroid Carcinoma (PTC) is the most common type of cancer affecting the thyroid. It is a slow-growing cancer and, thus, it can usually be cured. However, given the worrying increase in the diagnosis of this type of cancer, the discovery of new genetic markers for accurate treatment and prognostic is crucial. In the present study, the aim is to identify putative genes that may be specifically relevant in PTC through bioinformatic analysis of several gene expression public datasets and clinical information. Two datasets from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) dataset were studied. Statistics and machine learning methods were sequentially employed to retrieve a final small cluster of genes of interest: PTGFR, ZMAT3, GABRB2, and DPP6. Kaplan-Meier plots were employed to assess the expression levels regarding overall survival and relapse-free survival. Furthermore, a manual bibliographic search for each gene was carried out, and a Protein-Protein Interaction (PPI) network was built to verify existing associations among them, followed by a new enrichment analysis. The results revealed that all the genes are highly relevant in the context of thyroid cancer and, more particularly interesting, PTGFR and DPP6 have not yet been associated with the disease up to date, thus making them worthy of further investigation as to their relationship to PTC.
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Affiliation(s)
- Iván Petrini
- Department of Computer Science and Engineering, Universidad Nacional del Sur, Bahía Blanca 8000, Argentina
| | - Rocío L Cecchini
- Department of Computer Science and Engineering, Universidad Nacional del Sur, Bahía Blanca 8000, Argentina
- Institute for Computer Science and Engineering (UNS-CONICET), Bahía Blanca 8000, Argentina
| | - Marilina Mascaró
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca 8000, Argentina
| | - Ignacio Ponzoni
- Department of Computer Science and Engineering, Universidad Nacional del Sur, Bahía Blanca 8000, Argentina
- Institute for Computer Science and Engineering (UNS-CONICET), Bahía Blanca 8000, Argentina
| | - Jessica A Carballido
- Department of Computer Science and Engineering, Universidad Nacional del Sur, Bahía Blanca 8000, Argentina
- Institute for Computer Science and Engineering (UNS-CONICET), Bahía Blanca 8000, Argentina
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7
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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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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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9
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Sallam M, Mysara M, Benotmane MA, Crijns APG, Spoor D, Van Nieuwerburgh F, Deforce D, Baatout S, Guns PJ, Aerts A, Ramadan R. DNA Methylation Alterations in Fractionally Irradiated Rats and Breast Cancer Patients Receiving Radiotherapy. Int J Mol Sci 2022; 23:16214. [PMID: 36555856 PMCID: PMC9783664 DOI: 10.3390/ijms232416214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Radiation-Induced CardioVascular Disease (RICVD) is an important concern in thoracic radiotherapy with complex underlying pathophysiology. Recently, we proposed DNA methylation as a possible mechanism contributing to RICVD. The current study investigates DNA methylation in heart-irradiated rats and radiotherapy-treated breast cancer (BC) patients. Rats received fractionated whole heart X-irradiation (0, 0.92, 6.9 and 27.6 Gy total doses) and blood was collected after 1.5, 3, 7 and 12 months. Global and gene-specific methylation of the samples were evaluated; and gene expression of selected differentially methylated regions (DMRs) was validated in rat and BC patient blood. In rats receiving an absorbed dose of 27.6 Gy, DNA methylation alterations were detected up to 7 months with differential expression of cardiac-relevant DMRs. Of those, SLMAP showed increased expression at 1.5 months, which correlated with hypomethylation. Furthermore, E2F6 inversely correlated with a decreased global longitudinal strain. In BC patients, E2F6 and SLMAP exhibited differential expression directly and 6 months after radiotherapy, respectively. This study describes a systemic radiation fingerprint at the DNA methylation level, elucidating a possible association of DNA methylation to RICVD pathophysiology, to be validated in future mechanistic studies.
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Affiliation(s)
- Magy Sallam
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Mohamed Mysara
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | | | - Anne P. G. Crijns
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Daan Spoor
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Pieter-Jan Guns
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium
| | - An Aerts
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Raghda Ramadan
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
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Ma B, Chai B, Dong H, Qi J, Wang P, Xiong T, Gong Y, Li D, Liu S, Song F. Diagnostic classification of cancers using DNA methylation of paracancerous tissues. Sci Rep 2022; 12:10646. [PMID: 35739223 PMCID: PMC9226137 DOI: 10.1038/s41598-022-14786-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The potential role of DNA methylation from paracancerous tissues in cancer diagnosis has not been explored until now. In this study, we built classification models using well-known machine learning models based on DNA methylation profiles of paracancerous tissues. We evaluated our methods on nine cancer datasets collected from The Cancer Genome Atlas (TCGA) and utilized fivefold cross-validation to assess the performance of models. Additionally, we performed gene ontology (GO) enrichment analysis on the basis of the significant CpG sites selected by feature importance scores of XGBoost model, aiming to identify biological pathways involved in cancer progression. We also exploited the XGBoost algorithm to classify cancer types using DNA methylation profiles of paracancerous tissues in external validation datasets. Comparative experiments suggested that XGBoost achieved better predictive performance than the other four machine learning methods in predicting cancer stage. GO enrichment analysis revealed key pathways involved, highlighting the importance of paracancerous tissues in cancer progression. Furthermore, XGBoost model can accurately classify nine different cancers from TCGA, and the feature sets selected by XGBoost can also effectively predict seven cancer types on independent GEO datasets. This study provided new insights into cancer diagnosis from an epigenetic perspective and may facilitate the development of personalized diagnosis and treatment strategies.
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Affiliation(s)
- Baoshan Ma
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China.
| | - Bingjie Chai
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Heng Dong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Jishuang Qi
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Pengcheng Wang
- Department of Mechanical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Tong Xiong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yi Gong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Di Li
- Department of Neuro Intervention, Dalian Medical University Affiliated Dalian Municipal Central Hospital, Dalian, 116033, China
| | - Shuxin Liu
- Department of Nephrology, Dalian Medical University Affiliated Dalian Municipal Central Hospital, Dalian, 116033, China.
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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11
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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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England-Mason G, Merrill SM, Gladish N, Moore SR, Giesbrecht GF, Letourneau N, MacIsaac JL, MacDonald AM, Kinniburgh DW, Ponsonby AL, Saffery R, Martin JW, Kobor MS, Dewey D. Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: An epigenome-wide association study. ENVIRONMENT INTERNATIONAL 2022; 163:107183. [PMID: 35325772 DOI: 10.1016/j.envint.2022.107183] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Prenatal exposure to phthalates has been associated with adverse health and neurodevelopmental outcomes. DNA methylation (DNAm) alterations may be a mechanism underlying these effects, but prior investigations of prenatal exposure to phthalates and neonatal DNAm profiles are limited to placental tissue and umbilical cord blood. OBJECTIVE Conduct an epigenome-wide association study (EWAS) of the associations between prenatal exposure to phthalates and DNAm in two accessible infant tissues, venous buffy coat blood and buccal epithelial cells (BECs). METHODS Participants included 152 maternal-infant pairs from the Alberta Pregnancy Outcomes and Nutrition (APrON) study. Maternal second trimester urine samples were analyzed for nine phthalate metabolites. Blood (n = 74) or BECs (n = 78) were collected from 3-month-old infants and profiled for DNAm using the Infinium HumanMethylation450 (450K) BeadChip. Robust linear regressions were used to investigate the associations between high (HMWPs) and low molecular weight phthalates (LMWPs) and change in methylation levels at variable Cytosine-phosphate-Guanine (CpG) sites in infant tissues, as well as the sensitivity of associations to potential confounders. RESULTS One candidate CpG in gene RNF39 reported by a previous study examining prenatal exposure to phthalates and cord blood DNAm was replicated. The EWAS identified 12 high-confidence CpGs in blood and another 12 in BECs associated with HMWPs and/or LMWPs. Prenatal exposure to bisphenol A (BPA) associated with two of the CpGs associated with HMWPs in BECs. DISCUSSION Prenatal exposure to phthalates was associated with DNAm variation at CpGs annotated to genes associated with endocrine hormone activity (i.e., SLCO4A1, TPO), immune pathways and DNA damage (i.e., RASGEF1B, KAZN, HLA-A, MYO18A, DIP2C, C1or109), and neurodevelopment (i.e., AMPH, NOTCH3, DNAJC5). Future studies that characterize the stability of these associations in larger samples, multiple cohorts, across tissues, and investigate the potential associations between these biomarkers and relevant health and neurodevelopmental outcomes are needed.
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Affiliation(s)
- Gillian England-Mason
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sarah M Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Nicole Gladish
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Sarah R Moore
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald F Giesbrecht
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Psychology, Faculty of Arts, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nicole Letourneau
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Faculty of Nursing, University of Calgary, Calgary, Alberta, Canada; Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Amy M MacDonald
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada
| | - David W Kinniburgh
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan W Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Södermanland, Sweden
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; Program in Child and Brain Development, CIFAR, Toronto, Ontario, Canada
| | - Deborah Dewey
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada.
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13
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Barki M, Xue H. GABRB2, a key player in neuropsychiatric disorders and beyond. Gene 2022; 809:146021. [PMID: 34673206 DOI: 10.1016/j.gene.2021.146021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 01/11/2023]
Abstract
The GABA receptors represent the main inhibitory system in the central nervous system that ensure synaptogenesis, neurogenesis, and the regulation of neuronal plasticity and learning. GABAA receptors are pentameric in structure and belong to the Cys-loop superfamily. The GABRB2 gene, located on chromosome 5q34, encodes the β2 subunit that combines with the α and γ subunits to form the major subtype of GABAA receptors, which account for 43% of all GABAA receptors in the mammalian brain. Each subunit probably consists of an extracellular N-terminal domain, four membrane-spanning segments, a large intracellular loop between TM3 and TM4, and an extracellular C-terminal domain. Alternative splicing of the RNA transcript of the GABRB2 gene gives rise at least to four long and short isoforms with dissimilar electrophysiological properties. Furthermore, GABRB2 is imprinted and subjected to epigenetic regulation and positive selection. It has been associated with schizophrenia first in Han Chinese, and subsequently validated in other populations. Gabrb2 knockout mice also exhibited schizophrenia-like behavior and neuroinflammation that were ameliorated by the antipsychotic drug risperidone. GABRB2 was also associated with other neuropsychiatric disorders including bipolar disorder, epilepsy, autism spectrum disorder, Alzheimer's disease, frontotemporal dementia, substance dependence, depression, internet gaming disorder, and premenstrual dysphoric disorder. Recently, it has been postulated that GABRB2 might be a potential marker for different cancer types. As GABRB2 has a pivotal role in the central nervous system and is increasingly recognized to contribute to human diseases, further understanding of its structure and function may expedite the generation of new therapeutic approaches.
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Affiliation(s)
- Manel Barki
- Center for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Hong Xue
- Center for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China; Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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14
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[Detection of DNA methylation of HYAL2 gene for differentiating malignant from benign thyroid tumors]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:123-129. [PMID: 35249879 PMCID: PMC8901399 DOI: 10.12122/j.issn.1673-4254.2022.01.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To assess the value of DNA methylation level of HYAL2 gene as a molecular marker for differential diagnosis of malignant and benign thyroid tumors. METHODS DNA methylation of HYAL2 gene in tissue specimens of 190 patients with papillary thyroid cancer (PTC) and 190 age- and gender-matched patients with benign thyroid tumors was examined by mass spectrometry, and the protein expression of HYAL2 was detected immunohistochemically for another 55 pairs of patients. Logistic regression analysis was performed to calculate the odds ratio (OR) and evaluate the correlation of per 10% reduction in DNA methylation with PTC. Receiver operating characteristic (ROC) curve analysis was performed and the area under curve (AUC) was calculated to assess the predictive value of alterations in HYAL2 methylation. RESULTS Hypomethylation of HYAL2_CpG_3 was significantly correlated with early-stage PTC (OR=1.51, P=0.001), even in stage I cancer (OR=1.42, P=0.007). Age-stratified analysis revealed a significantly stronger correlation between increased HYAL2_CpG_ 3 methylation and early-stage PTC in patients below 50 years than in those older than 50 years (OR: 1.89 vs 1.37, P < 0.05); ROC analysis also showed a larger AUC of 0.787 in younger patients. The results of immunohistochemistry showed that patients with PTC had significantly higher protein expressions of HYAL2 than patients with benign tumors. CONCLUSION The alterations of DNA methylation level of HYAL2 gene is significantly correlated with early-stage PTC, suggesting the value of DNA methylation level as a potential biomarker for differentiation of malignant from benign thyroid tumors.
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Gu P, Zeng Y, Ma W, Zhang W, Liu Y, Guo F, Ruan X, Chi J, Zheng X, Gao M. Characterization of the CpG island methylator phenotype subclass in papillary thyroid carcinoma. Front Endocrinol (Lausanne) 2022; 13:1008301. [PMID: 36353231 PMCID: PMC9637834 DOI: 10.3389/fendo.2022.1008301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
CpG island methylator phenotype (CIMP), characterized by the concurrent and widespread hypermethylation of a cluster of CpGs, has been reported to play an important role in carcinogenesis. Limited studies have explored the role of CIMP in papillary thyroid carcinomas (PTCs). Here, in genome-wide DNA methylation analysis of 350 primary PTCs from the Cancer Genome Atlas database that were assessed using the Illumina HumanMethylation450K platform, our study helps to identify two subtypes displayed markedly distinct DNA methylation levels, termed CIMP (high levels of DNA methylation) and nCIMP subgroup (low levels of DNA methylation). Interestingly, PTCs with CIMP tend to have a higher degree of malignancy, since this subtype was tightly associated with older age, advanced pathological stage, and lymph node metastasis (all P < 0.05). Differential methylation analysis showed a broad methylation gain in CIMP and subsequent generalized gene set testing analysis based on the significantly methylated probes in CIMP showed remarkable enrichment in epithelial mesenchymal transition and angiogenesis hallmark pathways, confirming that the CIMP phenotype may promote the tumor progression from another perspective. Analysis of tumor microenvironment showed that CIMP PTCs are in an immune-depletion status, which may affect the effectiveness of immunotherapy. Genetically, the significantly higher tumor mutation burden and copy number alteration both at the genome and focal level confirmed the genomic heterogeneity and chromosomal instability of CIMP. tumor Corresponding to the above findings, PTC patients with CIMP showed remarkable poor clinical outcome as compared to nCIMP regarding overall survival and progression-free survival. More importantly, CIMP was associated with worse survival independent of known prognostic factors.
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Affiliation(s)
- Pengfei Gu
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yu Zeng
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Weike Ma
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Wei Zhang
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yu Liu
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Fengli Guo
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Xianhui Ruan
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Jiadong Chi
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- *Correspondence: Jiadong Chi, ; Xiangqian Zheng, ; Ming Gao,
| | - Xiangqian Zheng
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- *Correspondence: Jiadong Chi, ; Xiangqian Zheng, ; Ming Gao,
| | - Ming Gao
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Thyroid and Breast Surgery, Tianjin Union Medical Center, Tianjin, China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center, Tianjin, China
- *Correspondence: Jiadong Chi, ; Xiangqian Zheng, ; Ming Gao,
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Liu T, Wang J, Xiu Y, Wu Y, Xu D. DNA Methylation Age Drift Is Associated with Poor Outcomes and De-Differentiation in Papillary and Follicular Thyroid Carcinomas. Cancers (Basel) 2021; 13:cancers13194827. [PMID: 34638311 PMCID: PMC8508076 DOI: 10.3390/cancers13194827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Normal human tissues contain an epigenetic clock resulting from the age-dependent DNA methylation signature, which is the so-called DNA methylation (DNAm) age and can be used to precisely predict chronological age of healthy individuals. Abnormal DNAm age drift has been implicated in cancer risk and pathogenesis. Here, we observed that highly drifted DNAm age (HDDA) occurred in approximately 1/3 tumors derived from patients with papillary and follicular thyroid carcinomas. HDDA is significantly associated with dedifferentiation of tumor cells and poor patient outcomes. Thus, HDDA may serve as a new prognostic factor for thyroid carcinoma. Abstract Alterations in global DNA methylation play a critical role in both aging and cancer, and DNA methylation (DNAm) age drift has been implicated in cancer risk and pathogenesis. In the present study, we analyzed the TCGA cohort of papillary and follicular thyroid carcinoma (PTC and FTC) for their DNAm age and association with clinic-pathological features. In 54 noncancerous thyroid (NT) samples, DNAm age was highly correlated with patient chronological age (R2 = 0.928, p = 2.6 × 10−31), but drifted to younger than chronological age in most specimens, especially those from patients >50 years old. DNAm age in 502 tumors was also correlated with patient chronological age, but to a much lesser extent (R2 = 0.403). Highly drifted DNAm age (HDDA) was identified in 161 tumors, among which were 101 with DNAm age acceleration while 60 with DNAm age deceleration. Tumors with HDDA were characterized by the robust aberrations in metabolic activities, extracellular microenvironment components and inflammation/immunology responses, and dedifferentiation. Importantly, HDDA in tumors independently predicted shorter disease-free survival of patients. Collectively, NT thyroids from TC patients have younger DNAm age, while HDDA frequently occurs in TCs, and contributes to the TC progression and poor patient outcomes. HDDA may serve as a new prognostic factor for TCs.
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Affiliation(s)
- Tiantian Liu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
- Correspondence:
| | - Jiansheng Wang
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yuchen Xiu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yujiao Wu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
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Suteau V, Seegers V, Munier M, Ben Boubaker R, Reyes C, Gentien D, Wery M, Croué A, Illouz F, Hamy A, Rodien P, Briet C. G Protein-coupled Receptors in Radioiodine-refractory Thyroid Cancer in the Era of Precision Medicine. J Clin Endocrinol Metab 2021; 106:2221-2232. [PMID: 34000025 DOI: 10.1210/clinem/dgab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 12/11/2022]
Abstract
CONTEXT Radioiodine-refractory thyroid cancers have poor outcomes and limited therapeutic options (tyrosine kinase inhibitors) due to transient efficacy and toxicity of treatments. Therefore, combinatorial treatments with new therapeutic approaches are needed. Many studies link G protein-coupled receptors (GPCRs) to cancer cell biology. OBJECTIVE To perform a specific atlas of GPCR expression in progressive and refractory thyroid cancer to identify potential targets among GPCRs aiming at drug repositioning. METHODS We analyzed samples from tumor and normal thyroid tissues from 17 patients with refractory thyroid cancer (12 papillary thyroid cancers [PTCs] and 5 follicular thyroid cancers [FTCs]). We assessed GPCR mRNA expression using NanoString technology with a custom panel of 371 GPCRs. The data were compared with public repositories and pharmacological databases to identify eligible drugs. The analysis of prognostic value of genes was also performed with TCGA datasets. RESULTS With our transcriptomic analysis, 4 receptors were found to be downregulated in FTC (VIPR1, ADGRL2/LPHN2, ADGRA3, and ADGRV1). In PTC, 24 receptors were deregulated, 7 of which were also identified by bioinformatics analyses of publicly available datasets on primary thyroid cancers (VIPR1, ADORA1, GPRC5B, P2RY8, GABBR2, CYSLTR2, and LPAR5). Among all the differentially expressed genes, 22 GPCRs are the target of approved drugs and some GPCRs are also associated with prognostic factors. DISCUSSION For the first time, we performed GPCR mRNA expression profiling in progressive and refractory thyroid cancers. These findings provide an opportunity to identify potential therapeutic targets for drug repositioning and precision medicine in radioiodine-refractory thyroid cancer.
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Affiliation(s)
- Valentine Suteau
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
| | - Valérie Seegers
- Institut de Cancérologie de l'Ouest, Service de Biométrie, Angers, France
| | - Mathilde Munier
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
| | - Rym Ben Boubaker
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
| | - Cécile Reyes
- Institut Curie, Plateforme Génomique, Paris, France
| | | | - Méline Wery
- Faculty of Health, University of Angers (CHU Angers), SFR ICAT, Angers, France
| | - Anne Croué
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France
| | - Frédéric Illouz
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
| | - Antoine Hamy
- Service de chirurgie viscérale, CHU d'Angers, Angers, France
| | - Patrice Rodien
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
| | - Claire Briet
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
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18
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Jurado-Escobar R, Doña I, Perkins JR, Laguna JJ, Muñoz-Cano R, García-Sánchez A, Ayuso P, Torres MJ, Mayorga C, Cornejo-García JA. Polymorphisms in eicosanoid-related biosynthesis enzymes associated with acute urticaria/angioedema induced by nonsteroidal anti-inflammatory drug hypersensitivity. Br J Dermatol 2021; 185:815-824. [PMID: 33955560 DOI: 10.1111/bjd.20440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND Nonsteroidal anti-inflammatory drugs (NSAIDs) are the main triggers of drug hypersensitivity, with NSAID-induced acute urticaria/angioedema (NIUA) the most frequent phenotype. NSAID hypersensitivity is caused by cyclooxygenase 1 inhibition, which leads to an imbalance in prostaglandin (PG) and cysteinyl leukotriene (CysLT) synthesis. As only susceptible individuals develop NSAID hypersensitivity, genetic factors are believed to be involved; however, no study has assessed the overall genetic variability of key enzymes in PG and CysLT synthesis in NSAID hypersensitivity. OBJECTIVES To evaluate simultaneously variants in the main genes involved in PG and CysLT biosynthesis in NIUA. METHODS Two independent cohorts of patients were recruited in Spain, alongside NSAID-tolerant controls. The discovery cohort included only patients with NIUA; the replication cohort included patients with NSAID-exacerbated respiratory disease (NERD). A set of tagging single-nucleotide polymorphisms (tagSNPs) in PTGS1, PTGS2, ALOX5 and LTC4S was genotyped using mass spectrometry coupled with endpoint polymerase chain reaction. RESULTS The study included 1272 individuals. Thirty-five tagSNPs were successfully genotyped in the discovery cohort, with three being significantly associated after Bonferroni correction (rs10306194 and rs1330344 in PTGS1; rs28395868 in ALOX5). These polymorphisms were genotyped in the replication cohort: rs10306194 and rs28395868 remained associated with NIUA, and rs28395868 was marginally associated with NERD. Odds ratios (ORs) in the combined analysis (discovery and replication NIUA populations) were 1·7 for rs10306194 [95% confidence interval (CI) 1·34-2·14; Pcorrected = 2·83 × 10-4 ) and 2·19 for rs28395868 (95% CI 1·43-3·36; Pcorrected = 0·002). CONCLUSIONS Variants of PTGS1 and ALOX5 may play a role in NIUA and NERD, supporting the proposed mechanisms of NSAID-hypersensitivity and shedding light on their genetic basis.
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Affiliation(s)
- R Jurado-Escobar
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Departments of, Department of, Medicine, University of Malaga, Malaga, Spain
| | - I Doña
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario de Málaga, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain
| | - J R Perkins
- Department of, Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain.,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.,The Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain
| | - J J Laguna
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Unidad de Alergia, Hospital Central de la Cruz Roja, Madrid, Spain
| | - R Muñoz-Cano
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Allergy Section, Pneumology Department, Hospital Clinic, Universitat de Barcelona, ARADyAL, Barcelona, Spain
| | - A García-Sánchez
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Biochemistry, Pharmacogenetics Unit, University Hospital of Salamanca, Salamanca, Spain
| | - P Ayuso
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Department of Pharmacology, University of Extremadura, Caceres, Spain
| | - M J Torres
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Departments of, Department of, Medicine, University of Malaga, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario de Málaga, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Malaga, Spain
| | - C Mayorga
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario de Málaga, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Malaga, Spain
| | - J A Cornejo-García
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain
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19
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Jurado-Escobar R, Doña I, Triano-Cornejo J, Perkins JR, Pérez-Sánchez N, Testera-Montes A, Labella M, Bartra J, Laguna JJ, Estravís M, Agúndez JAG, Torres MJ, Cornejo-García JA. Genetic Variants in Cytosolic Phospholipase A2 Associated With Nonsteroidal Anti-Inflammatory Drug-Induced Acute Urticaria/Angioedema. Front Pharmacol 2021; 12:667824. [PMID: 33995098 PMCID: PMC8120030 DOI: 10.3389/fphar.2021.667824] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the main triggers of drug hypersensitivity reactions, probably due to their high consumption worldwide. The most frequent type of NSAID hypersensitivity is NSAID cross-hypersensitivity, in which patients react to NSAIDs from different chemical groups in the absence of a specific immunological response. The underlying mechanism of NSAID cross-hypersensitivity has been linked to cyclooxygenase (COX)-1 inhibition causing an imbalance in the arachidonic acid pathway. Despite NSAID-induced acute urticaria/angioedema (NIUA) being the most frequent clinical phenotype, most studies have focused on NSAID-exacerbated respiratory disease. As NSAID cross-hypersensitivity reactions are idiosyncratic, only appearing in some subjects, it is believed that individual susceptibility is under the influence of genetic factors. Although associations with polymorphisms in genes from the AA pathway have been described, no previous study has evaluated the potential role of cytosolic phospholipase A2 (cPLA2) variants. This enzyme catalyzes the initial hydrolysis of membrane phospholipids to release AA, which can be subsequently metabolized into eicosanoids. Here, we analyzed for the first time the overall genetic variation in the cPLA2 gene (PLA2G4A) in NIUA patients. For this purpose, a set of tagging single nucleotide polymorphisms (tagSNPs) in PLA2G4A were selected using data from Europeans subjects in the 1,000 Genomes Project, and genotyped with the iPlex Sequenom MassArray technology. Two independent populations, each comprising NIUA patients and NSAID-tolerant controls, were recruited in Spain, for the purposes of discovery and replication, comprising a total of 1,128 individuals. Fifty-eight tagSNPs were successfully genotyped in the discovery cohort, of which four were significantly associated with NIUA after Bonferroni correction (rs2049963, rs2064471, rs12088010, and rs12746200). These polymorphisms were then genotyped in the replication cohort: rs2049963 was associated with increased risk for NIUA after Bonferroni correction under the dominant and additive models, whereas rs12088010 and rs12746200 were protective under these two inheritance models. Our results suggest a role for PLA2G4A polymorphisms in NIUA. However, further studies are required to replicate our findings, elucidate the mechanistic role, and evaluate the participation of PLA2G4A variants in other phenotypes induced by NSAID cross-hypersensitivity.
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Affiliation(s)
- Raquel Jurado-Escobar
- Allergy Research Group, Instituto De Investigación Biomédica De Málaga-IBIMA, Malaga, Spain.,Departamento De Medicina, Universidad De Málaga, Malaga, Spain
| | - Inmaculada Doña
- Allergy Research Group, Instituto De Investigación Biomédica De Málaga-IBIMA, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario De Málaga, Malaga, Spain.,ARADyAL Network, Instituto De Salud Carlos III, Madrid, Spain
| | - José Triano-Cornejo
- Allergy Research Group, Instituto De Investigación Biomédica De Málaga-IBIMA, Malaga, Spain
| | - James R Perkins
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain.,CIBER De Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.,The Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain
| | | | | | - Marina Labella
- Allergy Unit, Hospital Regional Universitario De Málaga, Malaga, Spain
| | - Joan Bartra
- ARADyAL Network, Instituto De Salud Carlos III, Madrid, Spain.,Allergy Section, Pneumology Department, Hospital Clinic, Universitat De Barcelona, Barcelona, Spain
| | - José J Laguna
- ARADyAL Network, Instituto De Salud Carlos III, Madrid, Spain.,Allergy Unit, Allergo-Anaesthesia Unit, Hospital Central De La Cruz Roja, Faculty of Medicine, Alfonso X El Sabio University, Madrid, Spain
| | - Miguel Estravís
- ARADyAL Network, Instituto De Salud Carlos III, Madrid, Spain.,Instituto De Investigación Biomédica De Salamanca (IBSAL), Salamanca, Spain
| | - José A G Agúndez
- ARADyAL Network, Instituto De Salud Carlos III, Madrid, Spain.,Institute of Molecular Pathology Biomarkers, UEx, Cáceres, Spain
| | - María J Torres
- Allergy Research Group, Instituto De Investigación Biomédica De Málaga-IBIMA, Malaga, Spain.,Departamento De Medicina, Universidad De Málaga, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario De Málaga, Malaga, Spain.,ARADyAL Network, Instituto De Salud Carlos III, Madrid, Spain.,Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Andalusian Center for Nanomedicine and Biotechnology-BIONAND, Malaga, Spain
| | - José A Cornejo-García
- Allergy Research Group, Instituto De Investigación Biomédica De Málaga-IBIMA, Malaga, Spain.,ARADyAL Network, Instituto De Salud Carlos III, Madrid, Spain
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20
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Ham J, Wang B, Po JW, Singh A, Niles N, Lee CS. Cancer-associated fibroblasts (CAFs) in thyroid papillary carcinoma: molecular networks and interactions. J Clin Pathol 2021; 74:759-765. [PMID: 33619218 DOI: 10.1136/jclinpath-2020-207357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/04/2021] [Indexed: 01/17/2023]
Abstract
In 1989, Stephen Paget proposed the 'seed and soil' theory of cancer metastasis. This theory has led to previous researchers focusing on the role of a tumour as a cancer seed and antiangiogenesis agents as cancer soil fumigant; for the latter to be effective, it is important for them to be able to distinguish cancer cells from stromal cells. However, antiangiogenesis agents have not produced dramatic survival benefits in vivo. This may be related to their inability to destroy the supporting stroma that promote cancer cell growth. Therefore, in order to effectively arrest cancer cell growth for therapeutic purposes, a paradigm shift is required in our fundamental approach to decipher the molecular events and networks in the stromal environment that cancer cells can thrive and proliferate. The pathogenesis of cancer is a multidimensional process of pathological molecular and cellular pathways, influencing different stromal properties and achieving a mutually negotiated crosstalk between cancer cells and stromal cells. This review summarises the clinical presentation of current knowledge of classical papillary thyroid carcinoma (PTC), emerging molecular diagnostics and future directions of classical PTC research.
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Affiliation(s)
- Jeehoon Ham
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia.,Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia.,CONCERT Biobank, Ingham Institute, Liverpool, New South Wales, Australia
| | - Bin Wang
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia.,Centre for Oncology Education and Research Translation (CONCERT), Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia.,South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Joseph William Po
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia.,CONCERT Biobank, Ingham Institute, Liverpool, New South Wales, Australia.,Centre for Oncology Education and Research Translation (CONCERT), Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia.,Surgical Innovation Unit, Department of Surgery, Westmead Hospital, Sydney, New South Wales, Australia
| | - Amandeep Singh
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia.,Thyroid Cancer Group, Ingham Institute, Liverpool, New South Wales, Australia.,Department of Head & Neck Surgery, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Navin Niles
- CONCERT Biobank, Ingham Institute, Liverpool, New South Wales, Australia.,Thyroid Cancer Group, Ingham Institute, Liverpool, New South Wales, Australia.,Department of Head & Neck Surgery, Liverpool Hospital, Liverpool, New South Wales, Australia.,School of Medicine, Western Sydney University, Campbelltown Campus, Campbelltown, New South Wales, Australia
| | - Cheok Soon Lee
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia .,Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia.,CONCERT Biobank, Ingham Institute, Liverpool, New South Wales, Australia.,South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia.,School of Medicine, Western Sydney University, Campbelltown Campus, Campbelltown, New South Wales, Australia.,Central Clinical School, University of Sydney, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,Department of Anatomical Pathology, Liverpool Hospital, Liverpool, New South Wales, Australia
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21
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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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22
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Yao Y, Xu P, Ying T, Wang Y, Wang X, Shu L, Mo Z, Chen Z, Wang X, Wang W, Teng L, Lou X. Integrative Analysis of DNA Methylation and Gene Expression Identified Follicular Thyroid Cancer-Specific Diagnostic Biomarkers. Front Endocrinol (Lausanne) 2021; 12:736068. [PMID: 35370931 PMCID: PMC8964406 DOI: 10.3389/fendo.2021.736068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
The diagnosis of follicular thyroid carcinoma (FTC) prior surgical resection remains a challenge, as routine screening methods, such as ultrasound or even FNAB, could not diagnose FTC preoperatively. Here, we performed an integrative analysis of DNA methylation and RNA array data from our own cohort (14 Follicular thyroid carcinoma vs 16 Benign thyroid lesion) to identify thyroid cancer-specific DNA methylation markers. We first identified differentially methylated and expressed genes and examined their correlations. Candidate DNA methylation sites were selected and further verified in validation set. Among all candidate methylation sites, cg06928209 was the most promising site as a molecular marker for early diagnosis, with a sensitivity of 90%, a specificity of 80% and an AUC of 0.77. Overall, our study demonstrates the potential use of methylation markers in FTC diagnosis and may boost the development of new epigenetic therapies.
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Affiliation(s)
- Yunjin Yao
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Peiwei Xu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Tianxing Ying
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yue Wang
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xumeng Wang
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Liqi Shu
- Warren Alpert School of Medicine, Brown University, Providence, RI, United States
| | - Zhe Mo
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhijian Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaofeng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Weibin Wang
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Xiaoming Lou, ; Lisong Teng, ; Weibin Wang,
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Xiaoming Lou, ; Lisong Teng, ; Weibin Wang,
| | - Xiaoming Lou
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- *Correspondence: Xiaoming Lou, ; Lisong Teng, ; Weibin Wang,
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23
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Lin L, Wen J, Lin B, Bhandari A, Zheng D, Kong L, Wang Y, Wang O, Chen Y. Immortalization up-regulated protein promotes tumorigenesis and inhibits apoptosis of papillary thyroid cancer. J Cell Mol Med 2020; 24:14059-14072. [PMID: 33094920 PMCID: PMC7754061 DOI: 10.1111/jcmm.16018] [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: 03/04/2020] [Revised: 09/14/2020] [Accepted: 09/29/2020] [Indexed: 11/28/2022] Open
Abstract
The incidence of thyroid cancer is increasing in recent years worldwide, but the underlying mechanisms await further exploration. We utilized the bioinformatic analysis to discover that Immortalization up‐regulated protein (IMUP) could be a potential oncogene in the papillary thyroid cancer (PTC). We verified this finding in several databases and locally validated cohorts. Clinicopathological features analyses showed that high expression of IMUP is positively related to malignant clinicopathological features in PTC. Braf‐like PTC patients with higher IMUP expression had shorter disease‐free survival. The biological function of IMUP in PTC cell lines (KTC‐1 and TPC‐1) was investigated using small interfering RNA. Our results showed that silencing IMUP suppresses proliferation, migration and invasion while inducing apoptosis in PTC cell lines. Changes of the expression of apoptosis‐related molecules were identified by real‐time quantitative polymerase chain reaction and Western blotting. We also found that YAP1 and TAZ, the critical effectors in the Hippo pathway, were down‐regulated when the IMUP is silenced. Rescue experiments showed that overexpression of YAP1 reverses the tumour inhibitory effect caused by IMUP knockdown. Our study demonstrated that IMUP has an oncogenic function in PTC and might be a new target gene in the treatment of PTC.
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Affiliation(s)
- Lizhi Lin
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Jialiang Wen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Bangyi Lin
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Adheesh Bhandari
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Danni Zheng
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Lingguo Kong
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Yinghao Wang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Ouchen Wang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Yizuo Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
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24
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do Canto LM, Barros-Filho MC, Rainho CA, Marinho D, Kupper BEC, Begnami MDFDS, Scapulatempo-Neto C, Havelund BM, Lindebjerg J, Marchi FA, Baumbach J, Aguiar S, Rogatto SR. Comprehensive Analysis of DNA Methylation and Prediction of Response to NeoadjuvantTherapy in Locally Advanced Rectal Cancer. Cancers (Basel) 2020; 12:cancers12113079. [PMID: 33105711 PMCID: PMC7690383 DOI: 10.3390/cancers12113079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 12/19/2022] Open
Abstract
The treatment for locally advanced rectal carcinomas (LARC) is based on neoadjuvant chemoradiotherapy (nCRT) and surgery, which results in pathological complete response (pCR) in up to 30% of patients. Since epigenetic changes may influence response to therapy, we aimed to identify DNA methylation markers predictive of pCR in LARC patients treated with nCRT. We used high-throughput DNA methylation analysis of 32 treatment-naïve LARC biopsies and five normal rectal tissues to explore the predictive value of differentially methylated (DM) CpGs. External validation was carried out with The Cancer Genome Atlas-Rectal Adenocarcinoma (TCGA-READ 99 cases). A classifier based on three-CpGs DM (linked to OBSL1, GPR1, and INSIG1 genes) was able to discriminate pCR from incomplete responders with high sensitivity and specificity. The methylation levels of the selected CpGs confirmed the predictive value of our classifier in 77 LARCs evaluated by bisulfite pyrosequencing. Evaluation of external datasets (TCGA-READ, GSE81006, GSE75546, and GSE39958) reproduced our results. As the three CpGs were mapped near to regulatory elements, we performed an integrative analysis in regions associated with predicted cis-regulatory elements. A positive and inverse correlation between DNA methylation and gene expression was found in two CpGs. We propose a novel predictive tool based on three CpGs potentially useful for pretreatment screening of LARC patients and guide the selection of treatment modality.
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Affiliation(s)
- Luisa Matos do Canto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- International Research Center–CIPE, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (M.C.B.-F.); (F.A.M.)
| | - Mateus Camargo Barros-Filho
- International Research Center–CIPE, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (M.C.B.-F.); (F.A.M.)
- Department of Head and Neck Surgery, Hospital das Clinicas HCFMUSP, Sao Paulo 01246-903, Brazil
| | - Cláudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University (Unesp), Botucatu 18618-689, Brazil;
| | - Diogo Marinho
- Institute of Biological Psychiatry, Psykiatrisk Center Sct. Hans, 4000 Roskilde, Denmark;
| | - Bruna Elisa Catin Kupper
- Colorectal Cancer Service, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (B.E.C.K.); (S.A.J.)
| | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos – 14784-400, and Diagnósticos da América (DASA), Barueri 06455010, Brazil;
| | - Birgitte Mayland Havelund
- Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark;
| | - Jan Lindebjerg
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark;
- Department of Pathology, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Fabio Albuquerque Marchi
- International Research Center–CIPE, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (M.C.B.-F.); (F.A.M.)
| | - Jan Baumbach
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany;
| | - Samuel Aguiar
- Colorectal Cancer Service, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (B.E.C.K.); (S.A.J.)
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark;
- Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense, Denmark
- Correspondence: ; Tel.: +45-7940-6669
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Guo D, Li F, Zhao X, Long B, Zhang S, Wang A, Cao D, Sun J, Li B. Circular RNA expression and association with the clinicopathological characteristics in papillary thyroid carcinoma. Oncol Rep 2020; 44:519-532. [PMID: 32468074 PMCID: PMC7336492 DOI: 10.3892/or.2020.7626] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Circular RNAs (circRNAs) are a novel class of RNAs, with higher stability and tissue specificity, which may be of value as novel clinical markers. High-throughput RNA sequencing was used to profile the expression of circRNAs in 5 pairs of cancer and normal tissues, and reverse transcription-quantitative PCR (RT-qPCR) analysis was employed to verify the results of the RNA sequencing in 45 cases of PTC. The dysregulated circRNA expression and clinicopathological characteristics were assessed and the potential roles of circRNAs in the cellular miRNA and mRNA network were predicted using bioinformatics analysis. The results demonstrated that, compared with normal tissues, a total of 53 circRNAs were dysregulated in tumour tissues, and 8 circRNAs were validated at the mRNA level (P<0.001 and P<0.01). Among those, the expression of chr5:161330882-161336769- (P=0.015), chr9:22046750-22097364+ (P=0.041) and chr8:18765448-18804898- (P=0.036) were obviously associated with the BRAFV600E mutation, chr12:129699809-129700698- was associated with capsular invasion (P=0.025) and chr5:38523418-38530666- was associated with pT stage (P=0.037) and lymph node metastasis (P=0.002). Therefore, some dysregulated circRNAs were found to be associated with BRAFV600E mutation, capsular invasion, advanced pT stage and lymph node metastasis of PTC, indicating that circRNAs may be involved in tumourigenesis and cancer progression, and they may be putative biomarkers for the diagnosis and evaluation of progression of PTC.
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Affiliation(s)
- Dan Guo
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Fangyuan Li
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Xiaoxiao Zhao
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Bo Long
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Sumei Zhang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Anqi Wang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Dingyan Cao
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Jian Sun
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Binglu Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
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26
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Song F, Li L, Zhang B, Zhao Y, Zheng H, Yang M, Li X, Tian J, Huang C, Liu L, Wang Q, Zhang W, Chen K. Tumor specific methylome in Chinese high-grade serous ovarian cancer characterized by gene expression profile and tumor genotype. Gynecol Oncol 2020; 158:178-187. [PMID: 32362568 DOI: 10.1016/j.ygyno.2020.04.688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/11/2020] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Extensive genetic and limited epigenetics have been characterized by the Cancer Genome Atlas (TCGA) among Western High-grade serous ovarian cancer (HGSOC). The present study aimed to characterize Chinese HGSOC at genome scale. METHODS We used reduced representation bisulfite sequencing to investigate whole-genome and tumor-specific DNA methylation in 21 HGSOC tumors paired with their normal tissues, followed by a replication study involving additional 41 HGSOC patients. Altered methylation patterns in HGSOC were further characterized by gene expression profiles and whole-exome sequencing data. RESULTS Comparing HGSOC tumors with normal tissues we observed global hypomethylation but with more specific hypermethylation in gene promoter. Totally, we revealed 159,881 differentially methylated regions (DMRs) and 4060 differentially expressed genes (DEGs). By integrating DNA methylation and mRNA expression data, we identified 153 negative (mainly in the upstream region) and 115 positive (mainly in the CDS regions) DMRs-DEGs correlated pairs, respectively. The negatively correlated DMRs-DEGs underlined Wnt and cell adhesion molecule binding as critical canonical pathways disrupted by DNA methylation. Eleven DMRs (in CAPS, FZD7, CDKN2A, PON3, KLF4, etc.), accompanied with a global DNA methylation marker, were validated in the replication samples. Whole-exome sequencing presented a relatively less dominated TP53 mutation in Chinese HGSOC compared to TCGA dataset. Unsupervised analysis of the three-level omics data identified differential methylation and expression subgroups based on tumor genetics, one of which presented increased DNA methylation and significantly associated with TP53 mutation. CONCLUSIONS Our individual and integrated analyses contribute details about the tissue-specific genetic and DNA methylation landscape of Chinese HGSOC.
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Affiliation(s)
- Fangfang Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | | | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Meng Yang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Xiangchun Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Jing Tian
- Department of Gynecological Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Caiyun Huang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Luyang Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Qinghua Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Wei Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.
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27
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Lv L, Cao L, Hu G, Shen Q, Wu J. Methylation-Driven Genes Identified as Novel Prognostic Indicators for Thyroid Carcinoma. Front Genet 2020; 11:294. [PMID: 32296463 PMCID: PMC7136565 DOI: 10.3389/fgene.2020.00294] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation plays an crucial role in tumorigenesis through regulating gene expression. Nevertheless, the exact role of methylation in the carcinogenesis of thyroid cancer and its association with prognosis remains unclear. The purpose of this study is to explore the DNA methylation-driven genes in thyroid cancer by integrative bioinformatics analysis. METHODS The transcriptome profiling data and DNA methylation data of thyroid cancer were downloaded from The Cancer Genome Atlas (TCGA) database. The methylmix R package was used to screen DNA methylation-driven genes in thyroid cancer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted to annotate the function of methylation-driven genes. Univariate Cox regression analyses was performed to distinguish prognosis-related methylation-driven genes. Multivariate Cox regression analyses was utilized to build a prognostic multi-gene signature. A survival analysis was carried out to determine the individual prognostic significance of this multi-gene signature. RESULTS A total of 51 methylation-driven genes were identified. The functional analysis indicated that these genes were significantly enriched in diverse biological processes (BP) and pathways related to the malignancy processes. Four of these genes (RDH5, TREM1, BIRC7, and SLC26A7) were selected to construct the risk evaluation model. Patients in the low-risk group had an conspicuously better overall survival (OS) than those in high-risk group (p < 0.001). The area under the receiver operating characteristic (ROC) curve for this model was 0.836, suggesting a good specificity and sensitivity. Subsequent survival analysis revealed that this four-gene signature served as an independent indicator for the prognosis of thyroid cancer. Moreover, the prognostic signature was well validated in a external thyroid cancer cohort. CONCLUSION We identified methylation-driven genes in thyroid cancer with independent prognostic value, which may offer new insight into molecular mechanisms of thyroid cancer and provide new possibility for individualized treatment of thyroid cancer patients.
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Affiliation(s)
- Liting Lv
- Department of Thyroid and Breast Surgery, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
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28
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Ding W, Feng G, Hu Y, Chen G, Shi T. Co-occurrence and Mutual Exclusivity Analysis of DNA Methylation Reveals Distinct Subtypes in Multiple Cancers. Front Cell Dev Biol 2020; 8:20. [PMID: 32064261 PMCID: PMC7000380 DOI: 10.3389/fcell.2020.00020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Co-occurrence and mutual exclusivity (COME) of DNA methylation refer to two or more genes that tend to be positively or negatively correlated in DNA methylation among different samples. Although COME of gene mutations in pan-cancer have been well explored, little is known about the COME of DNA methylation in pan-cancer. Here, we systematically explored the COME of DNA methylation profile in diverse human cancer. A total of 5,128,332 COME events were identified in 14 main cancers types in The Cancer Genome Atlas (TCGA). We also identified functional epigenetic modules of the zinc finger gene family in six cancer types by integrating the gene expression and DNA methylation data and the frequently occurred COME network. Interestingly, most of the genes in those functional epigenetic modules are epigenetically repressed. Strikingly, those frequently occurred COME events could be used to classify the patients into several subtypes with significant different clinical outcomes in six cancers as well as pan-cancer (p-value ≤ = 0.05). Moreover, we observed significant associations between different COME subtypes and clinical features (e.g., age, gender, histological type, neoplasm histologic grade, and pathologic stage) in distinct cancers. Taken together, we identified millions of COME events of DNA methylation in pan-cancer and detected functional epigenetic COME events that could separate tumor patients into different subtypes, which may benefit the diagnosis and prognosis of pan-cancer.
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Affiliation(s)
- Wubin Ding
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Guoshuang Feng
- Big Data and Engineering Research Center, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yige Hu
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Big Data and Engineering Research Center, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, China
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29
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Zhang D, Shi G, Qiu J, Shi C, Liang Y, Yuan L, Yong Z, Li J, Cao Y. Overexpression of long noncoding RNA ENST433110 inhibits cell proliferation and migration and enhances cell apoptosis of thyroid cancer cells. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1763480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Dongxin Zhang
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Guangqing Shi
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Juan Qiu
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Can Shi
- Department of Radiology, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Yan Liang
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Li Yuan
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Zhong Yong
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Jian Li
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Yan Cao
- Department of Nuclear Medicine, the Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
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30
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Hu H, Xu L, Luo SJ, Xiang T, Chen Y, Cao ZR, Zhang YJ, Mo Z, Wang Y, Meng DF, Yu L, Lin LZ, Zhang SJ. Retinal dehydrogenase 5 (RHD5) attenuates metastasis via regulating HIPPO/YAP signaling pathway in Hepatocellular Carcinoma. Int J Med Sci 2020; 17:1897-1908. [PMID: 32788868 PMCID: PMC7415383 DOI: 10.7150/ijms.46091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
Abstract
Retinal dehydrogenase 5 (RDH5) is an important enzyme in the visual cycle. Several studies have reported that the RDH family may play crucial roles in tumor prognosis. However, the role of RDH5 in tumor prognosis is still unclear. We examined the mRNA level of RDH5 by using q-PCR in hepatocellular carcinoma (HCC) and adjacent non-cancerous tissues. The proliferation rate of HCC cells was detected by MTS assay, and the invasive ability was examined by transwell and scratch wound assays. The YAP protein localization and expression were visualized by immunofluorescence in two different cell lines. CpG islands in the promoter region were predicted by using the methprimer database. Clinical characteristics of a patient cohort data came from The Cancer Genome Atlas database. RDH5 was significantly downregulated in hepatocellular carcinoma tissues, and low RDH5 expression was associated with metastasis and poor patient prognosis. Functional assays revealed that the RDH5 promoter is methylated in HCC cell lines. Moreover, overexpressing RDH5 can suppress metastasis by reversing the epithelial-mesenchymal transition (EMT) process, and RDH5 also inhibits cell proliferation in HCC cell lines. Furthermore, suppressing RDH5 can activate the Hippo/YAP signaling pathway and promote the nuclear translocation of YAP. Clinical data demonstrated that RDH5 is an independent prognostic factor in HCC. In our study, we provided the first evidence that RDH5 plays a crucial role in suppressing proliferation and metastasis, and the RDH5 promoter is methylated in hepatocellular carcinoma. And as an important regulator, RDH5 can suppress the Hippo/YAP signaling pathway. Taken together, it revealed that RDH5 might be a potential therapeutic target in HCC patients.
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Affiliation(s)
- Hao Hu
- Department of Oncology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou (510407), China.,The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Liang Xu
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Shao-Ju Luo
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Ting Xiang
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Yan Chen
- Department of Chinese Medicine, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, Guangdong, P. R. China
| | - Zhi-Rui Cao
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Yu-Jian Zhang
- Department of Oncology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou (510407), China
| | - Zhuomao Mo
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Yongdan Wang
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Dong-Fang Meng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, P. R. China
| | - Ling Yu
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
| | - Li-Zhu Lin
- Department of Oncology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou (510407), China
| | - Shi-Jun Zhang
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, P. R. China
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Feng SJ, Liu XS, Ma LY, Khan IU, Rono JK, Yang ZM. Identification of epigenetic mechanisms in paddy crop associated with lowering environmentally related cadmium risks to food safety. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 256:113464. [PMID: 31677869 DOI: 10.1016/j.envpol.2019.113464] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Cadmium (Cd) is a toxic metal that contributes to human diseases such as pediatric cancer and cardiovascular dysfunction. Epigenetic modification caused by Cd exposure is the major factor in etiology of environmentally-relevant diseases. However, the underlying epigenetic mechanism for Cd uptake and accumulation in food crops, particularly those growing in Cd-contaminated environments, is largely unknown. This study investigated uncharacterized regulatory mechanisms and biological functions of global DNA hypomethylation at CG sites that are associated with gene expression for Cd detoxification and accumulation in the food crop rice. Mutation of the CG maintenance enzyme OsMET1 confers rice tolerance to Cd exposure. Genome-wide analysis of OsMET1 loss of function mutant Osmet1 and its wild type shows numerous loci differentially methylated and upregulated genes for Cd detoxification, transport and accumulation. We functionally identified a new locus for a putative cadmium tolerance factor (here termed as OsCTF) and demonstrated that Cd-induced DNA demethylation is the drive of OsCTF expression. The 3'-UTR of OsCTF is the primary site of DNA and histone (H3K9me2) demethylation, which is associated with higher levels of OsCTF transcripts detected in the Osmet1 and Ossdg714 mutant lines. Mutation of OsCTF in rice led to hypersensitivity to Cd and the Osctf line accumulated more Cd, whereas transfer of OsCTF back to the Osctf mutant completely restored the normal phenotype. Our work unveiled an important epigenetic mechanism and will help develop breeding crops that contribute to food security and better human health.
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Affiliation(s)
- Sheng Jun Feng
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xue Song Liu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Ya Ma
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Irfan Ullah Khan
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Justice Kipkoir Rono
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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32
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Barros-Filho MC, de Mello JBH, Marchi FA, Pinto CAL, da Silva IC, Damasceno PKF, Soares MBP, Kowalski LP, Rogatto SR. GADD45B Transcript Is a Prognostic Marker in Papillary Thyroid Carcinoma Patients Treated With Total Thyroidectomy and Radioiodine Therapy. Front Endocrinol (Lausanne) 2020; 11:269. [PMID: 32425887 PMCID: PMC7203742 DOI: 10.3389/fendo.2020.00269] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
Currently, there is a lack of efficient recurrence prediction methods for papillary thyroid carcinoma (PTC). In this study, we enrolled 202 PTC patients submitted to total thyroidectomy and radioiodine therapy with long-term follow-up (median = 10.7 years). The patients were classified as having favorable clinical outcome (PTC-FCO, no disease in the follow-up) or recurrence (PTC-RE). Alterations in BRAF, RAS, RET, and TERT were investigated (n = 202) and the transcriptome of 48 PTC (>10 years of follow-up) samples was profiled. Although no mutation was associated with the recurrence risk, 68 genes were found as differentially expressed in PTC-RE compared to PTC-FCO. Pathway analysis highlighted a potential role of cancer-related pathways, including signal transduction and FoxO signaling. Among the eight selected genes evaluated by RT-qPCR, SLC2A4 and GADD45B showed down-expression exclusively in the PTC-FCO group compared to non-neoplastic tissues (NT). Increased expression of GADD45B was an independent marker of shorter disease-free survival [hazard ratio (HR) 2.9; 95% confidence interval (CI95) 1.2-7.0] in our cohort and with overall survival in the TCGA dataset (HR = 4.38, CI95 1.2-15.5). In conclusion, GADD45B transcript was identified as a novel prognostic marker candidate in PTC patients treated with total thyroidectomy and radioiodine therapy.
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MESH Headings
- Antigens, Differentiation/genetics
- Antigens, Differentiation/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Combined Modality Therapy
- Female
- Follow-Up Studies
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Iodine Radioisotopes/therapeutic use
- Male
- Middle Aged
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/therapy
- Prognosis
- Retrospective Studies
- Survival Rate
- Thyroid Cancer, Papillary/genetics
- Thyroid Cancer, Papillary/metabolism
- Thyroid Cancer, Papillary/pathology
- Thyroid Cancer, Papillary/therapy
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
- Thyroid Neoplasms/therapy
- Thyroidectomy/mortality
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Affiliation(s)
- Mateus C. Barros-Filho
- International Research Center–CIPE, A. C. Camargo Cancer Center, São Paulo, Brazil
- *Correspondence: Mateus C. Barros-Filho
| | - Julia B. H. de Mello
- International Research Center–CIPE, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Fabio A. Marchi
- International Research Center–CIPE, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | | | | | - Milena B. P. Soares
- Gonçalo Moniz Institute, Fiocruz, Salvador, Brazil
- Health Technology Institute, SENAI CIMATEC, Salvador, Brazil
| | - Luiz P. Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Silvia R. Rogatto
- Department of Clinical Genetics, Vejle University Hospital, Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Silvia R. Rogatto
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33
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Wang W, Wang S, Chu X, Liu H, Xiang M. Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique DNA Methylation and Gene Expression Profiles. J Comput Biol 2019; 27:1041-1054. [PMID: 31710242 DOI: 10.1089/cmb.2019.0138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The early diagnosis of lung squamous cell carcinoma (LUSC) is difficult, causing an unsatisfactory prognosis. Therefore, the 5-year survival rate of LUSC is poor. This study aimed at screening the potential diagnostic and prognostic markers for LUSC. The data of LUSC gene expression profiles and DNA methylation were obtained from The Cancer Genome Atlas (TCGA) database; the differentially expressed genes (DEGs) and the differentially methylated genes (DMGs) were screened out by an independent t-test and Benjamini/Hochberg methods. Further, the classifiers of the gene expression and DNA methylation markers in LUSC were constructed. After that, diagnostic and prognostic markers in LUSC were analyzed by the protein-protein interaction (PPI) network. The DEGs and the DMGs from TCGA database of LUSC were screened out. After strict filtration, we identified three potential DMGs (POU domain, class 4, transcription factor 2 [POU4F2], EN1, single-minded homolog 1 [SIM1]) for early diagnosis and seven potential DEGs (G-protein coupled receptor 78 [GPR78], PCDHA5, myosin binding protein H [MYBPH], RTL3, KIAA0408, HSD3B2, PCDHA12) for prognosis of LUSC. The tumor-normal tissue classification model and prognosis model were validated in two independent datasets. In addition, the PPI network was constructed, including three DMGs and the five DEGs (GPR78, MYBPH, KIAA0408, HSD3B2, PCDHA12) of the seven DEGs. The potential DMGs (POU4F2, EN1, SIM1) and DEGs (GPR78, MYBPH, KIAA0408, HSD3B2, PCDHA12) for the diagnosis and prognosis of LUSC identified in this article are expected to be further applied in clinical practice of the treatment of LUSC.
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Affiliation(s)
- Weiqing Wang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Shaohua Wang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Xiao Chu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Hui Liu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Ming Xiang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
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Wei S, Yun X, Ruan X, Wei X, Zheng X, Gao M. Identification of potential pathogenic candidates or diagnostic biomarkers in papillary thyroid carcinoma using expression and methylation profiles. Oncol Lett 2019; 18:6670-6678. [PMID: 31814850 PMCID: PMC6888281 DOI: 10.3892/ol.2019.11059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 09/20/2019] [Indexed: 01/15/2023] Open
Abstract
The mechanisms underlying the pathogenesis of papillary thyroid carcinoma (PTC) have not yet been elucidated. The aim of the current study was to identify potential pathogenic biomarkers in PTC by comprehensively analyzing gene expression and methylation profiles, and to increase the understanding of PTC pathogenesis. The gene expression profiles of the GSE97001 and GSE83520 datasets, the miRNA expression profiles of the GSE73182 dataset, and the DNA methylation profiles of the GSE86961 and GSE97466 datasets were downloaded from Gene Expression Omnibus database. The differentially expressed genes (DEGs) and the differentially expressed microRNAs (DEMs) were identified using the limma package in R, and the differentially methylated sites (DMSs) were identified using the β distribution and two-sample t-tests. The Database for Annotation, Visualization and Integrated Discovery, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome were subsequently used to perform functional and pathway enrichment analysis. The miRNA target genes were predicted using the online databases miRWalk. The protein-protein interactions (PPI) were analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins. The regulatory network was constructed, and the gene expression and methylation levels of the key nodes were detected using reverse-transcription quantitative-polymerase chain reaction (PCR) and methylation-specific PCR. A total of 155 overlapping DEGs were identified between the GSE97001 and GSE83520 datasets, and 19 DEMs between PTC tissue and normal tissue samples were identified in the GSE73182 set. In the GSE86961 and GSE97466 datasets, 2,910 overlapping DMSs that were associated with 38 downregulated methylated genes were identified. The overlapping DEGs were enriched in 46 Gene Ontology terms and one KEGG pathway. A total of 60 PPI pairs were identified for the overlapping DEGs and 12 negative miRNA-gene pairs were identified for the DEMs. The expression levels of hsa-miR-199a-5p and decorin (DCN) were decreased in patients with PTC. C-X-C motif chemokine ligand 12 (CXCL12) was hypermethylated and had a decreased expression level in PTC tissues. LDL receptor related protein 4 (LRP4) and carbonic anhydrase 12 (CA12) were hypomethylated and had an increased expression level. The present study revealed that hsa-miR-199a-5p, DCN, CXCL12, LRP4 and CA12 may serve important roles in the pathogenesis of PTC.
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Affiliation(s)
- Songfeng Wei
- Department of Thyroid and Neck Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Xinwei Yun
- Department of Thyroid and Neck Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Xianhui Ruan
- Department of Thyroid and Neck Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Xi Wei
- Department of Ultrasonic Diagnosis and Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Ming Gao
- Department of Thyroid and Neck Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
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Barros-Filho MC, Dos Reis MB, Beltrami CM, de Mello JBH, Marchi FA, Kuasne H, Drigo SA, de Andrade VP, Saieg MA, Pinto CAL, Kowalski LP, Rogatto SR. DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions. Thyroid 2019; 29:1244-1254. [PMID: 31328658 DOI: 10.1089/thy.2018.0458] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3% sensitivity and 82.4% specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4% sensitivity and 87.5% specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7% sensitivity and 75.4% specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7% sensitivity and 89.5% specificity in confirmed malignant tumors, and 100% sensitivity and 89% specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.
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Affiliation(s)
| | - Mariana Bisarro Dos Reis
- International Research Center - CIPE-A.C.Camargo Cancer Center, São Paulo, Brazil
- Faculty of Medicine, University of Sao Paulo State-UNESP, Botucatu, Brazil
| | | | | | | | - Hellen Kuasne
- International Research Center - CIPE-A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | | | - Mauro Ajaj Saieg
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
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Yang Q, Wu F, Wang F, Cai K, Zhang Y, Sun Q, Zhao X, Gui Y, Li Q. Impact of DNA methyltransferase inhibitor 5-azacytidine on cardiac development of zebrafish in vivo and cardiomyocyte proliferation, apoptosis, and the homeostasis of gene expression in vitro. J Cell Biochem 2019; 120:17459-17471. [PMID: 31271227 DOI: 10.1002/jcb.29010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/15/2022]
Abstract
Cardiac development is a peculiar process involving coordinated cellular differentiation, migration, proliferation, and apoptosis. DNA methylation plays a key role in genomic stability, tissue-specific gene expression, cell proliferation, and apoptosis. Hypomethylation in the global genome has been reported in cardiovascular diseases. However, little is known about the impact and specific mechanism of global hypomethylation on cardiomyocytes. In the present study, we explored the impact of DNA methyltransferase inhibitors 5-azacytidine on cardiac development. In vivo experiment showed that hypomethylation of zebrafish embryos with 5-azacytidine exposure significantly reduced survival, induced malformations, and delayed general development process. Furthermore, zebrafish embryos injected with 5-azacytidine developed pericardial edema, ventricular volume reduction, looping deformity, and reduction in heart rate and ventricular shortening fraction. Cardiomyocytes treated with 5-azacytidine in vitro decreased proliferation and induced apoptosis in a concentration-dependent manner. Furthermore, 5-azacytidine treatment in cardiomyocytes resulted in 20 downregulated genes expression and two upregulated genes expression in 45 candidate genes, which indicated that DNA methylation functions as a bidirectional modulator in regulating gene expression. In conclusion, these results show the regulative effects of the epigenetic modifier 5-azacytidine in cardiac development of zebrafish embryos in vivo and cardiomyocyte proliferation and apoptosis and the homeostasis of gene expression in vitro, which offer a novel understanding of aberrant DNA methylation in the etiology of cardiovascular disease.
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Affiliation(s)
- Qian Yang
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Fang Wu
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Feng Wang
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Ke Cai
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yawen Zhang
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Quanya Sun
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaolong Zhao
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yonghao Gui
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Qiang Li
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
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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: 63] [Impact Index Per Article: 12.6] [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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38
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Lapa RML, Barros-Filho MC, Marchi FA, Domingues MAC, de Carvalho GB, Drigo SA, Kowalski LP, Rogatto SR. Integrated miRNA and mRNA expression analysis uncovers drug targets in laryngeal squamous cell carcinoma patients. Oral Oncol 2019; 93:76-84. [PMID: 31109699 DOI: 10.1016/j.oraloncology.2019.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/20/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVES The current treatment of laryngeal squamous cell carcinoma (LSCC) is based on radical surgery and radiotherapy resulting in high morbidity. Chemoradiotherapy has been used as alternative to organ sparing; however, several advanced cases presented resistance to treatment, which contributes to a high risk of recurrence and mortality. Coding RNAs and miRNAs have potential to be used as biomarkers or targets for cancer therapy. MATERIALS AND METHODS In this study, 36 LSCC and 5 non-neoplastic control samples were investigated using miRNA and mRNA large-scale expression analysis and a cross-validation was performed using the TCGA database (116 LSCC and 12 surrounding normal tissues). RESULTS The large-scale profiling revealed the involvement of 28 miRNAs and 817 genes differentially expressed in LSCC. An integrative analysis comprising predicted and experimentally validated miRNA/mRNA interactions (negatively correlated), resulted in 28 miRNAs and 543 mRNAs. Decreased expression of miR-199b was significantly associated with shorter disease-free survival in LSCC (internal and TCGA datasets). The expression levels of selected miRNAs (miR-199b-5p, miR-29c-3p, miR-204-5p, miR-125b-5p and miR-92a-3p) and genes (COL3A1, COL10A1, ERBB4, HMGA2, HLF, TOP2A, MMP3, MMP13, MMP10 and PPP1R3) were confirmed as altered in LSCC by RT-qPCR. Additionally, a drug target prediction analysis revealed drug combinations based on miRNA and mRNA expression, pointing out novel alternatives to optimize the LSCC treatment. CONCLUSION Collectively, these findings provide new insights in the LSCC transcriptional deregulation and potential drug targets.
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Affiliation(s)
- Rainer Marco Lopez Lapa
- International Research Center, CIPE - A.C.Camargo Cancer Center, São Paulo, Brazil; Department of Genetics, Institute of Bioscience, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | | | | | | | | | - Sandra Aparecida Drigo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo Brazil
| | - Silvia Regina Rogatto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University - UNESP, Botucatu, SP, Brazil; Department of Clinical Genetics, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Denmark.
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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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PFKFB2 Promoter Hypomethylation as Recurrence Predictive Marker in Well-Differentiated Thyroid Carcinomas. Int J Mol Sci 2019; 20:ijms20061334. [PMID: 30884810 PMCID: PMC6471408 DOI: 10.3390/ijms20061334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Despite the low mortality rates, well-differentiated thyroid carcinomas (WDTC) frequently relapse. BRAF and TERT mutations have been extensively related to prognosis in thyroid cancer. In this study, the methylation levels of selected CpGs (5-cytosine-phosphate-guanine-3) comprising a classifier, previously reported by our group, were assessed in combination with BRAF and TERT mutations. We evaluated 121 WDTC, three poorly-differentiated/anaplastic thyroid carcinomas (PDTC/ATC), 22 benign thyroid lesions (BTL), and 13 non-neoplastic thyroid (NT) tissues. BRAF (V600E) and TERT promoter (C228T and C250T) mutations were tested by pyrosequencing and Sanger sequencing, respectively. Three CpGs mapped in PFKFB2, ATP6V0C, and CXXC5 were evaluated by bisulfite pyrosequencing. ATP6V0C hypermethylation and PFKFB2 hypomethylation were detected in poor-prognosis (PDTC/ATC and relapsed WDTC) compared with good-prognosis (no relapsed WDTC) and non-malignant cases (NT/BTL). CXXC5 was hypomethylated in both poor and good-prognosis cases. Shorter disease-free survival was observed in WDTC patients presenting lower PFKFB2 methylation levels (p = 0.004). No association was observed on comparing BRAF (60.7%) and TERT (3.4%) mutations and prognosis. Lower PFKFB2 methylation levels was an independent factor of high relapse risk (Hazard Ratio = 3.2; CI95% = 1.1–9.5). PFKFB2 promoter methylation analysis has potential applicability to better stratify WDTC patients according to the recurrence risk, independently of BRAF and TERT mutations.
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Barros-Filho MC, Pewarchuk M, Minatel BDC, Sage AP, Marshall EA, Martinez VD, Rock LD, MacAulay G, Kowalski LP, Rogatto SR, Garnis C, Lam WL. Previously undescribed thyroid-specific miRNA sequences in papillary thyroid carcinoma. J Hum Genet 2019; 64:505-508. [DOI: 10.1038/s10038-019-0583-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 12/12/2022]
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Loss of DNA methylation is related to increased expression of miR-21 and miR-146b in papillary thyroid carcinoma. Clin Epigenetics 2018; 10:144. [PMID: 30454026 PMCID: PMC6245861 DOI: 10.1186/s13148-018-0579-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/06/2018] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation in miRNA genes has been reported as a mechanism that may cause dysregulation of mature miRNAs and consequently impact the gene expression. This mechanism is largely unstudied in papillary thyroid carcinomas (PTC). Methods To identify differentially methylated miRNA-encoding genes, we performed global methylation analysis (Illumina 450 K), integrative analysis (TCGA database), data confirmation (pyrosequencing and RT-qPCR), and functional assays. Results Methylation analysis revealed 27 differentially methylated miRNA genes. The integrative analyses pointed out miR-21 and miR-146b as potentially regulated by methylation (hypomethylation and increased expression). DNA methylation and expression patterns of miR-21 and miR-146b were confirmed as altered, as well as seven of 452 mRNAs targets were down-expressed. The combined methylation and expression levels of miR-21 and miR-146b showed potential to discriminate malignant from benign lesions (91–96% sensitivity and 96–97% specificity). An increased expression of miR-146b due to methylation loss was detected in the TPC1 cell line. The miRNA mimic transfection highlighted putative target mRNAs. Conclusions The increased expression of miR-21 and miR-146b due to loss of DNA methylation in PTC resulted in the disruption of the transcription machinery and biological pathways. These miRNAs are potential diagnostic biomarkers, and these findings provide support for future development of targeted therapies. Electronic supplementary material The online version of this article (10.1186/s13148-018-0579-8) contains supplementary material, which is available to authorized users.
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Lamartina L, Grani G, Durante C, Borget I, Filetti S, Schlumberger M. Follow-up of differentiated thyroid cancer - what should (and what should not) be done. Nat Rev Endocrinol 2018; 14:538-551. [PMID: 30069030 DOI: 10.1038/s41574-018-0068-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The treatment paradigm for thyroid cancer has shifted from a one-size-fits-all approach to more personalized protocols that range from active surveillance to total thyroidectomy followed by radioiodine remnant ablation. Accurate surveillance tools are available, but follow-up protocols vary widely between centres and clinicians, owing to the lack of clear, straightforward recommendations on the instruments and assessment schedule that health-care professionals should adopt. For most patients (that is, those who have had an excellent response to the initial treatment and have a low or intermediate risk of tumour recurrence), an infrequent assessment schedule is sufficient (such as a yearly determination of serum levels of TSH and thyroglobulin). Select patients will benefit from second-line imaging and more frequent assessments. This Review discusses the strengths and weaknesses of the surveillance tools and follow-up strategies that clinicians use as a function of the initial treatment and each patient's risk of recurrence.
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Affiliation(s)
- Livia Lamartina
- Dipartimento di Medicina Interna e Specialità Mediche, Università di Roma "Sapienza", Rome, Italy
| | - Giorgio Grani
- Dipartimento di Medicina Interna e Specialità Mediche, Università di Roma "Sapienza", Rome, Italy
| | - Cosimo Durante
- Dipartimento di Medicina Interna e Specialità Mediche, Università di Roma "Sapienza", Rome, Italy
| | - Isabelle Borget
- Department of Biostatistic and Epidemiology, Gustave Roussy and University Paris-Saclay, Villejuif, France
| | - Sebastiano Filetti
- Dipartimento di Medicina Interna e Specialità Mediche, Università di Roma "Sapienza", Rome, Italy
| | - Martin Schlumberger
- Department of Nuclear Medicine and Endocrine Oncology, Gustave Roussy and University Paris-Saclay, Villejuif, France.
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Thyroid cancers of follicular origin in a genomic light: in-depth overview of common and unique molecular marker candidates. Mol Cancer 2018; 17:116. [PMID: 30089490 PMCID: PMC6081953 DOI: 10.1186/s12943-018-0866-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
In recent years, thyroid malignances have become more prevalent, especially among women. The most common sporadic types of thyroid tumors of follicular origin include papillary, follicular and anaplastic thyroid carcinomas. Although modern diagnosis methods enable the identification of tumors of small diameter, tumor subtype differentiation, which is imperative for the correct choice of treatment, is still troublesome. This review discusses the recent advances in the field of molecular marker identification via next-generation sequencing and microarrays. The potential use of these biomarkers to distinguish among the most commonly occurring sporadic thyroid cancers is presented and compared. Geographical heterogeneity might be a differentiator, although not necessarily a limiting factor, in biomarker selection. The available data advocate for a subset of mutations common for the three subtypes as well as mutations that are unique for a particular tumor subtype. Tumor heterogeneity, a known issue occurring within solid malignancies, is also discussed where applicable. Public databases with datasets derived from high-throughput experiments are a valuable source of information that aid biomarker research in general, including the identification of molecular hallmarks of thyroid cancer.
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45
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Xin Z, Hua L, Shi TT, Tuo X, Yang FY, Li Y, Cao X, Yang JK. A genome-wide DNA methylation analysis in peripheral blood from patients identifies risk loci associated with Graves' orbitopathy. J Endocrinol Invest 2018; 41:719-727. [PMID: 29190000 DOI: 10.1007/s40618-017-0796-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 11/14/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Graves' orbitopathy (GO) is an inflammatory orbital disease of autoimmune origin with the potential to cause severe functional and psychosocial effects. The pathogenesis has not been fully elucidated. We investigated whether DNA methylation was associated with GO incidence in Chinese patients. MATERIALS AND METHODS Six GO patients and six age-matched controls were recruited, and genome-wide DNA methylation patterns were analyzed in their peripheral blood. t tests were performed to determine differential methylated sites in genomic regions and the univariable logistic regression analyses was performed to evaluate their risk with GO incidence. Cluster analysis and principal component analysis (PCA) were performed to determine the effects of the extracted differentially methylated sites. RESULTS One hundred and forty-eight differentially methylated sites were identified, including CD14 (fold change = 4.31, p = 0.005), IL17RE (fold change = 2.128, p = 0.005), and DRD4 (fold change = 0.25, p = 0.004), and were supported by cluster and PCA analyses. Univariable logistic regression analyses showed that the methylation patterns at 12 loci were associated with GO incidence. The relative risk per 1% decrease in methylation at ZCCHC6 and GLI3 was 0.15 (95% CI 0.03-0.91; p = 0.039) and 0.65 (95% CI 0.42-0.98; p = 0.042), respectively. Pearson correlation analyses demonstrated that methylation levels at IL17RE were positively associated with Clinical Activity Score (CAS) (r = 0.967, p < 0.05). CONCLUSIONS Our results demonstrate that differential methylation levels at analyzed sites (genes) may be risk markers of GO. DNA methylation analysis could provide new insights into understanding the disease and provide new treatment strategies for GO in Chinese patients.
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Affiliation(s)
- Z Xin
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
| | - L Hua
- Department of Mathematics, School of Biomedical Engineering, Capital Medical University, Beijing, China
| | - T-T Shi
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - X Tuo
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - F-Y Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Y Li
- Physical Examination Department, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - X Cao
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - J-K Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
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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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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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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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