1
|
Zhou Z, Liu J, Chen Y, Ren B, Wan S, Chen Y, He Y, Wei Q, Gao H, Liu L, Shen H. Genome-wide DNA methylation pattern in whole blood of patients with Hashimoto thyroiditis. Front Endocrinol (Lausanne) 2023; 14:1259903. [PMID: 38075038 PMCID: PMC10704911 DOI: 10.3389/fendo.2023.1259903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Background Hashimoto thyroiditis (HT), a prevalent autoimmune disorder, is not yet thoroughly understood, especially when it comes to the influence of epigenetics in its pathogenesis. The primary goal of this research was to probe the DNAm profile across the genome in the whole blood derived from patients suffering from HT. Method Using the Illumina 850K BeadChip, we conducted a genome-wide DNAm assessment on 10 matched pairs of HT sufferers and healthy individuals. Genes with differential methylation (DMGs) were identified and underwent functional annotation via the databases of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The transcriptional significance of potential epigenetic biomarker genes was corroborated through qRT-PCR. Results The DNAm profiling across the genome indicated an overall reduction in methylation in HT subjects in comparison with their healthy counterparts. We detected 283 DMPs (adjusted P < 0.05 and |Δβ| > 0.1), among which 152 exhibited hypomethylation and 131 demonstrated hypermethylation. Further analysis exposed a noteworthy concentration of hypermethylated DMPs in the 3´UTR, North Shore, and CpG islands, while there was a significant decrease in the Open Sea (all P < 0.001). The 283 DMPs were broadly distributed from chromosome 1 to 22, with chromosome 6 harboring the most DMPs (n = 51) and chromosome 12 carrying the most DMGs (n = 15). The SLFN12 gene, which presented with extreme hypomethylation in its promoter DMPs among HT patients, was identified as the epigenetic marker gene. Consequently, the SLFN12 mRNA expression was markedly upregulated in HT, displaying a negative relationship with its methylation levels. The area under curve (AUC) value for the SLFN12 gene among HT patients was 0.85 (sensitivity: 0.7, specificity: 0.7), a significant difference compared with healthy controls. The methylation levels of all DMPs in SLFN12 gene were negatively correlated with TSH and one CpG site (cg24470734) was positively assocciated with FT4. Conclusion This investigation presents an initial comprehensive DNAm blueprint for individuals with HT, which permits clear differentiation between HT subjects and normal controls through an epigenetic lens. The SLFN12 gene plays a pivotal role in the onset of HT, suggesting that the methylation status of this gene could serve as a potential epigenetic indicator for HT.
Collapse
Affiliation(s)
- Zheng Zhou
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinjin Liu
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yun Chen
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| | - Bingxuan Ren
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| | - Siyuan Wan
- Department of Preventive Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Yao Chen
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanhong He
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qiuyang Wei
- First Clinical Medical Department, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
- Second Department of Endocrinology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Haiyan Gao
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lixiang Liu
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongmei Shen
- Disorders Control, Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Etiology and Epidemiology, National Health Commission & Education Bureau of Heilongjiang Province, Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin, Heilongjiang, China
| |
Collapse
|
2
|
Wang J, Li J. Research progress in the pathogenesis of chronic urticaria. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2023; 48:1602-1610. [PMID: 38432889 PMCID: PMC10929888 DOI: 10.11817/j.issn.1672-7347.2023.230037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Indexed: 03/05/2024]
Abstract
Chronic urticaria is very common in clinic, but its pathogenesis is not fully elucidated. Most patients can't find the exact cause, resulting in misdiagnosis or delayed treatment. Previous studies have found that mast cell activation is the central link in the pathogenesis of chronic urticaria. Genetics, autoimmune, coagulation disorders, and infection may also be involved in the pathophysiological process of chronic urticaria. With the deepening of research, more immune and non-immune mechanisms have been gradually revealed in the pathogenesis of chronic urticaria, such as the interaction of immune cells in the microenvironment of urticaria, intestinal flora and metabolism, neuroimmunity, environmental factors and hormones. Clarifying the pathogenesis of chronic urticaria will help to find more treatment targets and provide more diversified ideas for clinical diagnosis and treatment.
Collapse
Affiliation(s)
- Jiayi Wang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Jie Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China.
| |
Collapse
|
3
|
Yang Z, Wen P, Chen J, Kang J, Xiang Y, Ding S, Gao L, Tong X, Guo A. DNA methylation regulatory patterns and underlying pathways behind the co-pathogenesis of allergic rhinitis and chronic spontaneous urticaria. Front Immunol 2023; 13:1053558. [PMID: 36713372 PMCID: PMC9875140 DOI: 10.3389/fimmu.2022.1053558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
Background Allergic rhinitis (AR) and chronic spontaneous urticaria (CSU) are often concurrent in patients. Changes in DNA methylation affect T cell biological processes, which may explain the occurrence and progression of comorbidity. However, downstream regulatory pathways of DNA methylation in two diseases and the underlying mechanisms have not been fully elucidated. Methods The GSE50101, GSE72541, GSE50222 and OEP002482 were mined for the identification of differentially expressed genes (DEGs) or co-expressed genes and differentially methylated genes (DMGs) in AR and CSU patients. We applied GO analysis and consensus clustering to study the potential functions and signal pathways of selected genes in two diseases. GSVA and logistic regression analysis were used to find the regulatory pathway between DNA methylation and activation patterns of CD4+ T cells. Besides, we used the Illumina 850k chip to detect DNA methylation expression profiles and recognize the differentially methylated CpG positions (DMPs) on corresponding genes. Finally, we annotated the biological process of these genes using GO and KEGG pathway analysis. Result The AR-related DEGs were found closely related to the differentiation and activation of CD4+ T cells. The DEGs or co-expressed genes of CD4+ T cells in AR and CSU patients were also clustered using GO and KEGG analysis and we got 57 co-regulatory pathways. Furthermore, logistic regression analysis showed that the regulation of cellular component size was closely related to the activation of CD4+ T cells regulated by DNA methylation. We got self-tested data using the Illumina 850k chip and identified 98 CpGs that were differentially methylated in patients. Finally, we mapped the DMPs to 15 genes and found that they were mainly enriched in the same CD4+T cell regulating pathway. Conclusion Our study indicated that DNA methylation affected by pollen participated in the activation patterns of CD4 + T cells, providing a novel direction for the symptomatic treatment of the co-occurrence of AR and CSU.
Collapse
Affiliation(s)
- Zijiang Yang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Puqiao Wen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Kang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yaping Xiang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shu Ding
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lihua Gao
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoliang Tong
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Aiyuan Guo
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Aiyuan Guo,
| |
Collapse
|