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Zouali M. Engineered immune cells as therapeutics for autoimmune diseases. Trends Biotechnol 2024; 42:842-858. [PMID: 38368169 DOI: 10.1016/j.tibtech.2024.01.006] [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: 10/13/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/19/2024]
Abstract
Current treatment options for autoimmune disease (AID) are essentially immunosuppressive, inhibiting the inflammatory cascade, without curing the disease. Therapeutic monoclonal antibodies (mAbs) that target B cells showed efficacy, emphasizing the importance of B lymphocytes in autoimmune pathogenesis. Treatments that eliminate more potently B cells would open a new therapeutic era for AID. Immune cells can now be bioengineered to express constructs that enable them to specifically eradicate pathogenic B lymphocytes. Engineered immune cells (EICs) have shown therapeutic promise in both experimental models and in clinical trials in AID. Next-generation platforms are under development to optimize their specificity and improve safety. The profound and durable B cell depletion achieved reinforces the view that this biotherapeutic option holds promise for treating AID.
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Affiliation(s)
- Moncef Zouali
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
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2
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Zhu X, Hong S, Bu J, Liu Y, Liu C, Li R, Zhang T, Zhang Z, Li L, Zhou X, Hua Z, Zhu B, Hou B. Antiviral memory B cells exhibit enhanced innate immune response facilitated by epigenetic memory. SCIENCE ADVANCES 2024; 10:eadk0858. [PMID: 38552009 PMCID: PMC10980274 DOI: 10.1126/sciadv.adk0858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/26/2024] [Indexed: 04/01/2024]
Abstract
The long-lasting humoral immunity induced by viral infections or vaccinations depends on memory B cells with greatly increased affinity to viral antigens, which are evolved from germinal center (GC) responses. However, it is unclear whether antiviral memory B cells represent a distinct subset among the highly heterogeneous memory B cell population. Here, we examined memory B cells induced by a virus-mimicking antigen at both transcriptome and epigenetic levels and found unexpectedly that antiviral memory B cells exhibit an enhanced innate immune response, which appeared to be facilitated by the epigenetic memory that is established through the memory B cell development. In addition, T-bet is associated with the altered chromatin architecture and is required for the formation of the antiviral memory B cells. Thus, antiviral memory B cells are distinct from other GC-derived memory B cells in both physiological functions and epigenetic landmarks.
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Affiliation(s)
- Xiping Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng Hong
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiachen Bu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingping Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runhan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiantian Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liping Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaolin Hua
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baidong Hou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Peters TJ, Meyer B, Ryan L, Achinger-Kawecka J, Song J, Campbell EM, Qu W, Nair S, Loi-Luu P, Stricker P, Lim E, Stirzaker C, Clark SJ, Pidsley R. Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics 2024; 25:251. [PMID: 38448820 PMCID: PMC10916044 DOI: 10.1186/s12864-024-10027-5] [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: 10/12/2023] [Accepted: 01/18/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples. RESULTS We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding. CONCLUSIONS Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.
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Affiliation(s)
- Timothy J Peters
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Braydon Meyer
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Lauren Ryan
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Jenny Song
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Elyssa M Campbell
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Shalima Nair
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Phuc Loi-Luu
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Phillip Stricker
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
- Department of Urology, St. Vincent's Prostate Cancer Centre, Sydney, NSW, 2050, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia.
| | - Ruth Pidsley
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia.
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Ferenc K, Sokal-Dembowska A, Helma K, Motyka E, Jarmakiewicz-Czaja S, Filip R. Modulation of the Gut Microbiota by Nutrition and Its Relationship to Epigenetics. Int J Mol Sci 2024; 25:1228. [PMID: 38279228 PMCID: PMC10816208 DOI: 10.3390/ijms25021228] [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: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
The intestinal microbiota is a community of microorganisms inhabiting the human intestines, potentially influencing both physiological and pathophysiological processes in the human body. Existing evidence suggests that nutrients can influence the modulation of the gut microbiota. However, there is still limited evidence regarding the effects of vitamin and mineral supplementation on the human gut microbiota through epigenetic modification. It is plausible that maintaining an adequate dietary intake of vitamin D, iron, fibre, zinc and magnesium may have a beneficial effect on alleviating inflammation in the body, reducing oxidative stress, and improving the condition of the intestinal microbiota through various epigenetic mechanisms. Moreover, epigenetics involves alterations in the phenotype of a cell without changing its fundamental DNA sequence. It appears that the modulation of the microbiota by various nutrients may lead to epigenetic regulation. The correlations between microbiota and epigenetics are potentially interdependent. Therefore, the primary objective of this review is to identify the complex relationships between diet, gut microbiota, and epigenetic regulation. These interactions could play a crucial role in systemic health.
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Affiliation(s)
- Katarzyna Ferenc
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Aneta Sokal-Dembowska
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Kacper Helma
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Elżbieta Motyka
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | | | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Gastroenterology with IBD Unit, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
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Singh S, Sarma DK, Verma V, Nagpal R, Kumar M. Unveiling the future of metabolic medicine: omics technologies driving personalized solutions for precision treatment of metabolic disorders. Biochem Biophys Res Commun 2023; 682:1-20. [PMID: 37788525 DOI: 10.1016/j.bbrc.2023.09.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Metabolic disorders are increasingly prevalent worldwide, leading to high rates of morbidity and mortality. The variety of metabolic illnesses can be addressed through personalized medicine. The goal of personalized medicine is to give doctors the ability to anticipate the best course of treatment for patients with metabolic problems. By analyzing a patient's metabolomic, proteomic, genetic profile, and clinical data, physicians can identify relevant diagnostic, and predictive biomarkers and develop treatment plans and therapy for acute and chronic metabolic diseases. To achieve this goal, real-time modeling of clinical data and multiple omics is essential to pinpoint underlying biological mechanisms, risk factors, and possibly useful data to promote early diagnosis and prevention of complex diseases. Incorporating cutting-edge technologies like artificial intelligence and machine learning is crucial for consolidating diverse forms of data, examining multiple variables, establishing databases of clinical indicators to aid decision-making, and formulating ethical protocols to address concerns. This review article aims to explore the potential of personalized medicine utilizing omics approaches for the treatment of metabolic disorders. It focuses on the recent advancements in genomics, epigenomics, proteomics, metabolomics, and nutrigenomics, emphasizing their role in revolutionizing personalized medicine.
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Affiliation(s)
- Samradhi Singh
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Ravinder Nagpal
- Department of Nutrition and Integrative Physiology, College of Health and Human Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Manoj Kumar
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India.
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Müller L, Di Benedetto S. From aging to long COVID: exploring the convergence of immunosenescence, inflammaging, and autoimmunity. Front Immunol 2023; 14:1298004. [PMID: 37942323 PMCID: PMC10628127 DOI: 10.3389/fimmu.2023.1298004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
The process of aging is accompanied by a dynamic restructuring of the immune response, a phenomenon known as immunosenescence. This mini-review navigates through the complex landscape of age-associated immune changes, chronic inflammation, age-related autoimmune tendencies, and their potential links with immunopathology of Long COVID. Immunosenescence serves as an introductory departure point, elucidating alterations in immune cell profiles and their functional dynamics, changes in T-cell receptor signaling, cytokine network dysregulation, and compromised regulatory T-cell function. Subsequent scrutiny of chronic inflammation, or "inflammaging," highlights its roles in age-related autoimmune susceptibilities and its potential as a mediator of the immune perturbations observed in Long COVID patients. The introduction of epigenetic facets further amplifies the potential interconnections. In this compact review, we consider the dynamic interactions between immunosenescence, inflammation, and autoimmunity. We aim to explore the multifaceted relationships that link these processes and shed light on the underlying mechanisms that drive their interconnectedness. With a focus on understanding the immunological changes in the context of aging, we seek to provide insights into how immunosenescence and inflammation contribute to the emergence and progression of autoimmune disorders in the elderly and may serve as potential mediator for Long COVID disturbances.
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Affiliation(s)
- Ludmila Müller
- Max Planck Institute for Human Development, Center for Lifespan Psychology, Berlin, Germany
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Gupta MK, Peng H, Li Y, Xu CJ. The role of DNA methylation in personalized medicine for immune-related diseases. Pharmacol Ther 2023; 250:108508. [PMID: 37567513 DOI: 10.1016/j.pharmthera.2023.108508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Epigenetics functions as a bridge between host genetic & environmental factors, aiding in human health and diseases. Many immune-related diseases, including infectious and allergic diseases, have been linked to epigenetic mechanisms, particularly DNA methylation. In this review, we summarized an updated overview of DNA methylation and its importance in personalized medicine, and demonstrated that DNA methylation has excellent potential for disease prevention, diagnosis, and treatment in a personalized manner. The future implications and limitations of the DNA methylation study have also been well-discussed.
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Affiliation(s)
- Manoj Kumar Gupta
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - He Peng
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
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Xu R, Hong X, Ladd-Acosta C, Buckley JP, Choi G, Wang G, Hou W, Wang X, Liang L, Ji H. Contrasting Association of Maternal Plasma Biomarkers of Smoking and 1-Carbon Micronutrients with Offspring DNA Methylation: Evidence of Aryl Hydrocarbon Receptor Repressor Gene-Smoking-Folate Interaction. J Nutr 2023; 153:2339-2351. [PMID: 37156443 PMCID: PMC10447613 DOI: 10.1016/j.tjnut.2023.05.002] [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: 01/12/2023] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Maternal prenatal smoking is known to alter offspring DNA methylation (DNAm). However, there are no effective interventions to mitigate smoking-induced DNAm alteration. OBJECTIVES This study investigated whether 1-carbon nutrients (folate, vitamins B6, and B12) can protect against prenatal smoking-induced offspring DNAm alterations in the aryl hydrocarbon receptor repressor (AHRR) (cg05575921), GFI1 (cg09935388), and CYP1A1 (cg05549655) genes. METHODS This study included mother-newborn dyads from a racially diverse US birth cohort. The cord blood DNAm at the above 3 sites were derived from a previous study using the Illumina Infinium MethylationEPIC BeadChip. Maternal smoking was assessed by self-report and plasma biomarkers (hydroxycotinine and cotinine). Maternal plasma folate, and vitamins B6 and B12 concentrations were obtained shortly after delivery. Linear regressions, Bayesian kernel machine regression, and quantile g-computation were applied to test the study hypothesis by adjusting for covariables and multiple testing. RESULTS The study included 834 mother-newborn dyads (16.7% of newborns exposed to maternal smoking). DNAm at cg05575921 (AHRR) and at cg09935388 (GFI1) was inversely associated with maternal smoking biomarkers in a dose-response fashion (all P < 7.01 × 10-13). In contrast, cg05549655 (CYP1A1) was positively associated with maternal smoking biomarkers (P < 2.4 × 10-6). Folate concentrations only affected DNAm levels at cg05575921 (AHRR, P = 0.014). Regression analyses showed that compared with offspring with low hydroxycotinine exposure (<0.494) and adequate maternal folate concentrations (quartiles 2-4), an offspring with high hydroxycotinine exposure (≥0.494) and low folate concentrations (quartile 1) had a significant reduction in DNAm at cg05575921 (M-value, ß ± SE = -0.801 ± 0.117, P = 1.44 × 10-11), whereas adequate folate concentrations could cut smoking-induced hypomethylation by almost half. Exposure mixture models further supported the protective role of adequate folate concentrations against smoking-induced aryl hydrocarbon receptor repressor (AHRR) hypomethylation. CONCLUSIONS This study found that adequate maternal folate can attenuate maternal smoking-induced offspring AHRR cg05575921 hypomethylation, which has been previously linked to a range of pediatric and adult diseases.
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Affiliation(s)
- Richard Xu
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Xiumei Hong
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States.
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Jessie P Buckley
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Giehae Choi
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Guoying Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Wenpin Hou
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, United States
| | - Xiaobin Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Liming Liang
- Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States; Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States.
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Jarmakiewicz-Czaja S, Sokal A, Ferenc K, Motyka E, Helma K, Filip R. The Role of Genetic and Epigenetic Regulation in Intestinal Fibrosis in Inflammatory Bowel Disease: A Descending Process or a Programmed Consequence? Genes (Basel) 2023; 14:1167. [PMID: 37372347 DOI: 10.3390/genes14061167] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic diseases characterized by recurring periods of exacerbation and remission. Fibrosis of the intestine is one of the most common complications of IBD. Based on current analyses, it is evident that genetic factors and mechanisms, as well as epigenetic factors, play a role in the induction and progression of intestinal fibrosis in IBD. Key genetic factors and mechanisms that appear to be significant include NOD2, TGF-β, TLRs, Il23R, and ATG16L1. Deoxyribonucleic acid (DNA) methylation, histone modification, and ribonucleic acid (RNA) interference are the primary epigenetic mechanisms. Genetic and epigenetic mechanisms, which seem to be important in the pathophysiology and progression of IBD, may potentially be used in targeted therapy in the future. Therefore, the aim of this study was to gather and discuss selected mechanisms and genetic factors, as well as epigenetic factors.
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Affiliation(s)
| | - Aneta Sokal
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Katarzyna Ferenc
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Elżbieta Motyka
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Kacper Helma
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Gastroenterology with IBD, Clinical Hospital No. 2 im. Św. Jadwigi Królowej, 35-301 Rzeszow, Poland
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Nikolova-Ganeva K, Bradyanova S, Manoylov I, Boneva G, Tchorbanov A. Methyl- rich diet ameliorates lupus-like disease in MRL/lpr mice. Immunobiology 2022; 227:152282. [DOI: 10.1016/j.imbio.2022.152282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/01/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022]
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Epigenetic regulation of B cells and its role in autoimmune pathogenesis. Cell Mol Immunol 2022; 19:1215-1234. [PMID: 36220996 PMCID: PMC9622816 DOI: 10.1038/s41423-022-00933-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022] Open
Abstract
B cells play a pivotal role in the pathogenesis of autoimmune diseases. Although previous studies have shown many genetic polymorphisms associated with B-cell activation in patients with various autoimmune disorders, progress in epigenetic research has revealed new mechanisms leading to B-cell hyperactivation. Epigenetic mechanisms, including those involving histone modifications, DNA methylation, and noncoding RNAs, regulate B-cell responses, and their dysregulation can contribute to the pathogenesis of autoimmune diseases. Patients with autoimmune diseases show epigenetic alterations that lead to the initiation and perpetuation of autoimmune inflammation. Moreover, many clinical and animal model studies have shown the promising potential of epigenetic therapies for patients. In this review, we present an up-to-date overview of epigenetic mechanisms with a focus on their roles in regulating functional B-cell subsets. Furthermore, we discuss epigenetic dysregulation in B cells and highlight its contribution to the development of autoimmune diseases. Based on clinical and preclinical evidence, we discuss novel epigenetic biomarkers and therapies for patients with autoimmune disorders.
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7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries Are Potent and Selective Inhibitors of DNA Methyltransferase 1. Molecules 2022; 27:molecules27092892. [PMID: 35566242 PMCID: PMC9102847 DOI: 10.3390/molecules27092892] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/24/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
Inhibitors of epigenetic writers such as DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug and probe discovery. To advance epigenetic probes and drug discovery, chemical companies are developing focused libraries for epigenetic targets. Based on a knowledge-based approach, herein we report the identification of two quinazoline-based derivatives identified in focused libraries with sub-micromolar inhibition of DNMT1 (30 and 81 nM), more potent than S-adenosylhomocysteine. Also, both compounds had a low micromolar affinity of DNMT3A and did not inhibit DNMT3B. The enzymatic inhibitory activity of DNMT1 and DNMT3A was rationalized with molecular modeling. The quinazolines reported in this work are known to have low cell toxicity and be potent inhibitors of the epigenetic target G9a. Therefore, the quinazoline-based compounds presented are attractive not only as novel potent inhibitors of DNMTs but also as dual and selective epigenetic agents targeting two families of epigenetic writers.
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Romano R, Cillo F, Moracas C, Pignata L, Nannola C, Toriello E, De Rosa A, Cirillo E, Coppola E, Giardino G, Brunetti-Pierri N, Riccio A, Pignata C. Epigenetic Alterations in Inborn Errors of Immunity. J Clin Med 2022; 11:1261. [PMID: 35268351 PMCID: PMC8910960 DOI: 10.3390/jcm11051261] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 02/07/2023] Open
Abstract
The epigenome bridges environmental factors and the genome, fine-tuning the process of gene transcription. Physiological programs, including the development, maturation and maintenance of cellular identity and function, are modulated by intricate epigenetic changes that encompass DNA methylation, chromatin remodeling, histone modifications and RNA processing. The collection of genome-wide DNA methylation data has recently shed new light into the potential contribution of epigenetics in pathophysiology, particularly in the field of immune system and host defense. The study of patients carrying mutations in genes encoding for molecules involved in the epigenetic machinery has allowed the identification and better characterization of environment-genome interactions via epigenetics as well as paving the way for the development of new potential therapeutic options. In this review, we summarize current knowledge of the role of epigenetic modifications in the immune system and outline their potential involvement in the pathogenesis of inborn errors of immunity.
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Affiliation(s)
- Roberta Romano
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Francesca Cillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Cristina Moracas
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Chiara Nannola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Elisabetta Toriello
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Antonio De Rosa
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emma Coppola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Nicola Brunetti-Pierri
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Claudio Pignata
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
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14
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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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15
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Li J, Li L, Wang Y, Huang G, Li X, Xie Z, Zhou Z. Insights Into the Role of DNA Methylation in Immune Cell Development and Autoimmune Disease. Front Cell Dev Biol 2021; 9:757318. [PMID: 34790667 PMCID: PMC8591242 DOI: 10.3389/fcell.2021.757318] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
To date, nearly 100 autoimmune diseases have been an area of focus, and these diseases bring health challenges to approximately 5% of the population worldwide. As a type of disease caused by tolerance breakdown, both environmental and genetic risk factors contribute to autoimmune disease development. However, in most cases, there are still gaps in our understanding of disease pathogenesis, diagnosis, and treatment. Therefore, more detailed knowledge of disease pathogenesis and potential therapies is indispensable. DNA methylation, which does not affect the DNA sequence, is one of the key epigenetic silencing mechanisms and has been indicated to play a key role in gene expression regulation and to participate in the development of certain autoimmune diseases. Potential epigenetic regulation via DNA methylation has garnered more attention as a disease biomarker in recent years. In this review, we clarify the basic function and distribution of DNA methylation, evaluate its effects on gene expression and discuss related key enzymes. In addition, we summarize recent aberrant DNA methylation modifications identified in the most important cell types related to several autoimmune diseases and then provide potential directions for better diagnosing and monitoring disease progression driven by epigenetic control, which may broaden our understanding and contribute to further epigenetic research in autoimmune diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yimeng Wang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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16
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Contribution of Dysregulated DNA Methylation to Autoimmunity. Int J Mol Sci 2021; 22:ijms222111892. [PMID: 34769338 PMCID: PMC8584328 DOI: 10.3390/ijms222111892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/22/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022] Open
Abstract
Epigenetic mechanisms, such as DNA methylation, histone modifications, and non-coding RNAs are known regulators of gene expression and genomic stability in cell growth, development, and differentiation. Because epigenetic mechanisms can regulate several immune system elements, epigenetic alterations have been found in several autoimmune diseases. The purpose of this review is to discuss the epigenetic modifications, mainly DNA methylation, involved in autoimmune diseases in which T cells play a significant role. For example, Rheumatoid Arthritis and Systemic Lupus Erythematosus display differential gene methylation, mostly hypomethylated 5′-C-phosphate-G-3′ (CpG) sites that may associate with disease activity. However, a clear association between DNA methylation, gene expression, and disease pathogenesis must be demonstrated. A better understanding of the impact of epigenetic modifications on the onset of autoimmunity will contribute to the design of novel therapeutic approaches for these diseases.
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17
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Functional Interplay between Methyltransferases and Inflammasomes in Inflammatory Responses and Diseases. Int J Mol Sci 2021; 22:ijms22147580. [PMID: 34299198 PMCID: PMC8306412 DOI: 10.3390/ijms22147580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 02/08/2023] Open
Abstract
An inflammasome is an intracellular protein complex that is activated in response to a pathogenic infection and cellular damage. It triggers inflammatory responses by promoting inflammatory cell death (called pyroptosis) and the secretion of pro-inflammatory cytokines, interleukin (IL)-1β and IL-18. Many types of inflammasomes have been identified and demonstrated to play a central role in inducing inflammatory responses, leading to the onset and progression of numerous inflammatory diseases. Methylation is a biological process by which methyl groups are transferred from methyl donors to proteins, nucleic acids, and other cellular molecules. Methylation plays critical roles in various biological functions by modulating gene expression, protein activity, protein localization, and molecular stability, and aberrant regulation of methylation causes deleterious outcomes in various human diseases. Methylation is a key determinant of inflammatory responses and diseases. This review highlights the current understanding of the functional relationship between inflammasome regulation and methylation of cellular molecules in inflammatory responses and diseases.
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18
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Qin M, Wang D, Fang Y, Zheng Z, Liu X, Wu F, Wang L, Li X, Hui B, Ma S, Tang W, Pan X. Current Perspectives on B Lymphocytes in the Immunobiology of Hepatocellular Carcinoma. Front Oncol 2021; 11:647854. [PMID: 34235074 PMCID: PMC8256159 DOI: 10.3389/fonc.2021.647854] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
Immune cells infiltrating tumors are capable of significantly impacting carcinogenesis through cancer promotion and anticancer responses. There are many aspects of hepatocellular carcinoma (HCC) related T lymphocytes that are undergoing extensive studies, whereas the effect exerted by B lymphocytes remains a less researched area. In this study, the latest research on the effect of B lymphocytes as they infiltrate tumors in relation to HCC is presented. Their prognosis-related importance is analyzed, along with their function in the tumor microenvironment (TME), as well as the way that B cell biology can be employed to help create a B cell therapy strategy for HCC.
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Affiliation(s)
- Miaomiao Qin
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Danping Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yijiao Fang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhiying Zheng
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xinyang Liu
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Liangliang Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiao Li
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bingqing Hui
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shijie Ma
- Department of Gastroenterology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Weiwei Tang
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Xiongxiong Pan
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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