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Lafontaine N, Shore CJ, Campbell PJ, Mullin BH, Brown SJ, Panicker V, Dudbridge F, Brix TH, Hegedüs L, Wilson SG, Bell JT, Walsh JP. Epigenome-wide Association Study Shows Differential DNA Methylation of MDC1, KLF9, and CUTA in Autoimmune Thyroid Disease. J Clin Endocrinol Metab 2024; 109:992-999. [PMID: 37962983 PMCID: PMC10940258 DOI: 10.1210/clinem/dgad659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023]
Abstract
CONTEXT Autoimmune thyroid disease (AITD) includes Graves disease (GD) and Hashimoto disease (HD), which often run in the same family. AITD etiology is incompletely understood: Genetic factors may account for up to 75% of phenotypic variance, whereas epigenetic effects (including DNA methylation [DNAm]) may contribute to the remaining variance (eg, why some individuals develop GD and others HD). OBJECTIVE This work aimed to identify differentially methylated positions (DMPs) and differentially methylated regions (DMRs) comparing GD to HD. METHODS Whole-blood DNAm was measured across the genome using the Infinium MethylationEPIC array in 32 Australian patients with GD and 30 with HD (discovery cohort) and 32 Danish patients with GD and 32 with HD (replication cohort). Linear mixed models were used to test for differences in quantile-normalized β values of DNAm between GD and HD and data were later meta-analyzed. Comb-p software was used to identify DMRs. RESULTS We identified epigenome-wide significant differences (P < 9E-8) and replicated (P < .05) 2 DMPs between GD and HD (cg06315208 within MDC1 and cg00049440 within KLF9). We identified and replicated a DMR within CUTA (5 CpGs at 6p21.32). We also identified 64 DMPs and 137 DMRs in the meta-analysis. CONCLUSION Our study reveals differences in DNAm between GD and HD, which may help explain why some people develop GD and others HD and provide a link to environmental risk factors. Additional research is needed to advance understanding of the role of DNAm in AITD and investigate its prognostic and therapeutic potential.
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Affiliation(s)
- Nicole Lafontaine
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Crawley, WA, 6009, Australia
| | - Christopher J Shore
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Purdey J Campbell
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
| | - Benjamin H Mullin
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, 6009, Australia
| | - Suzanne J Brown
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
| | - Vijay Panicker
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Crawley, WA, 6009, Australia
| | - Frank Dudbridge
- Population Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Thomas H Brix
- Department of Endocrinology and Metabolism, Odense University Hospital, Odense, 5000, Denmark
| | - Laszlo Hegedüs
- Department of Endocrinology and Metabolism, Odense University Hospital, Odense, 5000, Denmark
| | - Scott G Wilson
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
- School of Biomedical Sciences, University of Western Australia, Perth, 6009, Australia
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Crawley, WA, 6009, Australia
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Yoshioka S, Arakawa Y, Hasegawa M, Kato S, Hashimoto H, Mori S, Ueda H, Watanabe M. Twin study: genotype-dependent epigenetic factors affecting free thyroxine levels in the normal range. Epigenomics 2024; 16:147-158. [PMID: 38264851 DOI: 10.2217/epi-2023-0372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Aim: To explore the clinical application of DNA methylation affecting thyroid function, we evaluated the association of DNA methylation with free thyroxine (FT4) and TSH measurements in monozygotic twins. Materials & methods: Discordant pairs for FT4 or TSH levels were examined for the relationship between the within-pair difference of each measurement and the DNA methylation levels using epigenome-wide association studies. The contribution of polymorphisms to the methylation sensitivity was also examined. Results: We found two CpG sites significantly associated with FT4 levels, and also some CpG sites showing significant differences in their methylation levels within FT4-discordant pairs depending on the polymorphism in EPHB2. Conclusion: The FT4 level may be associated with a combination of methylation and polymorphisms in the EPHB2 gene.
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Affiliation(s)
- Saki Yoshioka
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Yuya Arakawa
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Mika Hasegawa
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Shiho Kato
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Hinako Hashimoto
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Saho Mori
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Hiromichi Ueda
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Mikio Watanabe
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
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Simmen FA, Alhallak I, Simmen RCM. Krüppel-like Factor-9 and Krüppel-like Factor-13: Highly Related, Multi-Functional, Transcriptional Repressors and Activators of Oncogenesis. Cancers (Basel) 2023; 15:5667. [PMID: 38067370 PMCID: PMC10705314 DOI: 10.3390/cancers15235667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 02/12/2024] Open
Abstract
Specificity Proteins/Krüppel-like Factors (SP/KLF family) are a conserved family of transcriptional regulators. These proteins share three highly conserved, contiguous zinc fingers in their carboxy-terminus, requisite for binding to cis elements in DNA. Each SP/KLF protein has unique primary sequence within its amino-terminal and carboxy-terminal regions, and it is these regions which interact with co-activators, co-repressors, and chromatin-modifying proteins to support the transcriptional activation and repression of target genes. Krüppel-like Factor 9 (KLF9) and Krüppel-like Factor 13 (KLF13) are two of the smallest members of the SP/KLF family, are paralogous, emerged early in metazoan evolution, and are highly conserved. Paradoxically, while most similar in primary sequence, KLF9 and KLF13 display many distinct roles in target cells. In this article, we summarize the work that has identified the roles of KLF9 (and to a lesser degree KLF13) in tumor suppression or promotion via unique effects on differentiation, pro- and anti-inflammatory pathways, oxidative stress, and tumor immune cell infiltration. We also highlight the great diversity of miRNAs, lncRNAs, and circular RNAs which provide mechanisms for the ubiquitous tumor-specific suppression of KLF9 mRNA and protein. Elucidation of KLF9 and KLF13 in cancer biology is likely to provide new inroads to the understanding of oncogenesis and its prevention and treatments.
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Affiliation(s)
- Frank A. Simmen
- Department of Physiology & Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (I.A.); (R.C.M.S.)
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Iad Alhallak
- Department of Physiology & Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (I.A.); (R.C.M.S.)
| | - Rosalia C. M. Simmen
- Department of Physiology & Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (I.A.); (R.C.M.S.)
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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