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Zhang S, Sui L, Kong X, Huang R, Li Z. HDAC6 decreases H4K16 and α-tubulin acetylation during porcine oocyte maturation. Cell Cycle 2023; 22:2057-2069. [PMID: 37904550 PMCID: PMC10761081 DOI: 10.1080/15384101.2023.2275907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/22/2023] [Indexed: 11/01/2023] Open
Abstract
HDAC6 is an essential factor in mouse oocyte maturation. However, the roles of HDAC6 in porcine oocyte maturation are still unclear. Therefore, we analyzed the roles of HDAC6 in porcine oocyte maturation by treatment with Tubastatin A (TubA) which is an HDAC6 inhibitor. Our results showed that treatment with 10 μg/ml TubA significantly decreased the rate of porcine oocyte maturation, but it did not influence the rate of germinal vesicle breakdown (GVBD). Then, we found that TubA treatment disrupted spindle organization by increasing the α-tubulin acetylation level during porcine oocyte maturation. Moreover, TubA treatment significantly increased H4K16 acetylation, which may compromise kinetochore and microtubule (K-MT) attachment during meiosis in porcine oocytes. We also analyzed the effects of TubA on meiosis-related (H3T3pho and H3S10pho) and transcription-related histone modifications (H3K4me3, H3K9me3 and H3K4ac) during porcine oocyte maturation. The results showed that TubA treatment increased H3S10pho and H3K4ac levels, but no influence was seen in H3T3pho, H3K4me3 and H3K9me3 levels in porcine oocytes. TubA treated oocytes also showed a compromised ability to develop after parthenogenetic activation. Finally, we found that HDAC6 exhibited higher mRNA levels and lower DNA methylation levels in porcine oocytes than it did in porcine embryonic fibroblasts (PEFs). These results indicate that the low level of DNA methylation in HDAC6 promoter ensures high expression. HDAC6 regulates the deacetylation of α-tubulin and H4K16, which promotes correct spindle organization and meiotic apparatus assembly during porcine oocyte maturation. This study illustrates a new pathway by which HDAC6 modulates mammalian oocyte maturation.
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Affiliation(s)
- Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin, China
| | - Liyan Sui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin, China
| | - Xiangjie Kong
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin, China
| | - Rong Huang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin, China
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2
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Ehtesham N, Habibi Kavashkohie MR, Mazhari SA, Azhdari S, Ranjbar H, Mosallaei M, Hazrati E, Behroozi J. DNA methylation alterations in systemic lupus erythematosus: A systematic review of case-control studies. Lupus 2023; 32:363-379. [PMID: 36573333 DOI: 10.1177/09612033221148099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Traditionally, the diagnosis and monitoring of disease activity in systemic lupus erythematosus (SLE) are contingent upon clinical manifestations and serological markers. However, researchers are struggling to find biomarkers with higher sensitivity and specificity. DNA methylation has been the most studied epigenetic feature in SLE. So, in this study, we performed a systematic review of studies about DNA methylation alterations in SLE patients compared to healthy controls. METHODS By searching PubMed, Scopus, and Google Scholar up to July 2022, all case-control studies in which DNA methylation of specific genes was assessed by a non-high-throughput technique and passed the quality of bias assessment were included. RESULTS In total, 44 eligible studies underwent a data extraction process. In all, 3471 SLE patients and 1028 healthy individuals were included. Among the studies that reported the patients' gender (n = 2853), 89.41% were female and 10.59% were male. Forty studies have been conducted on adult patients. The number of works on fractionated and unfractionated blood cells was almost equal. In this regard, 22 studies were conducted on whole blood or peripheral blood mononuclear cells and two studies on unfractionated white blood cells. Sorted blood cells were biological sources in 20 studies. The most investigated gene was IFI44L. Sensitivity, specificity, and diagnostic power of methylation levels were only reported for IFI44L in five studies. The most employed methylation profiling method was bisulfite sequencing polymerase chain reaction. The correlation between methylation patterns and clinical parameters was explored in 22 studies, which of them 16 publications displayed a remarkable association between DNA methylation status and clinical indices. CONCLUSIONS The methylation status of some genes especially IFI44L, FOXP3, and MX1 has been suggested as promising SLE biomarkers. However, given the conflicting findings between studies because of potential confounders such as different sample types, methylation profiling methods, and ethnicity as well as shared DNA methylation patterns of SLE and other autoimmune diseases, DNA methylation biomarkers are currently not reliable diagnostic biomarkers and do not represent surrogate markers of SLE disease activity. Future investigations on a larger scale with the discarding of limitations of previous studies would probably lead to a consensus.
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Affiliation(s)
- Naeim Ehtesham
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, 162996AJA University of Medical Sciences, Tehran, Iran.,Student Research Committee, 48533University of Social Welfare and Rehabilitation Science, Tehran, Iran
| | | | - Seyed Amirhossein Mazhari
- Department of Medical Biology and Genetics, 217747Azerbaijan Medical University (AMU), Baku, Azerbaijan
| | - Sara Azhdari
- Department of Anatomy and Embryology, School of Medicine, 394237Bam University of Medical Sciences, Bam, Iran
| | - Hamta Ranjbar
- Student Research Committee, 48463Kerman University of Medical Sciences, Kerman, Iran
| | - Meysam Mosallaei
- Student Research Committee, 48533University of Social Welfare and Rehabilitation Science, Tehran, Iran.,Department of Genetics and Molecular Biology, School of Medicine, 48455Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ebrahim Hazrati
- Department of Anesthesiology and Intensive Care, Medical Faculty, 162996AJA University of Medical Sciences, Tehran, Iran
| | - Javad Behroozi
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, 162996AJA University of Medical Sciences, Tehran, Iran.,Research Center for Cancer Screening and Epidemiology, 162996AJA University of Medical Sciences, Tehran, Iran
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Methyl Donor Micronutrients: A Potential Dietary Epigenetic Target in Systemic Lupus Erythematosus Patients. Int J Mol Sci 2023; 24:ijms24043171. [PMID: 36834583 PMCID: PMC9961281 DOI: 10.3390/ijms24043171] [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: 12/21/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by an aberrant immune response and persistent inflammation. Its pathogenesis remains unknown; however, a complex interaction between environmental, genetic, and epigenetic factors has been suggested to cause disease onset. Several studies have demonstrated that epigenetic alterations, such as DNA hypomethylation, miRNA overexpression, and altered histone acetylation, may contribute to SLE onset and the disease's clinical manifestations. Epigenetic changes, especially methylation patterns, are modifiable and susceptible to environmental factors such as diet. It is well known that methyl donor nutrients, such as folate, methionine, choline, and some B vitamins, play a relevant role in DNA methylation by participating as methyl donors or coenzymes in one-carbon metabolism. Based on this knowledge, this critical literature review aimed to integrate the evidence in animal models and humans regarding the role of nutrients in epigenetic homeostasis and their impact on immune system regulation to suggest a potential epigenetic diet that could serve as adjuvant therapy in SLE.
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4
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Liao L, Li S, Upreti B, Wang X, Yang Y, Lou X, Li L, Cui R, Liu S, Cheng Y, Xu J. Status of TWEAK DNA methylation and mRNA expression in systemic lupus erythematosus. Lupus 2023; 32:171-179. [PMID: 36418949 DOI: 10.1177/09612033221141261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Draw upon research into the serum concentration, mRNA expression, and DNA methylation of TNF-like weak inducer of apoptosis (TWEAK) in the peripheral blood of systemic lupus erythematosus patients and healthy controls in an attempt to investigate the epigenetics associated with TWEAK in the pathogenesis of systemic lupus erythematosus (SLE). METHODS A total of 178 SLE patients (SLE group) and 131 sex-age matched healthy controls (HC group) were recruited. Enzyme-linked immunosorbent assays (ELISA) was used to detect serum protein concentration of TWEAK. TWEAK mRNA expression was analyzed by Real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). Methylation levels of the promotor of TWEAK were measured using quantitative DNA methylation analysis on the MassARRAY spectrometry. RESULTS Serum TWEAK concentrations were not statistically significant in SLE patients and HCs. Nevertheless, serum TWEAK concentrations were significantly lower in patients with renal involvement when compared to those without it. Serum TWEAK concentrations were reduced in clinically active patients (SLEDAI ≥ 10) compared with clinically stable patients (SLEDAI < 10). It was also significantly associated with SLEDAI. Compared with the HC group, the TWEAK mRNA expression in the SLE group was significantly lower. The global DNA methylation levels of TWEAK in the SLE group were observed to be significantly higher than the HC group. SLE patients with renal involvement, and the clinically active patients had higher TWEAK global methylation as well as exhibited variation in certain CpG island methylation. Furthermore, TWEAK methylation negatively correlated with TWEAK mRNA expression. CONCLUSION This study suggests that TWEAK DNA methylation is a valuable as a focus for epigenetic studies because of it potentially influencing TWEAK gene expression in SLE patients. Aberrant DNA methylation of TWEAK may be involved in the initiation and development of SLE.
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Affiliation(s)
- Li Liao
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shu Li
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Bibhuti Upreti
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiangyu Wang
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yifan Yang
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xue Lou
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Luqiong Li
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruomei Cui
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shuang Liu
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuqi Cheng
- Department of Psychiatry, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jian Xu
- Department of Rheumatology and Immunology, 36657First Affiliated Hospital of Kunming Medical University, Kunming, China
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5
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Ning Y, Li Y, Wang H. ANXA2 is a potential biomarker for cancer prognosis and immune infiltration: A systematic pan-cancer analysis. Front Genet 2023; 14:1108167. [PMID: 36713082 PMCID: PMC9877333 DOI: 10.3389/fgene.2023.1108167] [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: 11/25/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
Background: Annexin A2 (ANXA2) belongs to the Annexin A family and plays a role in epithelial-mesenchymal transition, fibrinolysis, and other physiological processes. Annexin A2 has been extensively implicated in tumorigenesis and development in previous studies, but its precise role in pan-cancer remains largely unknown. Methods: We adopted bioinformatics methods to explore the oncogenic role of Annexin A2 using different databases, including the Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) biobank, the Human Protein Atlas (HPA), the Gene Expression Profiling Interaction Analysis (GEPIA) and cBioPortal. We analyzed the differential expression of Annexin A2 in different tumors and its relationship with cancer prognosis, immune cell infiltration, DNA methylation, tumor mutation burden (TMB), microsatellite instability (MSI) and mismatch repair (MMR). Furtherly, we conducted a Gene Set Enrichment Analysis (GSEA) to identify the Annexin A2-related pathways. Results: Annexin A2 expression was upregulated in most cancers, except in kidney chromophobe (KICH) and prostate adenocarcinoma (PRAD). Annexin A2 showed a good diagnostic efficacy in twelve types of cancer. The high expression of Annexin A2 was significantly associated with a reduced overall survival, disease-specific survival and progression-free interval in seven cancers. The Annexin A2 expression was variably associated with infiltration of 24 types of immune cells in 32 tumor microenvironments. In addition, Annexin A2 expression was differently associated with 47 immune checkpoints, immunoregulators, DNA methylation, tumor mutation burden, microsatellite instability and mismatch repair in pan-cancer. Gene Set Enrichment Analysis revealed that Annexin A2 was significantly correlated with immune-related pathways in fifteen cancers. Conclusion: Annexin A2 widely correlates with immune infiltration and may function as a promising prognostic biomarker in many tumors, showing its potential as a target for immunotherapy in pan-cancer.
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Affiliation(s)
- Yijie Ning
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yufei Li
- Department of Neurosurgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongqin Wang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, China,*Correspondence: Hongqin Wang,
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Liotti A, Ferrara AL, Loffredo S, Galdiero MR, Varricchi G, Di Rella F, Maniscalco GT, Belardo M, Vastano R, Prencipe R, Pignata L, Romano R, Spadaro G, de Candia P, Pezone A, De Rosa V. Epigenetics: an Opportunity to Shape Innate and Adaptive Immune Responses. Immunol Suppl 2022; 167:451-470. [PMID: 36043705 DOI: 10.1111/imm.13571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
Epigenetics connects genetic and environmental factors: it includes DNA methylation, histone post-translational modifications and the regulation of chromatin accessibility by non-coding RNAs, all of which control constitutive or inducible gene transcription. This plays a key role in harnessing the transcriptional programs of both innate and adaptive immune cells due to its plasticity and environmental-driven nature, piloting myeloid and lymphoid cell fate decision with no change in their genomic sequence. In particular, epigenetic marks at the site of lineage specific transcription factors and maintenance of cell type-specific epigenetic modifications, referred to as "epigenetic memory", dictate cell differentiation, cytokine production and functional capacity following repeated antigenic exposure in memory T cells. Moreover, metabolic and epigenetic reprogramming occurring during a primary innate immune response leads to enhanced responses to secondary challenges, a phenomenon known as "trained immunity". Here we discuss how stable and dynamic epigenetic states control immune cell identity and plasticity in physiological and pathological conditions. Dissecting the regulatory circuits of cell fate determination and maintenance is of paramount importance for understanding the delicate balance between immune cell activation and tolerance, in healthy conditions and in autoimmune diseases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Antonietta Liotti
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Anne Lise Ferrara
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Stefania Loffredo
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Maria Rosaria Galdiero
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Gilda Varricchi
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Francesca Di Rella
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori IRCCS Fondazione Pascale, Naples, Italy
| | - Giorgia Teresa Maniscalco
- Neurological Clinic and Stroke Unit and Multiple Sclerosis Center "A. Cardarelli" Hospital, Naples, Italy
| | - Martina Belardo
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Roberta Vastano
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Rosaria Prencipe
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roberta Romano
- Department of Translational Medical Sciences, Pediatric Section, University of Naples "Federico II", Naples, Italy
| | - Giuseppe Spadaro
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Paola de Candia
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Antonio Pezone
- Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Veronica De Rosa
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
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Yang D, Li H, Chen Y, Li C, Ren W, Huang Y. A Pan-Cancer Analysis of the Oncogenic Role of BCL7B: A Potential Biomarker for Prognosis and Immunotherapy. Front Genet 2022; 13:906174. [PMID: 35910232 PMCID: PMC9334570 DOI: 10.3389/fgene.2022.906174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Previous studies have partly explored the role of B-cell CLL/lymphoma 7 protein family member B (BCL7B) in tumorigenesis and development. However, the prognosis and immunoregulatory value of BCL7B in pan-cancer patients remains unclear. Methods: Through The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, the distinct expression of BCL7B gene in 33 tumors and adjacent normal tissues was analyzed. The Kaplan–Meier method (univariate Cox regression analysis and Kaplan–Meier curve) was used to identify the cancer types whose BCL7B gene expression was related to prognosis. The receiver operating characteristic (ROC) curve was used to elucidate the diagnosis value of BCL7B gene. Spearman’s rank correlation coefficient was used to explore the relationship between BCL7B gene expression and immune cell infiltration, immune checkpoints, DNA methylation, DNA repair genes, immune-activating genes, immune-suppressing genes, immune subtypes, tumor mutation burden (TMB), and microsatellite instability (MSI). The Wilcoxon rank sum test and Kruskal–Wallis test were used to compare the expression of BCL7B gene in tumor tissues with different clinicopathological features. Gene set enrichment analysis (GSEA) was conducted to identify the tumor-related pathways in pan-cancer. The Human Protein Atlas (HPA) database was used to verify the BCL7B gene expression at the protein level. Results: High expression of BCL7B was associated with an inferior prognosis in glioblastoma multiforme (GBM), glioma (GBMLGG), kidney chromophobe (KICH), brain lower grade glioma (LGG), oral squamous cell carcinoma (OSCC), rectum adenocarcinoma (READ), and uveal melanoma (UVM). Low expression of BCL7B was associated with a poor prognosis in kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), skin cutaneous melanoma (SKCM), thyroid carcinoma (THCA), and sarcoma (SARC). The BCL7B gene expression had varying degrees of correlation with 24 immune cell subsets in 37 tumor environments such as adrenocortical carcinoma (ACC) and bladder urothelial carcinoma (BCLA). Spearman’s rank correlation coefficient showed that BCL7B gene expression had different degrees of correlation with 47 immune checkpoints, 46 immune-activating genes, 24 immune-suppressing genes, 5 DNA repair genes, and DNA methylation, TMB, and MSI in 39 tumors. GSEA suggested that BCL7B was notably associated with cancer-related and immune-related pathways. Conclusion: In summary, BCL7B gene has a high diagnostic and prognostic value in pan-cancer and is related to the infiltration of 24 immune cell subsets in pan-cancer.
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Affiliation(s)
- Dinglong Yang
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Hetong Li
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Yujing Chen
- School of Public Health, Xi’an Jiaotong University, Xian, China
| | - Chunjiang Li
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Weiping Ren
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yongbo Huang
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Yongbo Huang,
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Establishment of DNA Methylation Profile Associated with TCM Syndrome in Endometriosis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4866360. [PMID: 35449808 PMCID: PMC9017494 DOI: 10.1155/2022/4866360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022]
Abstract
Objectives To screen the potential epigenetic biomarkers associated with endometriosis (EMS) and traditional Chinese medicine (TCM) syndrome EMS types. Methods A cohort of 99 participants comprising 42 EMS patients with cold coagulation blood stasis (CCBS) syndrome, 35 EMS patients with Qi stagnation blood stasis (QSBS) syndrome, and 22 women of childbearing age without EMS were recruited. Reduced representation bisulfite sequencing (RRBS) was used to establish the differential DNA methylation profiles in human peripheral blood samples obtained from four non-EMS and four EMS patients with CCBS or QSBS syndrome, respectively. Differentially expressed genes (DEGs) were verified in 18 non-EMS, 38 CCBS-EMS, and 31 QSBS-EMS using pyrosequencing. Results Methylation sites of 123942, 127229, and 115961 were found in peripheral blood DNA of non-EMS, CCBS-EMS, and QSBS-EMS patients, respectively. GO and KEGG analyses showed that the pathological process of EMS may be closely related to the nervous system development, cell junctions, GABA-gated chloride ion channel activity, nicotine addiction, Hippo signaling pathway, mRNA surveillance pathway, and Wnt signaling pathway. The methylation level at CpG site within HDAC6 gene in QSBS-EMS patients was significantly different from that in control women. Conclusions The changes in DNA methylation in peripheral blood samples may be associated with EMS and TCM syndrome EMS types. The methylation level of HDAC6 gene may be used to distinguish QSBS-EMS patients from women without EMS.
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Fang TJ, Lin CH, Lin YZ, Chiu MHS, Li RN, Chan HC, Yeh YT, Yen JH. Lower HDAC6 mRNA expression and promoter hypomethylation are associated with RA susceptibility. J Formos Med Assoc 2021; 121:1431-1441. [PMID: 34732304 DOI: 10.1016/j.jfma.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/25/2021] [Accepted: 10/12/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/PURPOSE Recent studies showed that Histone deacetylases 6 (HDAC6) inhibitors could improve arthritis in rheumatoid arthritis (RA) rodent models, whereas lower HDAC6 expression was observed in RA patients' synovial fibroblasts, raising the concerns to use HDAC6 inhibitors to treat RA patients. In the present study, we investigated the involvement of HDAC6 mRNA expression and promoter methylation in RA. METHODS The DNA and RNAs were extracted from the peripheral blood mononuclear cells (PBMCs) from 138 RA patients and 102 healthy controls. The pyrosequencing technique was used for promoter methylation analysis. The quantitative real-time polymerase chain reaction was used to determine the HDAC6 mRNA expression. The patients' clinical characteristics and disease biomarkers were recorded when blood sampling. RESULTS The HDAC6 mRNA expression was lower in the RA patients than controls (p = 0.001). The RA patients had significant hypomethylation of the HDAC6 promoter (p < 0.001). The HDAC6 promoter was hypo-methylated in the -229, -225, -144, and -142 CpG sites in RA patients (p < 0.05). Unexpectedly, promoter methylation and mRNA expression of the HDAC6 gene were positively associated (p < 0.001). The HDAC6 mRNA expression and promoter methylation status were associated with the risk of RA (p = 0.006 and 0.002, respectively). The inflammatory cytokines, TNF-α and IL-6, were significantly increased after HDAC6 knockdown in PMA-stimulated THP1 cells and SW982 cells (p < 0.05). CONCLUSION The HDAC6 mRNA expression and promoter methylation were lower in RA patients. Both HDAC6 mRNA expression level and promoter hypomethylation were associated the susceptibility of RA. HDAC6 inhibitors seem not proper for RA patients' treatment.
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Affiliation(s)
- Tzu-Jung Fang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Taiwan; Division of Geriatrics and Gerontology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Taiwan
| | - Chia-Hui Lin
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Taiwan
| | - Yuan-Zhao Lin
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Taiwan
| | - Min-HSi Chiu
- Aging and Disease Prevention Research Center, Fooyin University, Taiwan; Biomedical Analysis Center, Fooyin University Hospital, Taiwan
| | - Ruei-Nian Li
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Taiwan
| | - Hua-Chen Chan
- Center for Lipid Biosciences, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medical Laboratory Science and Biotechnology, School of Medical and Health Sciences, Fooyin University, Kaohsiung, Taiwan
| | - Yao-Tsung Yeh
- Aging and Disease Prevention Research Center, Fooyin University, Taiwan; Biomedical Analysis Center, Fooyin University Hospital, Taiwan
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Taiwan; Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Taiwan; College of Biological Science and Technology, National Yang Ming Chiao Tung University, Taiwan; Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan.
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10
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Song W, Qiu J, Yin L, Hong X, Dai W, Tang D, Liu D, Dai Y. Integrated analysis of competing endogenous RNA networks in peripheral blood mononuclear cells of systemic lupus erythematosus. J Transl Med 2021; 19:362. [PMID: 34419106 PMCID: PMC8380341 DOI: 10.1186/s12967-021-03033-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/07/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is an autoimmune disease with a complicated pathogenesis, and its aetiology has not been clearly unveiled. The lack of effective diagnosis and treatment methods makes it necessary to explore the molecular mechanism of SLE. We aimed to identify some critical signalling pathways and key competing endogenous RNAs (ceRNAs) underlying the molecular mechanism of SLE and to map out the systematic signalling networks by integrating the data on different kinds of RNAs. METHODS Peripheral blood mononuclear cells (PBMCs) were collected from both SLE patients and healthy subjects, RNA was extracted from the PBMCs, and RNA libraries including ribosomal RNA-depleted strand-specific libraries and small RNA libraries were built for deep RNA sequencing (RNA-seq). RNA-seq yielded differential expression profiles of lncRNAs/circRNAs/miRNAs/mRNAs related to SLE. The DAVID database (v. 6.8) was employed for Gene Ontology (GO) and KEGG pathway analysis. ceRNA networks (circRNA/lncRNA-miRNA-mRNA) were constructed and visualized using Cytoscape software (v. 3.5.0). The TargetScan and miRanda databases were used to predict target relationships in ceRNA networks. qRT-PCR was used to verify our data. RESULTS Differential expression of ceRNAs related to SLE was detected in SLE patients' PBMCs: 644 mRNAs (384 upregulated, 260 downregulated), 326 miRNAs (223 upregulated, 103 downregulated), 221 lncRNAs (79 upregulated, 142 downregulated), and 31 circRNAs (21 upregulated, 10 downregulated). We drew ceRNA signalling networks made up of the differentially expressed mRNAs/miRNAs/lncRNAs/circRNAs mentioned above, and the hub genes included IRF5, IFNAR2, TLR7, IRAK4, STAT1, STAT2, C2, and Tyk2. These hub genes were involved in ceRNA signalling pathways, such as the IL-17 signalling pathway and type I interferon signalling pathway. CONCLUSIONS We explored the differential expression profiles of various kinds of ceRNAs and integrated signalling networks constructed by ceRNAs. Our findings offer new insights into the pathogenesis of SLE and hint at therapeutic strategies.
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Affiliation(s)
- Wencong Song
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China
- The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Jie Qiu
- School of Computer Science and Engineering, Yulin Normal University, Yulin, China
| | - Lianghong Yin
- The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Xiaoping Hong
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, 78712, USA
| | - Donge Tang
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China.
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin NO. 924 Hospital, Guilin, 541002, China.
| | - Dongzhou Liu
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China.
| | - Yong Dai
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China.
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin NO. 924 Hospital, Guilin, 541002, China.
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Abstract
The term "epigenetics" refers to a series of meiotically/mitotically inheritable alterations in gene expression, related to environmental factors, without disruption on DNA sequences of bases. Recently, the pathophysiology of autoimmune diseases (ADs) has been closely linked to epigenetic modifications. Actually, epigenetic mechanisms can modulate gene expression or repression of targeted cells and tissues involved in autoimmune/inflammatory conditions acting as keys effectors in regulation of adaptive and innate responses. ADs, as systemic lupus erythematosus (SLE), a rare disease that still lacks effective treatment, is characterized by epigenetic marks in affected cells.Taking into account that epigenetic mechanisms have been proposed as a winning strategy in the search of new more specific and personalized therapeutics agents. Thus, pharmacology and pharmacoepigenetic studies about epigenetic regulations of ADs may provide novel individualized therapies. Focussing in possible implicated factors on development and predisposition of SLE, diet is feasibly one of the most important factors since it is linked directly to epigenetic alterations and these epigenetic changes may augment or diminish the risk of SLE. Nevertheless, several studies have guaranteed that dietary therapy could be a promise to SLE patients via prophylactic actions deprived of side effects of pharmacology, decreasing co-morbidities and improving lifestyle of SLE sufferers.Herein, we review and discuss the cross-link between epigenetic mechanisms on SLE predisposition and development, as well as the influence of dietary factors on regulation epigenetic modifications that would eventually make a positive impact on SLE patients.
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12
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The epigenetic face of lupus: Focus on antigen-presenting cells. Int Immunopharmacol 2020; 81:106262. [PMID: 32045873 DOI: 10.1016/j.intimp.2020.106262] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022]
Abstract
In recent years, epigenetic mechanisms became widely known due to their ability to regulate and maintain physiological processes such as cell growth, development, differentiation and genomic stability. When dysregulated, epigenetic mechanisms, may introduce gene expression changes and disturbance in immune homeostasis leading to autoimmune diseases. Systemic lupus erythematosus (SLE), the most extensively studied autoimmune disorder, has already been correlated with epigenetic modifications, especially in T cells. Since these cell rely on antigen presentation, it may be assumed that erroneous activity of antigen-presenting cells (APCs), culminates in T cell abnormalities. In this review we summarize and discuss the epigenetic modifications in SLE affected APCs, with the focus on dendritic cells (DCs), B cells and monocytes. Unravelling this aspect of SLE pathogenesis, might result in identification of new disease biomarkers and putative therapeutic approaches.
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13
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Mazzone R, Zwergel C, Artico M, Taurone S, Ralli M, Greco A, Mai A. The emerging role of epigenetics in human autoimmune disorders. Clin Epigenetics 2019; 11:34. [PMID: 30808407 PMCID: PMC6390373 DOI: 10.1186/s13148-019-0632-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 02/12/2019] [Indexed: 02/06/2023] Open
Abstract
Epigenetic pathways play a pivotal role in the development and function of the immune system. Over the last decade, a growing body of studies has been published out seeking to explain a correlation between epigenetic modifications and the development of autoimmune disorders. Epigenetic changes, such as DNA methylation, histone modifications, and noncoding RNAs, are involved in the pathogenesis of autoimmune diseases mainly by regulating gene expression. This paper reviews the importance of epigenetic alterations during the development of the most prevalent human autoimmune diseases, such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), systemic sclerosis (SSc), Sjogren’s syndrome (SS), autoimmune thyroid diseases (AITD), and type 1 diabetes (T1D), aiming to provide new insights in the pathogenesis of autoimmune diseases and the possibility to develop novel therapeutic approaches targeting the epigenome.
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Affiliation(s)
- Roberta Mazzone
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.,Center for Life Nano Science@Sapienza, Italian Institute of Technology, Viale Regina Elena 291, 00161, Rome, Italy
| | - Clemens Zwergel
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Marco Artico
- Department of Sense Organs, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Samanta Taurone
- IRCCS G.B. Bietti Foundation, Via Livenza, 3, 00198, Rome, Italy
| | - Massimo Ralli
- Department of Sense Organs, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Antonio Greco
- Department of Sense Organs, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy. .,Pasteur Institute - Cenci Bolognetti Foundation, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy.
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14
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Abstract
PURPOSE OF REVIEW Epigenetics is defined as mitotically heritable changes in gene expression that do not directly alter the DNA sequence. By implication, such epigenetic changes are non-genetically determined, although they can be affected by inherited genetic variation. Extensive evidence indicates that autoimmune diseases including type 1 diabetes are determined by the interaction of genetic and non-genetic factors. Much is known of the genetic causes of these diseases, but the non-genetic effects are less clear-cut. Further, it remains unclear how they interact to cause the destructive autoimmune process. This review identifies the key issues in the genetic/non-genetic interaction, examining the most recent evidence of the role of non-genetic effects in the disease process, including the impact of epigenetic effects on key pathways. RECENT FINDINGS Recent research indicates that these pathways likely involve immune effector cells both of the innate and adaptive immune response. Specifically, there is evidence of cell type-specific enrichment in altered DNA methylation, changes which were temporally stable and enriched at gene regulatory elements. Epigenomics remains in its infancy, and we anticipate further studies will define how the interaction of genetic and non-genetic effects induces tissue-specific destruction and enhances our ability to predict, and possibly even modify that process.
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Affiliation(s)
| | - Mary N. Dang
- Queen Mary University of London, Mile End Rd, London, E1 4NS UK
| | - R. David Leslie
- Queen Mary University of London, Mile End Rd, London, E1 4NS UK
- The Blizard Institute, London, UK
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15
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Foma AM, Aslani S, Karami J, Jamshidi A, Mahmoudi M. Epigenetic involvement in etiopathogenesis and implications in treatment of systemic lupus erythematous. Inflamm Res 2017; 66:1057-1073. [DOI: 10.1007/s00011-017-1082-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/22/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022] Open
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16
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Wu DJ, Adamopoulos IE. Autophagy and autoimmunity. Clin Immunol 2017; 176:55-62. [PMID: 28095319 DOI: 10.1016/j.clim.2017.01.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 12/19/2022]
Abstract
Autophagy is a highly conserved protein degradation pathway from yeasts to humans that is essential for removing protein aggregates and misfolded proteins in healthy cells. Recently, autophagy-related genes polymorphisms have been implicated in several autoimmune diseases including systemic lupus erythematosus, rheumatoid arthritis, psoriasis, and multiple sclerosis. Numerous studies reveal autophagy and autophagy-related proteins also participate in immune regulation. Conditional deletions of autophagy-related proteins in mice have rendered protection from experimental autoimmune encephalomyelitis, and TNF-mediated joint destruction in animal models of multiple sclerosis and experimental arthritis respectively. As autophagy is strongly implicated in immune functions such as removal of intracellular bacteria, inflammatory cytokine secretion, antigen presentation, and lymphocyte development, in this review we summarized current understanding of the roles of autophagy and autophagy proteins in autoimmune diseases.
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Affiliation(s)
- Dennis J Wu
- Graduate Group in Immunology, University of California at Davis, USA; Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, USA
| | - Iannis E Adamopoulos
- Graduate Group in Immunology, University of California at Davis, USA; Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, USA; Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, USA.
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