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Zhang S, Shao H, Shi W, Li KB, You N, Han DM, Mo J. Asymmetric Nanopore Sensor for Logic Detection of Dam and M.SssI Methyltransferases in Combination of DNA Walker and Autocatalytic Hybridization Reaction. Anal Chem 2024. [PMID: 39358840 DOI: 10.1021/acs.analchem.4c04092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
The detection of DNA methyltransferase (MTase) was crucial for understanding gene expression regulation, cancer mechanisms, and various biological processes, contributing significantly to disease diagnosis and drug development. Herein, a nanopore sensor based on cascaded signal amplification of DNA walker and autocatalytic hybridization reaction (AHR) was developed for the ultrasensitive determination of various MTases. In the presence of Dam MTase, the hairpin structure HD underwent methylation and cleavage by DpnI endonuclease, forming T-DNA fragments. These T-DNA fragments were used to activate the DNA walker, which moved across the surface of magnetic beads step by step, generating a large quantity of initiator I by cleaving the substrate. The initiator I subsequently activated the AHR. The AHR included a hybridization chain reaction (HCR) amplifier and a catalytic hairpin assembly (CHA) convertor. The HCR amplifier generated multiple novel CHA triggers, which activated the CHA convertor. This, in turn, stimulated the HCR amplifier, creating an AHR circuit that resulted in the formation of numerous DNA nanowires. These DNA nanowires were adsorbed onto the G4-PAMAM-modified nanopore surface under the influence of an electric field, thereby altering the surface charge of the nanopore and changing the ionic rectification curve. The detection limit of the Dam MTase nanopore sensor reached 0.0002 U/mL. By modification of the recognition sites of the probes, this nanopore system could also be used for the detection of M.SssI MTase. Moreover, a four-input parallel concatenated logic circuit (AND//INHIBIT-OR) had been constructed and applied for the multivariate detection of Dam MTase and M.SssI MTase, presenting a novel conceptual model for advancing the construction of nanopore logic gate systems and their applications in biosensing.
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Affiliation(s)
- Siqi Zhang
- Department of Hepatobiliary, Taizhou Central Hospital, Taizhou University, Taizhou, Zhejiang 318000, China
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Taizhou 318000, Zhejiang, China
| | - Huahao Shao
- Zhijiang College of Zhejiang University of Technology, Shaoxing, Zhejiang 312000, China
| | - Wei Shi
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Taizhou 318000, Zhejiang, China
| | - Kai-Bin Li
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Taizhou 318000, Zhejiang, China
| | - Nan You
- College of Petrochemical Engineering, Liaoning Petrochemical University, Fushun 113001, China
| | - De-Man Han
- Department of Hepatobiliary, Taizhou Central Hospital, Taizhou University, Taizhou, Zhejiang 318000, China
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Taizhou 318000, Zhejiang, China
| | - Jinggang Mo
- Department of Hepatobiliary, Taizhou Central Hospital, Taizhou University, Taizhou, Zhejiang 318000, China
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Zhou Z, Jin M, Li B, He Y, Liu L, Ren B, Li J, Li F, Liu J, Chen Y, Wan S, Shen H. Effects of different iodine levels on the DNA methylation of intrinsic apoptosis-associated genes and analysis of gene-environment interactions in patients with autoimmune thyroiditis. Br J Nutr 2023; 130:2039-2052. [PMID: 37183696 DOI: 10.1017/s0007114523001216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Iodine is an essential nutrient that may change the occurrence of autoimmune thyroiditis (AIT). Apoptosis and DNA methylation participate in the pathogenesis and destructive mechanism of AIT. We detected the methylation and the expression of mRNA of intrinsic apoptosis-associated genes (YWHAG, ING4, BRSK2 and GJA1) to identify the potential interactions between the levels of methylation in these genes and different levels of iodine. 176 adult patients with AIT in Shandong Province, China, were included. The MethylTargetTM assay was used to verify the levels of methylation. We used PCR to detect the mRNA levels of the candidate genes. Interactions between methylation levels of the candidate genes and iodine levels were evaluated with multiplicative and addictive interaction models and GMDR. In the AIT group, YWHAG_1 and six CpG sites and BRSK2_1 and eight CpG sites were hypermethylated, whereas ING4_1 and one CpG site were hypomethylated. A negative correlation was found between methylation levels of YWHAG and mRNA expression. The combination of iodine fortification, YWHAG_1 hypermethylation and BRSK2_1 hypermethylation was significantly associated with elevated AIT risk. A four-locus model (YWHAG_1 × ING4_1 × BRSK2_1 × iodine level) was found to be the best model of the gene-environment interactions. We identified abnormal changes in the methylation status of YWHAG, ING4 and BRSK2 in patients with AIT in different iodine levels. Iodine fortification not only affected the methylation levels of YWHAG and BRSK2 but also interacted with the methylation levels of these genes and may ultimately increase the risk of AIT.
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Affiliation(s)
- Zheng Zhou
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Meihui Jin
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Baoxiang Li
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Yanhong He
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Lixiang Liu
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Bingxuan Ren
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Jianshuang Li
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, People's Republic of China
| | - Fan Li
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Jinjin Liu
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Yun Chen
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
| | - Siyuan Wan
- Department of Preventive Medicine, Qiqihar Medical University, Qiqihar City, Heilongjiang Province161006, People's Republic of China
| | - Hongmei Shen
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, Heilongjiang Province150081, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin City, Heilongjiang Province, People's Republic of China
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Li F, Zhou Z, Wang L, Li B, Jin M, Liu J, Chen Y, He Y, Ren B, Shen H, Liu L. A study of programmed death-1/programmed death ligand and iodine-induced autoimmune thyroiditis in NOD.H-2h4 mice. ENVIRONMENTAL TOXICOLOGY 2023; 38:2574-2584. [PMID: 37598415 DOI: 10.1002/tox.23893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/14/2023] [Accepted: 07/01/2023] [Indexed: 08/22/2023]
Abstract
Excess iodine will trigger the occurrence of autoimmune thyroiditis (AIT), and programmed death-1 (PD-1)/programmed death ligand (PD-L) will also contribute to the development of AIT. The purpose of this study was to explore the role that negative regulatory signals mediated by PD-1/PD-L play in the development of spontaneous autoimmune thyroiditis (SAT) in NOD.H-2h4 mice when they are exposed to iodine. Programmed death ligand 1 (PD-L1) antibody was administered intraperitoneally to NOD.H-2h4 mice. The relevant indicators were determined by flow cytometry, real-time quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, immunohistochemistry, pathological hematoxylin and eosin staining, and arsenic-cerium catalytic spectrophotometry. Results showed that the level of urinary iodine, the level of thyroid lymphocyte infiltration, the level of thyroglobulin antibodies (TgAb) and interferon (IFN-γ)/tumor necrosis factor (TNF-α)/interleukin (IL-2)/IL-17, and the relative expression of PD-1/PD-L1/programmed death-2 (PD-L2) increased with the intervention of excess iodine. After the intervention of the PD-L1 antibody, the expression of PD-1/PD-L1/PD-L2 in different degrees was inhibited, but the level of thyroid lymphocyte infiltration and serum TgAb/IFN-γ/TNF-α/ IL-2/IL-17 did not decrease. Collectively, although PD-1/PD-L participates in the occurrence of SAT and induces inflammation, administration of the PD-L1 antibody does not effectively improve the pathological process of SAT. More research is needed to determine whether PD-1/PD-L intervention can treat autoimmune thyroid disease.
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Affiliation(s)
- Fan Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
- Control Infection Department, Xi'an First Hospital, Xi'an, People's Republic of China
| | - Zheng Zhou
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Lingbo Wang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Baoxiang Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Meihui Jin
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Jinjin Liu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Yun Chen
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Yanhong He
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Bingxuan Ren
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Hongmei Shen
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
| | - Lixiang Liu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, People's Republic of China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, People's Republic of China
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Cai Y, Su H, Si Y, Ni N. Machine learning-based prediction of diagnostic markers for Graves' orbitopathy. Endocrine 2023:10.1007/s12020-023-03349-z. [PMID: 37059863 PMCID: PMC10293385 DOI: 10.1007/s12020-023-03349-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/26/2023] [Indexed: 04/16/2023]
Abstract
PURPOSE The pathogenesis of Graves' orbitopathy/thyroid-associated orbitopathy (TAO) is still unclear, and abnormal DNA methylation in TAO has been reported. Thus, selecting and exploring TAO biomarkers associated with DNA methylation may provide a reference for new therapeutic targets. METHODS The TAO-associated expression data and methylation data were downloaded from The Gene Expression Omnibus database. Firstly, weighted gene co-expression network analysis was used to obtain the TAO-related genes, which were intersected with differentially methylated genes (DMGs), and differentially expressed genes between TAO samples and normal samples to obtain TAO-associated DMGs (TA-DMGs). Thereafter, the functions of the TA-DMGs were analyzed, and diagnostic markers were screened by least absolute shrinkage and selection operator (Lasso) regression analysis and support vector machine (SVM) analysis. The expression levels and diagnostic values of the diagnostic markers were also analyzed. Furthermore, single gene pathway enrichment analysis was performed for each diagnostic marker separately using gene set enrichment analysis (GSEA) software. Next, we also performed immune infiltration analysis for each sample in the GSE58331 dataset using the single-sample GSEA algorithm, and the correlation between diagnostic markers and differential immune cells was explored. Lastly, the expressions of diagnostic markers were explored by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS A total of 125 TA-DMGs were obtained. The enrichment analysis results indicated that these TA-DMGs were mainly involved in immune-related pathways, such as Th1 and Th2 cell differentiation and the regulation of innate immune response. Moreover, two diagnostic markers, including S100A11 and NKD2, were obtained by Lasso regression analysis and SVM analysis. Single gene pathway enrichment analysis showed that S100A11 was involved in protein polyufmylation, pancreatic-mediated proteolysis, and NKD2 was involved in innate immune response in mucosa, Wnt signaling pathway, etc. Meanwhile, immune cell infiltration analysis screened 12 immune cells, including CD56 dim natural killer cells and Neutrophil cells that significantly differed between TAO and normal samples, with the strongest positive correlation between NKD2 and CD56 dim natural killer cells. Finally, the qRT-PCR illustrated the expressions of NKD2 and S100A11 between normal and TAO. CONCLUSION NKD2 and S100A11 were screened as biomarkers of TAO and might be regulated by DNA methylation in TAO, providing a new reference for the diagnosis and treatment of TAO patients.
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Affiliation(s)
- Yunying Cai
- Department of Endocrinology, The First People's Hospital of Yunnan Province. The Affiliated Hospital of Kunming University of Science and Technology, Kunming City, Yunnan Provence, China
| | - Heng Su
- Department of Endocrinology, The First People's Hospital of Yunnan Province. The Affiliated Hospital of Kunming University of Science and Technology, Kunming City, Yunnan Provence, China.
| | - Yongting Si
- Department of Endocrinology, The First People's Hospital of Yunnan Province. The Affiliated Hospital of Kunming University of Science and Technology, Kunming City, Yunnan Provence, China
| | - Ninghua Ni
- Department of Ophthalmology, The First People's Hospital of Yunnan Province. The Affiliated Hospital of Kunming University of Science and Technology, Kunming City, Yunnan Provence, China
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Lafontaine N, Wilson SG, Walsh JP. DNA Methylation in Autoimmune Thyroid Disease. J Clin Endocrinol Metab 2023; 108:604-613. [PMID: 36420742 DOI: 10.1210/clinem/dgac664] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/02/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022]
Abstract
Graves disease and Hashimoto disease form part of the spectrum of autoimmune thyroid disease (AITD), to which genetic and environmental factors are recognized contributors. Epigenetics provides a potential link between environmental influences, gene expression, and thyroid autoimmunity. DNA methylation (DNAm) is the best studied epigenetic process, and global hypomethylation of leukocyte DNA is reported in several autoimmune disorders. This review summarizes the current understanding of DNAm in AITD. Targeted DNAm studies of blood samples from AITD patients have reported differential DNAm in the promoter regions of several genes implicated in AITD, including TNF, IFNG, IL2RA, IL6, ICAM1, and PTPN22. In many cases, however, the findings await replication and are unsupported by functional studies to support causal roles in AITD pathogenesis. Furthermore, thyroid hormones affect DNAm, and in many studies confounding by reverse causation has not been considered. Recent studies have shown that DNAm patterns in candidate genes including ITGA6, PRKAA2, and DAPK1 differ between AITD patients from regions with different iodine status, providing a potential mechanism for associations between iodine and AITD. Research focus in the field is moving from candidate gene studies to an epigenome-wide approach. Genome-wide methylation studies of AITD patients have demonstrated multiple differentially methylated positions, including some in immunoregulatory genes such as NOTCH1, HLA-DRB1, TNF, and ICAM1. Large, epigenome-wide studies are required to elucidate the pathophysiological role of DNAm in AITD, with the potential to provide novel diagnostic and prognostic biomarkers as well as therapeutic targets.
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Affiliation(s)
- Nicole Lafontaine
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
- Medical School, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Scott G Wilson
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
- Medical School, University of Western Australia, Crawley, Western Australia 6009, Australia
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Ren B, Wan S, Wu H, Qu M, Chen Y, Liu L, Jin M, Zhou Z, Shen H. Effect of different iodine levels on the DNA methylation of PRKAA2, ITGA6, THEM4 and PRL genes in PI3K-AKT signaling pathway and population-based validation from autoimmune thyroiditis patients. Eur J Nutr 2022; 61:3571-3583. [PMID: 35622138 DOI: 10.1007/s00394-022-02907-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/05/2022] [Indexed: 11/04/2022]
Abstract
PURPOSE Autoimmune thyroiditis (AIT) is one of the most common autoimmune endocrine diseases. The currently recognized causes are genetic susceptibility, environmental factors and immune disorders. It is important to clarify the pathogenesis for the prevention, diagnosis, treatment of AIT and scientific iodine supplementation. This study analyzed the DNA methylation levels of PRKAA2, ITGA6, PRL and THEM4 genes related to PI3K-AKT signaling pathway, compared the DNA methylation levels between cases and controls from different water iodine levels in Shandong Province of China, and evaluated the contribution of PI3K-AKT signaling pathway-related genes in AIT. METHODS A total of 176 adult AIT patients were included from three different water iodine areas, and 176 healthy controls were included according to gender, age and BMI. According to the results of the Illumina Methylation 850 K BeadChip in our previous research, the significant methylation differences of genes on the PI3K-AKT signaling pathway related to AIT were determined. The MethylTarget™ assay was used to detect the methylation levels of the target genes, and real-time PCR experiments were used to verify the mRNA expression levels. RESULTS Compared with the control group, PRKAA2_3 and 15 CpG sites were hyper-methylated. ITGA6 gene and 2 CpG sites were hypo-methylated in AIT cases. The mRNA expression of ITGA6 gene was negatively correlated with the DNA methylation levels of ITGA6 gene and 2 CpG sites. Compared with cases and controls in areas with different water iodine levels, methylation differences were mainly in PRKAA2 and ITGA6 genes. The methylation levels of PRKAA2_1 and PRKAA2_3 were positively correlated with age. The methylation levels of PRL and THEM4 genes were negatively correlated with age. The methylation level of PRKAA2_3 was positively correlated with FT4. CONCLUSION In summary, we identified aberrant DNA methylation levels of PRKAA2 and ITGA6 genes related to PI3K-AKT signaling pathway in the blood of AIT patients. Both iodine supplementation after long-term iodine deficiency and iodine excess can affect the DNA methylation levels of PRKAA2 and ITGA6 genes, and the former affects more obviously. In ITGA6 gene, this aberrant epigenetic modification is associated with the increased mRNA expression.
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Affiliation(s)
- Bingxuan Ren
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Siyuan Wan
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,Department of Preventive Medicine, Qiqihar Medical University, Qiqihar City, 161006, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Huaiyong Wu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Mengying Qu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Yao Chen
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Lixiang Liu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Meihui Jin
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Zheng Zhou
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China.,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China
| | - Hongmei Shen
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin City, 150081, Heilongjiang Province, People's Republic of China. .,National Health Commission and Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University, Harbin, China. .,Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, China.
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7
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Sun H, Xu J, Hu B, Liu Y, Zhai Y, Sun Y, Sun H, Li F, Wang J, Feng A, Tang Y, Zhao J. Association of DNA Methylation Patterns in 7 Novel Genes With Ischemic Stroke in the Northern Chinese Population. Front Genet 2022; 13:844141. [PMID: 35480311 PMCID: PMC9035884 DOI: 10.3389/fgene.2022.844141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Ischemic stroke is a highly complex disorder. This study aims to identify novel methylation changes in ischemic stroke.Methods: We carried out an epigenome-wide study of ischemic stroke using an Infinium HumanMethylation 850K array (cases:controls = 4:4). 10 CpG sites in 8 candidate genes from gene ontology analytics top-ranked pathway were selected to validate 850K BeadChip results (cases:controls = 20:20). We further qualified the methylation level of promoter regions in 8 candidate genes (cases:controls = 188:188). Besides, we performed subgroup analysis, dose-response relationship and diagnostic prediction polygenic model of candidate genes.Results: In the discovery stage, we found 462 functional DNA methylation positions to be associated with ischemic stroke. Gene ontology analysis highlighted the “calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules” item, including 8 candidate genes (CDH2/PCDHB10/PCDHB11/PCDHB14/PCDHB16/PCDHB3/PCDHB6/PCDHB9). In the replication stage, we identified 5 differentially methylated loci in 20 paired samples and 7 differentially methylated genes (CDH2/PCDHB10/PCDHB11/PCDHB14/PCDHB16/PCDHB3/PCDHB9) in 188 paired samples. Subgroup analysis showed that the methylation level of above 7 genes remained significantly different in the male subgroup, large-artery atherosclerosis subgroup and right hemisphere subgroup. The methylation level of each gene was grouped into quartiles, and Q4 groups of the 7 genes were associated with higher risk of ischemic stroke than Q1 groups (p < 0.05). Besides, the polygenic model showed high diagnostic specificity (0.8723), sensitivity (0.883), and accuracy (0.8777).Conclusion: Our results demonstrate that DNA methylation plays a crucial part in ischemic stroke. The methylation of these 7 genes may be potential diagnostic biomarker for ischemic stroke.
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Affiliation(s)
- Hongwei Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jia Xu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Bifeng Hu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yue Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yun Zhai
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanyan Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongwei Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fang Li
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiamin Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Anqi Feng
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Ying Tang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Jingbo Zhao, ; Ying Tang,
| | - Jingbo Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
- *Correspondence: Jingbo Zhao, ; Ying Tang,
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Qu M, Wan S, Wu H, Ren B, Chen Y, Liu L, Shen H. The Whole Blood DNA Methylation Patterns of Extrinsic Apoptotic Signaling Pathway Related Genes in Autoimmune Thyroiditis among Areas with Different Iodine Levels. Br J Nutr 2022; 129:1-35. [PMID: 35260211 DOI: 10.1017/s0007114522000721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Autoimmune thyroiditis (AIT) has a complex etiology and the susceptibility to it is determined by a combination of genetic and environmental factors, although these are not yet fully understood. The present research aimed to explore the DNA methylation patterns in whole blood of extrinsic apoptotic signaling pathway related genes in AIT among areas with different iodine levels. We selected the iodine-fortification areas (IFA), iodine-adequate areas (IAA) and water-based iodine-excess areas (IEA) from Shandong Province of China as survey sites. Totally 176 AIT cases and 176 controls were included. MethylTargetTM and QT-PCR technology were used to detect candidate genes' DNA methylation levels and mRNA expression levels, respectively. We found that DAPK1 DNA methylation levels in AIT cases (especially in female) were significantly higher than controls (t=2.7715, P=0.0059; t=2.4638, P=0.0143 in female). There were differences in DAPK1(t=2.5384, P=0.0121), TNFSF8(t=2.1667, P=0.0334) and TNFAIP8(t=2.5672, P=0.0121) genes methylation between cases and controls with different water iodine levels. The mRNA expression of DAPK1(t=4.329, P<0.001) and TNFAIP8(t=3.775, P<0.001) in the cases were increased. We identified the differences in the DNA methylation status of the extrinsic apoptotic signaling pathway related genes between AIT and controls and in different iodine levels areas. The results were verified at the mRNA level. The environmental iodine may affect DNA methylation to some extent.
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Affiliation(s)
- Mengying Qu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- Division of Health Risk Factor Monitoring and Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Siyuan Wan
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
- Department of Preventive Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, China
| | - Huaiyong Wu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Bingxuan Ren
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Yao Chen
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Lixiang Liu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Hongmei Shen
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
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