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Aourangzaib M, Chandra M, Maham R, Naz A, Malathi H, Qadeer S, Mateen RM, Parveen R. Solving the twin paradox-forensic strategies to identify the identical twins. Forensic Sci Int 2024; 363:112205. [PMID: 39213915 DOI: 10.1016/j.forsciint.2024.112205] [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: 07/31/2024] [Revised: 08/16/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Identical twins are also called monozygotic twins which originate from the same zygote that possesses the same genetic make-up. To discriminate between identical monozygotic twins, short tandem repeats has not been found effective, therefore, various techniques, including next-generation sequencing (NGS), are applied. Monozygotic twins can be identified through germ line genomes, through speech using deep learning networks, and through epigenetic analysis. Fingerprint analysis has also been used to distinguish between identical twins, as human beings have unique fingerprints. Two distinct levels of fingerprint are used to distinguish between monozygotic twins based upon the differences in the minutiae points. Examination of the methylation pattern of the genome has an enormous potential to differentiate between identical twins, as the methylation of DNA occurs uniquely to each individual. This article offers an insight into the latest methods and techniques used for the differentiation between the identical twins.
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Affiliation(s)
- Muhammad Aourangzaib
- Department of Life Sciences, School of Sciences, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
| | - Muktesh Chandra
- Marwadi University Research Centre, Department of Bioinformatics, Faculty of Engineering and Technology, Marwadi University, Rajkot, Gujrat 360003, India
| | - Rabiya Maham
- Department of Life Sciences, School of Sciences, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
| | - Alisha Naz
- Department of Life Sciences, School of Sciences, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
| | - H Malathi
- Department of Biotechnology and Genetics, School of Sciences, JAIN (Deemed to be University), Bangalore, Karnataka, India
| | - Saima Qadeer
- Department of Zoology, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Rana Muhammad Mateen
- Department of Life Sciences, School of Sciences, University of Management and Technology (UMT), Lahore, Punjab, Pakistan.
| | - Rukhsana Parveen
- Cenre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
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Ali F, Almuhaimeed A, Khalid M, Alshanbari H, Masmoudi A, Alsini R. DEEP-EP: Identification of epigenetic protein by ensemble residual convolutional neural network for drug discovery. Methods 2024; 226:49-53. [PMID: 38621436 DOI: 10.1016/j.ymeth.2024.04.004] [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: 02/27/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
Epigenetic proteins (EP) play a role in the progression of a wide range of diseases, including autoimmune disorders, neurological disorders, and cancer. Recognizing their different functions has prompted researchers to investigate them as potential therapeutic targets and pharmacological targets. This paper proposes a novel deep learning-based model that accurately predicts EP. This study introduces a novel deep learning-based model that accurately predicts EP. Our approach entails generating two distinct datasets for training and evaluating the model. We then use three distinct strategies to transform protein sequences to numerical representations: Dipeptide Deviation from Expected Mean (DDE), Dipeptide Composition (DPC), and Group Amino Acid (GAAC). Following that, we train and compare the performance of four advanced deep learning models algorithms: Ensemble Residual Convolutional Neural Network (ERCNN), Generative Adversarial Network (GAN), Convolutional Neural Network (CNN), and Gated Recurrent Unit (GRU). The DDE encoding combined with the ERCNN model demonstrates the best performance on both datasets. This study demonstrates deep learning's potential for precisely predicting EP, which can considerably accelerate research and streamline drug discovery efforts. This analytical method has the potential to find new therapeutic targets and advance our understanding of EP activities in disease.
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Affiliation(s)
- Farman Ali
- Department of Computer Science, Bahria University Islamabad Campus, Pakistan.
| | - Abdullah Almuhaimeed
- Digital Health Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Majdi Khalid
- Department of Computer Science and Artificial Intelligence, College of Computing, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hanan Alshanbari
- Department of Computer Science and Artificial Intelligence, College of Computing, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Atef Masmoudi
- College of Computer Science, King Khalid University, Abha, Saudi Arabia
| | - Raed Alsini
- Department of Information Systems, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Alsabri SG, Guedi GG, Najar M, Merimi M, Lavoie F, Grabs D, Fernandes J, Pelletier JP, Martel-Pelletier J, Benderdour M, Fahmi H. Epigenetic regulation of 15-lipoxygenase-1 expression in human chondrocytes by promoter methylation. Inflamm Res 2023; 72:2145-2153. [PMID: 37874359 DOI: 10.1007/s00011-023-01805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/23/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
OBJECTIVE AND DESIGN 15-Lipoxygenase-1 (15-LOX-1) catalyzes the biosynthesis of many anti-inflammatory and immunomodulatory lipid mediators and was reported to have protective properties in several inflammatory conditions, including osteoarthritis (OA). This study was designed to evaluate the expression of 15-LOX-1 in cartilage from normal donors and patients with OA, and to determine whether it is regulated by DNA methylation. METHODS Cartilage samples were obtained at autopsy from normal knee joints and from OA-affected joints at the time of total knee joint replacement surgery. The expression of 15-LOX-1 was evaluated using real-time polymerase chain reaction (PCR). The role of DNA methylation in 15-LOX-1 expression was assessed using the DNA methyltransferase inhibitor 5-Aza-2'-desoxycytidine (5-Aza-dC). The effect of CpG methylation on 15-LOX-1 promoter activity was evaluated using a CpG-free luciferase vector. The DNA methylation status of the 15-LOX-1 promoter was determined by pyrosequencing. RESULTS Expression of 15-LOX-1 was upregulated in OA compared to normal cartilage. Treatment with 5-Aza-dC increased 15-LOX-1 mRNA levels in chondrocytes, and in vitro methylation decreased 15-LOX-1 promoter activity. There was no difference in the methylation status of the 15-LOX-1 gene promoter between normal and OA cartilage. CONCLUSION The expression level of 15-LOX-1 was elevated in OA cartilage, which may be part of a repair process. The upregulation of 15-LOX-1 in OA cartilage was not associated with the methylation status of its promoter, suggesting that other mechanisms are involved in its upregulation.
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Affiliation(s)
- Sami G Alsabri
- Osteoarthritis Research Unit, University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Gadid G Guedi
- Osteoarthritis Research Unit, University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Mehdi Najar
- Osteoarthritis Research Unit, University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Makram Merimi
- LBEES, Genetics and Immune Cell Therapy Unit, Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Frédéric Lavoie
- Departement of Orthopedic Surgery, Centre Hospitalier de L'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Detlev Grabs
- Department of Anatomy, Research Unit in Clinical and Functional Anatomy, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Julio Fernandes
- Departement of Orthopedic Surgery, Centre Hospitalier de L'Université de Montréal (CHUM), Montréal, Québec, Canada
- Orthopedics Research Laboratory, Research Center, Hôpital du Sacré-Cœur de Montréal, Université de Montréal, Montréal, Québec, H4J 1C5, Canada
| | - Jean-Pierre Pelletier
- Osteoarthritis Research Unit, University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Johanne Martel-Pelletier
- Osteoarthritis Research Unit, University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Mohamed Benderdour
- Orthopedics Research Laboratory, Research Center, Hôpital du Sacré-Cœur de Montréal, Université de Montréal, Montréal, Québec, H4J 1C5, Canada
| | - Hassan Fahmi
- Osteoarthritis Research Unit, University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada.
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Riaz F, Huang Z, Pan F. Targeting post-translational modifications of Foxp3: a new paradigm for regulatory T cell-specific therapy. Front Immunol 2023; 14:1280741. [PMID: 37936703 PMCID: PMC10626496 DOI: 10.3389/fimmu.2023.1280741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
A healthy immune system is pivotal for the hosts to resist external pathogens and maintain homeostasis; however, the immunosuppressive tumor microenvironment (TME) damages the anti-tumor immunity and promotes tumor progression, invasion, and metastasis. Recently, many studies have found that Foxp3+ regulatory T (Treg) cells are the major immunosuppressive cells that facilitate the formation of TME by promoting the development of various tumor-associated cells and suppressing the activity of effector immune cells. Considering the role of Tregs in tumor progression, it is pivotal to identify new therapeutic drugs to target and deplete Tregs in tumors. Although several studies have developed strategies for targeted deletion of Treg to reduce the TME and support the accumulation of effector T cells in tumors, Treg-targeted therapy systematically affects the Treg population and may lead to the progression of autoimmune diseases. It has been understood that, nevertheless, in disease conditions, Foxp3 undergoes several definite post-translational modifications (PTMs), including acetylation, glycosylation, phosphorylation, ubiquitylation, and methylation. These PTMs not only elevate or mitigate the transcriptional activity of Foxp3 but also affect the stability and immunosuppressive function of Tregs. Various studies have shown that pharmacological targeting of enzymes involved in PTMs can significantly influence the PTMs of Foxp3; thus, it may influence the progression of cancers and/or autoimmune diseases. Overall, this review will help researchers to understand the advances in the immune-suppressive mechanisms of Tregs, the post-translational regulations of Foxp3, and the potential therapeutic targets and strategies to target the Tregs in TME to improve anti-tumor immunity.
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Affiliation(s)
| | | | - Fan Pan
- Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, China
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Su G, Du L, Yu H, Li M, Huang R, Yang X, Wang D, Wang Q, Yang P. Epigenome-wide association study identifies Vogt-Koyanagi-Harada disease-associated DNA methylation loci in Chinese. Exp Eye Res 2023:109553. [PMID: 37394087 DOI: 10.1016/j.exer.2023.109553] [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: 03/20/2023] [Revised: 06/11/2023] [Accepted: 06/23/2023] [Indexed: 07/04/2023]
Abstract
DNA methylation is one of the important epigenetic mechanisms for modulating gene expression. By performing a genome-wide methylation association analysis of whole peripheral blood from 60 Vogt-Koyanagi-Harada disease (VKH) patients and 60 healthy controls, we depicted the global DNA methylation status of VKH disease. Further pyrosequencing validation in 160 patients and 159 controls identified 3 aberrant CpG sites in HLA gene regions including cg04026937 and cg18052547 (located in HLA-DRB1 region), and cg13778567 (HLA-DQA1). We also identified 9 aberrant CpG sites in non-HLA gene regions including cg13979407, cg21075643, cg24290586, cg10135747 and cg22707857 (BTNL2), cg22155039 (NOTCH4), cg02605387 (TNXB), cg06255004 (AGPAT2) and cg18855195 (RIBC2). Increased mRNA levels of BTNL2, NOTCH4 and TNXB were identified in VKH patients when compared with healthy controls, consistent with the hypomethylated CpG status in these gene regions. Moreover, seven aberrantly methylated CpG sites may serve as a diagnostic marker for VKH disease (AUC = 84.95%, 95%CI: 79.49%-90.41%).
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Affiliation(s)
- Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Liping Du
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, China
| | - Hongsong Yu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Minghui Li
- Sinotech Genomics Ltd, Shanghai, 210000, China
| | | | | | - Detao Wang
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Qing Wang
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 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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DNA Methylation Expression Profile of Blood Heat Syndrome and Blood Stasis Syndrome in TCM Psoriasis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:9343285. [PMID: 36193156 PMCID: PMC9526661 DOI: 10.1155/2022/9343285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022]
Abstract
Objective Traditional Chinese medicine (TCM) emphasizes treatment based on syndrome differentiation. This study aimed to clarify the characteristics of DNA methylation expression profiles in peripheral blood mononuclear cells (PBMCs) in patients with psoriasis and analyze the differences in these profiles among different TCM syndromes of psoriasis in order to provide a material basis for the diversity of these syndromes. Methods Blood samples were collected from 32 participants, including 14 patients with psoriatic blood heat syndrome (BHS), 12 patients with psoriatic blood stasis syndrome (BSS), and 6 healthy controls. PBMCs were extracted and subjected to DNA quality inspection. An Illumina Human Methylation 850k chip was used to sequence each group of samples. According to gene annotation classification together with CpG island annotation classification, the differentially methylated regions between sample groups were screened, while Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were applied to perform functional analyses of DMGs. Finally, the DMGs closely correlating with psoriatic severity were screened using Spearman's correlation analysis. Results Compared with normal controls, patients with psoriasis showed an overall trend of hypermethylation. In psoriasis, the differential methylation probes were mainly distributed on gene body region on the genome, while those in CpG regions were mainly distributed in CpG islands. Compared with healthy controls, the overall trends in methylation were similar in psoriatic BHS and BSS patients compared to healthy controls. However, bioinformatic analysis revealed different functions of DMGs. We also found that the methylation levels of TRIM14 and PRDM16 were closely correlated with PASI scores and could serve as potential biomarkers to assess the severity of psoriasis. Conclusions Our study, for the first time, indicated the possible involvement of DNA methylation in regulating the characteristics of TCM syndromes of psoriasis, providing a new direction for research into TCM psoriatic syndromes.
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Ma L, Fang X, Zhang A. The hypermethylation of FOXP3 gene as an epigenetic marker for the identification of arsenic poisoning risk. Hum Exp Toxicol 2022; 41:9603271221142819. [PMID: 36464704 DOI: 10.1177/09603271221142819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background and Purpose: Arsenic exposure can lead to skin lesions and multiple organ damage, which are not easily reversible and for which there is no effective therapeutics. Identification of reliable epigenetic markers is essential for early recognition of arsenic poisoning risk. Anomalous DNA methylation of immune homeostasis regulator FOXP3 is a critical mechanism for triggering arsenic poisoning. This study aims to explore the value of FOXP3 methylation in the identification of arsenic poisoning risk.Methods: 88 arsenic poisoning subjects and 41 references were recruited. Urinary arsenic contents and FOXP3 methylation in PBLCs was measured by ICP-MS and pyrosequencing, respectively.Results: The results showed that the elevated FOXP3 methylation in PBLCs were associated with the increased levels of urinary arsenic and were positively associated with the increased risk of arsenic poisoning and its progression. The result of mediation analysis revealed that 24.3% of the effect of arsenic exposure on the risk of arsenic poisoning was mediated by increased FOXP3 methylation. Additionally, we constructed a nomogram model with FOXP3 methylation as an epigenetic predictor to assess the probability of individual arsenic poisoning. The model showed a robust ability in the discrimination of arsenic poisoning risk, with an area under receiver operating characteristics curve of 0.897(0.845-0.949) and more than 70% accuracy. The calibration curves and the Harrell concordance index showed that the consistency rate between the probability predicted by the nomogram model and the actual probability is 89.7%.Conclusions: Taken together, we found the great potential of FOXP3 methylation for the identification of arsenic poisoning risk and provided a new approach to the application of epigenetic markers in accurately quantifying the risk of adverse outcomes.
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Affiliation(s)
- Lu Ma
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, 74628Guizhou Medical University, Guiyang, China
| | - Xiaolin Fang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, 74628Guizhou Medical University, Guiyang, China
| | - Aihua Zhang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, 74628Guizhou Medical University, Guiyang, China
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Bertsias G. Dialogue: High-throughput studies in rheumatology: time for unsupervised clustering? Lupus Sci Med 2021; 8:8/1/e000643. [PMID: 34952891 PMCID: PMC8710894 DOI: 10.1136/lupus-2021-000643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Affiliation(s)
- George Bertsias
- Rheumatology, Clinical Immunology and Allergy, University of Crete School of Medicine, Heraklion, Crete, Greece .,Laboratory of Rheumatology, Autoimmunity and Inflammation, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Heraklion, Greece
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10
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He Z, Zhou S, Yang M, Zhao Z, Mei Y, Xin Y, Zhao M, Wu H, Lu Q. Comprehensive analysis of epigenetic modifications and immune-cell infiltration in tissues from patients with systemic lupus erythematosus. Epigenomics 2021; 14:81-100. [PMID: 34913398 DOI: 10.2217/epi-2021-0318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: To explore potential abnormal epigenetic modifications and immune-cell infiltration in tissues from systemic lupus erythematosus (SLE) patients. Materials & methods: To utilize bioinformatics analysis and 'wet lab' methods to identify and verify differentially expressed genes in multiple targeted organs in SLE. Results: Seven key genes, IFI44, IFI44L, IFIT1, IFIT3, PLSCR1, RSAD2 and OAS2, which are regulated by epigenetics and may be involved in the pathogenesis of SLE, are identified by combined long noncoding RNA-miRNA-mRNA network analysis and DNA methylation analysis. The results of quantitative reverse transcription PCR, immunohistochemistry and DNA methylation analysis confirmed the potential of these genes as biomarkers. Conclusion: This study reveals the potential mechanisms in SLE from epigenetic modifications and immune-cell infiltration, providing diagnostic biomarkers and therapeutic targets for SLE.
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Affiliation(s)
- Zhenghao He
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Shihang Zhou
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Ming Yang
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Zhidan Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Yang Mei
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Yue Xin
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Ming Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, 410000, Hunan, China.,Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, 210028, China
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11
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Epigenome association study for DNA methylation biomarkers in buccal and monocyte cells for female rheumatoid arthritis. Sci Rep 2021; 11:23789. [PMID: 34893669 PMCID: PMC8664902 DOI: 10.1038/s41598-021-03170-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/17/2021] [Indexed: 12/27/2022] Open
Abstract
Genetics (i.e., mutations) has been assumed to be the major factor in rheumatoid arthritis (RA) etiology, but accounts for a minority of the variance in disease risk for RA. In contrast to genetics, the environment can have dramatic impacts on epigenetics that associate with disease etiology. The current study used buccal cells and purified blood monocytes from two different clinical cohorts involving Caucasian or African American female populations with or without arthritis. The differential DNA methylation regions (DMRs) between the control and RA populations were identified with an epigenome-wide association study. The DMRs (i.e., epimutations) identified in the buccal cells and monocytes were found to be distinct. The DMR associated genes were identified and many have previously been shown to be associated with arthritis. Observations demonstrate DNA methylation epimutation RA biomarkers are cell type specific and similar findings were observed with the two racial background populations. Rheumatoid arthritis susceptibility epigenetic diagnosis appears feasible and may improve the clinical management of RA and allowpreventative medicine considerations.
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12
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Advanced genomics and clinical phenotypes in psoriatic arthritis. Semin Immunol 2021; 58:101665. [PMID: 36307312 DOI: 10.1016/j.smim.2022.101665] [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] [Indexed: 12/13/2022]
Abstract
Psoriatic Arthritis (PsA) is a complex polygenic inflammatory disease showing a variable musculoskeletal involvement in patients with skin psoriasis. PsA coexist in 25-40 % of patients with the dermatological manifestations, but PsA may also predate the appearance of psoriasis. Nonetheless, the immunopathogenesis of psoriasis and PsA manifest significant similarities, with a major role of the individual susceptibility in both cases. Genome wide association studies (GWAS) identified several genes/loci associated with the risk to develop PsA, both dependent and independent of psoriasis. The major challenge is thus represented by the need to translate the identification of functional polymorphisms and other genetics findings into biological mechanisms along with the identification of novel putative drug targets. A functional genomics approach aims to increase GWAS power and recent evidence supports the use of a multilayer process, including eQTL, methylome, chromatin conformation analysis and genome editing to discover novel genes that can be affected by disease-associated variants, such as PsA. The available data have considered PsA as a unique homogeneous clinical entity while the clinical experience supports a wide variability of skin and joint manifestations coexisting in diverse patients with different mechanisms underlying the musculoskeletal and dermatological domains. A better discrimination of the patient features is encouraged by the limited data on functional genomics. We provide herein a review of the latest findings on PsA functional genomics highlighting the exciting developments in the field and how these might lead to a better understanding of gene regulation underpinning disease mechanisms and ultimately refine clinical phenotyping.
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A Variant of sNASP Exacerbates Lymphocyte Subset Disorder and Nephritis in a Spontaneous Lupus Model Sle1.Yaa Mouse. Mediators Inflamm 2021; 2021:8175863. [PMID: 34720750 PMCID: PMC8553485 DOI: 10.1155/2021/8175863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/23/2021] [Indexed: 11/18/2022] Open
Abstract
A variant of somatic nuclear autoantigenic sperm protein (sNASP) was identified from the murine lupus susceptibility locus Sle2c1 by whole exome sequencing (WES). Previous studies have shown that mutant sNASP could synergize with the Faslpr mutation in exacerbating autoimmunity and aggravating end-organ inflammation. In the current study, the sNASP mutation was introduced into Sle1.Yaa mice to detect whether it has a synergistic effect with Sle1 or Yaa loci. As expected, compared with Sle1.Yaa mice, Sle1.Yaa.ΔsNASP mice showed enlarged lymph nodes, aggravated renal inflammation, and shortened survival time. The proportions of CD3+ T cells, activated CD19+CD86+ B cells, Th1 cells in the spleen and lymph nodes, and Th17 cells in lymph nodes in Sle1.Yaa.ΔsNASP mice were increased compared to those in Sle1.Yaa mice. The levels of IFN-γ and TNF-α in the serum of Sle1.Yaa.ΔsNASP mice were higher than those of Sle1.Yaa mice. The above results show that mutant sNASP can interact with different lupus susceptibility genes and promote the disease process of systemic lupus erythematosus.
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Chen Y, Xu X, Li X, Zhong J, Wu B, Shang J, Jiang N, Wang B, Zhong S, Lu H. Identification of circular RNAs hsa_circ_0140271 in peripheral blood mononuclear cells as a novel diagnostic biomarker for female rheumatoid arthritis. J Orthop Surg Res 2021; 16:647. [PMID: 34717684 PMCID: PMC8557002 DOI: 10.1186/s13018-021-02794-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is a chronic autoimmune disease, which commonly affects women. Accumulating evidence shows that differentially expressed circular RNAs (circRNAs) play crucial roles in the progress of RA. However, the roles of circRNAs in female RA remains unclear. This study explores potential role and diagnostic value of hsa_circ_0140271 from peripheral blood mononuclear cells (PBMC) in female RA. Methods Differential expression of circRNAs was determined by RNA-sequencing in PBMC from 4 healthy controls (HC) and 4 RA patients, and we further measured the level of hsa_circ_0140271 in a validation cohort consisting of 47 RA and 47 HC via RT-qPCR. Besides, correlation studies with clinical variables were also examined. What’s more, we performed bioinformatics analysis to predict the potential role of hsa_circ_0140271. Results PBMC expression of hsa_circ_0140271 of female RA was significantly higher than that of female HC, and it was positively correlated with antistreptolysin (ASO). Furthermore, the receiver operating characteristic (ROC) curve indicated that hsa_circ_0140271 could distinguish female RA from female HC and female patients with ankylosing spondylitis (AS) or osteoarthritis (OA). Besides, the combined diagnosis anti-cyclic citrullinated peptide (Anti-CCP) + hsa_circ_0140271 could improve diagnostic accuracy with an area under the curve (AUC) of 0.818 to compared with Anti-CCP. Furthermore, KEGG pathway enrichment analysis indicated hsa_circ_0140271 may act as microRNA sponge and participate in fatty acid metabolism pathways. Conclusion Hsa_circ_0140271 was likely to be used as a promising diagnostic biomarker for female RA; it may act as microRNA sponge to regulate fatty acid metabolism pathways in RA. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-021-02794-8.
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Affiliation(s)
- Yufeng Chen
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Xianghe Xu
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Xuegang Li
- Department of Rheumatology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Junlong Zhong
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Biao Wu
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Jie Shang
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Ning Jiang
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Bin Wang
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Shuping Zhong
- Department of Rheumatology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.
| | - Huading Lu
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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Peng H, Xiong S, Ding X, Tang X, Wang X, Wang L, Liu Y. Long non‑coding RNA expression profiles identify lncRNA‑XLOC_I2_006631 as a potential novel blood biomarker for Hashimoto's thyroiditis. Int J Mol Med 2020; 46:2172-2184. [PMID: 33125100 PMCID: PMC7595668 DOI: 10.3892/ijmm.2020.4755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/17/2020] [Indexed: 12/25/2022] Open
Abstract
Long non‑coding RNAs (lncRNAs) have been increasingly recognized as important immune checkpoints involved in the pathogenesis of autoimmune diseases. However, the exact role of lncRNAs in Hashimoto's thyroiditis (HT) has been rarely studied. The aim of the present study was to investigate the role of lncRNAs and the potential biomarkers in HT, a total of 33 patients with HT and 32 healthy volunteers were enrolled in the present study, and five patients and five healthy controls were investigated using next generation sequencing. A total of 218 dysregulated lncRNAs, including 94 upregulated and 124 downregulated lncRNAs, were identified and examined in the peripheral blood mononuclear cells (PBMCs) from patients with HT. The majority of the lncRNAs were intergenic and exonic (66.06%). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that abnormally expressed lncRNAs were enriched in the 'NF‑kB expression', in the 'TGF‑β signaling pathway' and in the 'JAK‑STAT signaling pathway', which are associated with the immunopathogenic mechanisms of HT. In total, three lncRNAs (LOC729737, XLOC_I2_006631 and BC041964) were validated and had a trend identical to that detected by the sequencing results. The expression of lncRNA‑XLOC_I2_006631 was upregulated and was positively correlated with the serum concentrations of anti‑thyroperoxidase antibody in patients with HT. Methyl‑CpG‑binding protein 2 (MECP2) was identified as the potential regulatory gene of lncRNA‑XLOC_I2_006631 using a prediction program. The expression of MECP2 was increased and was positively correlated with the elevated expression levels of lncRNA‑XLOC_I2_006631 and anti‑thyroperoxidase antibody in patients with HT. Furthermore, lncRNA‑XLOC_I2_006631 was able to regulate MECP2 expression in vitro. Receiver operating characteristic curve analysis suggested that lncRNA‑XLOC_I2_006631 has a potential diagnostic value. Collectively, the present results indicated the important role of dysregulated lncRNAs in HT and demonstrated that lncRNA‑XLOC_I2_006631 functioned as a positive regulator of MECP2 expression, suggesting a potential mechanism. Thus, lncRNA‑XLOC_I2_006631 may be used as a biomarker of HT.
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Affiliation(s)
- Huiyong Peng
- Department of Laboratory Medicine, The Affiliated People's Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Si Xiong
- Department of Endocrinology, The Fifth People's Hospital of Wuhan, Wuhan, Hubei 430050, P.R. China
| | - Xiangmei Ding
- Department of Endocrinology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Xinyi Tang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Xuehua Wang
- Department of Endocrinology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Li Wang
- Department of Endocrinology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Yingzhao Liu
- Department of Endocrinology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, Jiangsu 212002, P.R. China
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