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Danieli MG, Casciaro M, Paladini A, Bartolucci M, Sordoni M, Shoenfeld Y, Gangemi S. Exposome: Epigenetics and autoimmune diseases. Autoimmun Rev 2024; 23:103584. [PMID: 39097180 DOI: 10.1016/j.autrev.2024.103584] [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: 07/14/2024] [Revised: 07/27/2024] [Accepted: 07/27/2024] [Indexed: 08/05/2024]
Abstract
Systemic autoimmune diseases are complex conditions characterized by an immune system dysregulation and an aberrant activation against self-antigens, leading to tissue and organ damage. Even though genetic predisposition plays a role, it cannot fully explain the onset of these diseases, highlighting the significant impact of non-heritable influences such as environment, hormones and infections. The exposome represents all those factors, ranging from chemical pollutants and dietary components to psychological stressors and infectious agents. Epigenetics, which studies changes in gene expression without altering the DNA sequence, is a crucial link between exposome and the development of autoimmune diseases. Key epigenetic mechanisms include DNA methylation, histone modifications, and non-coding RNAs. These epigenetic modifications could provide a potential piece of the puzzle in understanding systemic autoimmune diseases and their connection with the exposome. In this work we have collected the most important and recent evidence in epigenetic changes linked to systemic autoimmune diseases (systemic lupus erythematosus, idiopathic inflammatory myopathies, ANCA-associated vasculitis, and rheumatoid arthritis), emphasizing the roles these changes may play in disease pathogenesis, their potential as diagnostic biomarkers and their prospective in the development of targeted therapies.
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Affiliation(s)
- Maria Giovanna Danieli
- SOS Immunologia delle Malattie Rare e dei Trapianti, AOU delle Marche & Dipartimento di Scienze Cliniche e Molecolari, Università Politecnica delle Marche, via Tronto 10/A, 60126 Torrette di Ancona, Italy; Postgraduate School of Allergy and Clinical Immunology, Università Politecnica delle Marche, via Tronto 10/A, 60126 Ancona, Italy.
| | - Marco Casciaro
- Operative Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy.
| | - Alberto Paladini
- PostGraduate School of Internal Medicine, Università Politecnica delle Marche, via Tronto 10/A, 60126 Ancona, Italy
| | - Martina Bartolucci
- Postgraduate School of Allergy and Clinical Immunology, Università Politecnica delle Marche, via Tronto 10/A, 60126 Ancona, Italy
| | - Martina Sordoni
- Postgraduate School of Allergy and Clinical Immunology, Università Politecnica delle Marche, via Tronto 10/A, 60126 Ancona, Italy
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Ramat Gan 52621, Israel; Reichman University, Herzelia 46101, Israel.
| | - Sebastiano Gangemi
- Operative Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy.
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Zhao N, Liu F, Dong W, Yu J, Halverson LJ, Xie B. Quantitative proteomics insights into Chlamydomonas reinhardtii thermal tolerance enhancement by a mutualistic interaction with Sinorhizobium meliloti. Microbiol Spectr 2024; 12:e0021924. [PMID: 39012118 DOI: 10.1128/spectrum.00219-24] [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: 01/24/2024] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Interactions between photosynthetic microalgae and bacteria impact the physiology of both partners, which influence the fitness and ecological trajectories of each partner in an environmental context-dependent manner. Thermal tolerance of Chlamydomonas reinhardtii can be enhanced through a mutualistic interaction with vitamin B12 (cobalamin)-producing Sinorhizobium meliloti. Here, we used label-free quantitative proteomics to reveal the metabolic networks altered by the interaction under normal and high temperatures. We created a scenario where the growth of Sinorhizobium requires carbon provided by Chlamydomonas for growth in co-cultures, and survival of Chlamydomonas under high temperatures relies on cobalamin and possibly other metabolites produced by Sinorhizobium. Differential abundance analysis identified proteins produced by each partner in co-cultures compared to mono-cultures at each temperature. Proteins involved in cobalamin production by Sinorhizobium increased in the presence of Chlamydomonas under elevated temperatures, whereas in Chlamydomonas, there was an increase in cobalamin-dependent methionine synthase and certain proteins associated with methylation reactions. Co-cultivation and heat stress strongly modulated the central metabolism of both partners as well as various transporters that could facilitate nutrient cross-utilization. Co-cultivation modulated expression of various components of two- or one-component signal transduction systems, transcriptional activators/regulators, or sigma factors, suggesting complex regulatory networks modulate the interaction in a temperature-dependent manner. Notably, heat and general stress-response and antioxidant proteins were upregulated in co-cultures, suggesting that the interaction is inherently stressful to each partner despite the benefits of mutualism. Our results shed insight into the metabolic tradeoffs required for mutualism and how metabolic networks are modulated by elevated temperature. IMPORTANCE Photosynthetic microalgae are key primary producers in aquatic ecosystems, playing an important role in the global carbon cycle. Nearly every alga lives in association with a diverse community of microorganisms that influence each other and their metabolic activities or survival. One chemical produced by bacteria that influence algae is vitamin B12, an enzyme cofactor used for a variety of metabolic functions. The alga Chlamydomonas reinhardtii benefits from vitamin B12 produced by Sinorhizobium meliloti by producing the amino acid methionine under high temperatures which are required for Chlamydomonas thermotolerance. Yet, our understanding of this interaction under normal and stressful temperatures is poor. Here, we used quantitative proteomics to identify differentially expressed proteins to reveal metabolic adjustments made by Chlamydomonas and Sinorhizobium that could facilitate this mutualism. These findings will enhance our understanding of how photosynthetic algae and their associated microbiomes will respond as global temperatures increase.
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Affiliation(s)
- Na Zhao
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
| | - Fei Liu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Wenxiu Dong
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Jie Yu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Larry J Halverson
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Bo Xie
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
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Russo C, Valle MS, D’Angeli F, Surdo S, Giunta S, Barbera AC, Malaguarnera L. Beneficial Effects of Manilkara zapota-Derived Bioactive Compounds in the Epigenetic Program of Neurodevelopment. Nutrients 2024; 16:2225. [PMID: 39064669 PMCID: PMC11280255 DOI: 10.3390/nu16142225] [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: 06/07/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Gestational diet has a long-dated effect not only on the disease risk in offspring but also on the occurrence of future neurological diseases. During ontogeny, changes in the epigenetic state that shape morphological and functional differentiation of several brain areas can affect embryonic fetal development. Many epigenetic mechanisms such as DNA methylation and hydroxymethylation, histone modifications, chromatin remodeling, and non-coding RNAs control brain gene expression, both in the course of neurodevelopment and in adult brain cognitive functions. Epigenetic alterations have been linked to neuro-evolutionary disorders with intellectual disability, plasticity, and memory and synaptic learning disorders. Epigenetic processes act specifically, affecting different regions based on the accessibility of chromatin and cell-specific states, facilitating the establishment of lost balance. Recent insights have underscored the interplay between epigenetic enzymes active during embryonic development and the presence of bioactive compounds, such as vitamins and polyphenols. The fruit of Manilkara zapota contains a rich array of these bioactive compounds, which are renowned for their beneficial properties for health. In this review, we delve into the action of each bioactive micronutrient found in Manilkara zapota, elucidating their roles in those epigenetic mechanisms crucial for neuronal development and programming. Through a comprehensive understanding of these interactions, we aim to shed light on potential avenues for harnessing dietary interventions to promote optimal neurodevelopment and mitigate the risk of neurological disorders.
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Affiliation(s)
- Cristina Russo
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, 95123 Catania, Italy; (C.R.); (L.M.)
| | - Maria Stella Valle
- Section of Physiology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Floriana D’Angeli
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy;
| | - Sofia Surdo
- Italian Center for the Study of Osteopathy (CSDOI), 95124 Catania, Italy;
| | - Salvatore Giunta
- Section of Anatomy, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy;
| | - Antonio Carlo Barbera
- Section of Agronomy and Field Crops, Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy;
| | - Lucia Malaguarnera
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, 95123 Catania, Italy; (C.R.); (L.M.)
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Ma S, Liu J, Zhao Y, Wang Y, Zhao R. In ovo betaine injection improves breast muscle growth in newly hatched goslings through FXR/IGF-2 pathway. Poult Sci 2024; 103:104075. [PMID: 39094501 DOI: 10.1016/j.psj.2024.104075] [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: 05/13/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024] Open
Abstract
Betaine has been shown to enhance growth performance and increase breast muscle yield in ducks and broilers through various mechanisms, including the modification of DNA methylation. However, the impact of in ovo betaine injection on muscle growth in newly hatched goslings remains unclear. In this study, fifty eggs were injected with saline or betaine at 7.5 mg/egg prior to incubation, and the subsequent effects on breast muscle growth in the newly hatched goslings were investigated. Betaine significantly increased (P < 0.05) the hatch weight, breast muscle weight, and breast muscle index, accompanied by an augmentation in muscle bundle cross-sectional area. Concurrently, betaine significantly upregulated (P < 0.05) the expression levels of myogenic regulatory factors, including myogenin (MyoG) and paired box 7 (Pax7) both mRNA and protein, while downregulating (P < 0.05) the mRNA and protein levels of myostatin (MSTN). Histological analysis revealed a higher abundance of proliferating cell nuclear antigen (PCNA) and Pax7 immune-positive cells in the breast muscle of the betaine group, consistent with elevated PCNA and Pax7 mRNA and protein levels. Additionally, significantly increased (P < 0.05) contents of insulin-like growth factor 1 (IGF-1) and insulin-like growth factor 2 (IGF-2) were observed in the breast muscle of the betaine group, so was mRNA expression of IGF-1, IGF-2, and insulin-like growth factor 1 receptor (IGF-1R). Betaine also significantly in8creased (P < 0.05) global DNA methylation of the breast muscle, accompanied by enhanced mRNA and protein levels of methionine cycle and DNA methylation-related enzymes, Interestingly, the promoter regions of IGF-1, IGF-2, and IGF-1R genes were significantly hypomethylated (P < 0.05). Moreover, in ovo betaine injection significantly upregulated (P < 0.05) the protein level of farnesoid X receptor (FXR) in breast muscle and FXR binding to the promoter of IGF-2 gene. These findings suggest that in ovo betaine injection promotes breast muscle growth during embryonic development in goslings through the FXR-mediated IGF-2 pathway, ultimately improving hatch weight and breast muscle weight.
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Affiliation(s)
- Shuai Ma
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Jie Liu
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yulan Zhao
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yan Wang
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Ruqian Zhao
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, P. R. China; National Key Laboratory of Meat Quality Control and Cultured Meat Development, Nanjing Agricultural University, Nanjing 210095, P. R. China.
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Zong Y, Zhu A, Liu P, Fu P, Li Y, Chen S, Gao X. Pan-cancer analysis of the disulfidptosis-related gene RPN1 and its potential biological function and prognostic significance in gliomas. Heliyon 2024; 10:e31875. [PMID: 38845861 PMCID: PMC11154626 DOI: 10.1016/j.heliyon.2024.e31875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Background Numerous studies have shown a strong correlation between disulfidptosis and various cancers. However, the expression and function of RPN1, a crucial gene in disulfidptosis, remain unclear in the context of cancer. Methods Gene expression and clinical information on lung adenocarcinoma were obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. RPN1 expression was analyzed using the Timer2.0 and the Human Protein Atlas (HPA) databases. Prognostic significance was assessed using Cox regression analysis and Kaplan-Meier curves. Genetic mutations and methylation levels were examined using the cBioPortal and UALCAN platforms, respectively. The relationship between RPN1 and tumor mutation burden (TMB) and microsatellite instability (MSI) across different cancer types was analyzed using the Spearman correlation coefficient. The relationship between RPN1 and immune cell infiltration was analyzed using the Timer2.0 database, whereas variations in drug sensitivity were explored using the CellMiner database. Receiver operating characteristic curves validated RPN1's diagnostic potential in glioma, and its correlation with immune checkpoint inhibitors (ICIs) was assessed using Spearman's correlation coefficient. Single-sample gene set enrichment analysis elucidated a link between RPN1 and immune cells and pathways. In addition, a nomogram based on RPN1 was developed to predict patient prognosis. The functional impact of RPN1 on glioma cells was confirmed using scratch and Transwell assays. Result RPN1 was aberrantly expressed in various cancers and affected patient prognosis. The main mutation type of RPN1 in the cancer was amplified. RPN1 exhibited a positive correlation with myeloid-derived suppressor cells, neutrophils, and macrophages, and a negative correlation with CD8+ T cells and hematopoietic stem cells. RPN1 expression was associated with TMB and MSI in various cancers. The expression of RPN1 affected drug sensitivity in cancer cells. RPN1 was positively correlated with multiple ICIs in gliomas. RPN1 also affected immune cell infiltration into the tumor microenvironment. RPN1 was an independent prognostic factor for gliomas, and the nomogram demonstrated excellent predictive performance. Interference with RPN1 expression reduces the migratory and invasive ability of glioma cells. Conclusion RPN1 exerts multifaceted effects on different stages of cancer, including immune infiltration, prognosis, and treatment outcomes. RPN1 expression affects the prognosis and immune microenvironment infiltration in patients with glioma, making RPN1 a potential target for the treatment of glioma.
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Affiliation(s)
- Yan Zong
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Ankang Zhu
- Department of Thoracic Surgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Peipei Liu
- Anhui BioX-Vision Biological Technology Co., Ltd., Anhui, China
| | - Peiji Fu
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yinuo Li
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shuai Chen
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xingcai Gao
- Department of Thoracic Surgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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Zhang L, Chen L, Jiang Y, Jin G, Yang J, Sun H, Liang J, Lv G, Yang Q, Yi S, Chen G, Liu W, Ou J, Yang Y. Cross-species metabolomic profiling reveals phosphocholine-mediated liver protection from cold and ischemia/reperfusion. Am J Transplant 2024:S1600-6135(24)00346-0. [PMID: 38878865 DOI: 10.1016/j.ajt.2024.05.018] [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: 11/18/2023] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 07/11/2024]
Abstract
Cold and ischemia/reperfusion (IR)-associated injuries are seemingly inevitable during liver transplantation and hepatectomy. Because Syrian hamsters demonstrate intrinsic tolerance to transplantation-like stimuli, cross-species comparative metabolomic analyses were conducted with hamster, rat, and donor liver samples to seek hepatic cold and IR-adaptive mechanisms. Lower hepatic phosphocholine contents were found in recipients with early graft-dysfunction and with virus-caused cirrhosis or high model for end-stage liver disease scores (≥30). Choline/phosphocholine deficiency in cultured human THLE-2 hepatocytes and animal models weakened hepatocellular cold tolerance and recovery of glutathione and ATP production, which was rescued by phosphocholine supplements. Among the biological processes impacted by choline/phosphocholine deficiency, 3 lipid-related metabolic processes were downregulated, whereas phosphocholine elevated the expression of genes in methylation processes. Consistently, in THLE-2, phosphocholine enhanced the overall RNA m6A methylation, among which the transcript stability of fatty acid desaturase 6 (FADS6) was improved. FADS6 functioned as a key phosphocholine effector in the production of polyunsaturated fatty acids, which may facilitate the hepatocellular recovery of energy and redox homeostasis. Thus, our study reveals the choline-phosphocholine metabolism and its downstream FADS6 functions in hepatic adaptation to cold and IR, which may inspire new strategies to monitor donor liver quality and improve recipient recovery from the liver transplantation process.
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Affiliation(s)
- Lele Zhang
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liang Chen
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Key Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education Institutes, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yong Jiang
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guanghui Jin
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jinghong Yang
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haobin Sun
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jinliang Liang
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guo Lv
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Key Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education Institutes, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qing Yang
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Key Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education Institutes, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuhong Yi
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Key Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education Institutes, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guihua Chen
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Key Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education Institutes, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Liu
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Key Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education Institutes, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Jingxing Ou
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Yang Yang
- Department of Hepatic Surgery and Liver Transplantation Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China; Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, China; Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Key Laboratory of Liver Disease Biotherapy and Translational Medicine of Guangdong Higher Education Institutes, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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Rogers PC, Cheng J, Lim A, Potts JE. Feasibility study of micronutrient status and body mass index of newly diagnosed pediatric oncology patients: Research commentary. Pediatr Blood Cancer 2024; 71:e30936. [PMID: 38462770 DOI: 10.1002/pbc.30936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/28/2024] [Accepted: 02/16/2024] [Indexed: 03/12/2024]
Abstract
We conducted a feasibility study to evaluate micronutrients and body mass index (BMI). Fat soluble vitamins A, D, E and trace elements copper (Cu), selenium (Se), and zinc (Zn) levels were evaluated. Weight, height, BMI, and Z-scores were recorded. Side effects or specific adverse events were documented. No patient had a Z-score for height, weight, or BMI of less than 2 SD or greater than 2 SD. Ninety percent of patients had one or more micronutrient levels below normal. These results suggest that micronutrient abnormalities are common despite no obvious evidence of malnutrition. Side effects of chemotherapy may be exacerbated by micronutrient depletion.
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Affiliation(s)
- Paul C Rogers
- Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey Cheng
- Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alecia Lim
- Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, British Columbia, Canada
| | - James E Potts
- Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, British Columbia, Canada
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Feng B, Zheng J, Cai Y, Han Y, Han Y, Wu J, Feng J, Zheng K. An Epigenetic Manifestation of Alzheimer's Disease: DNA Methylation. ACTAS ESPANOLAS DE PSIQUIATRIA 2024; 52:365-374. [PMID: 38863055 PMCID: PMC11190457 DOI: 10.62641/aep.v52i3.1595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Alzheimer's disease (AD), the most common form of dementia, has a complex pathogenesis. The number of AD patients has increased in recent years due to population aging, while a trend toward a younger age of onset has arisen, imposing a substantial burden on society and families, and garnering extensive attention. DNA methylation has recently been revealed to play an important role in AD onset and progression. DNA methylation is a critical mechanism regulating gene expression, and alterations in this mechanism dysregulate gene expression and disrupt important pathways, including oxidative stress responses, inflammatory reactions, and protein degradation processes, eventually resulting in disease. Studies have revealed widespread changes in AD patients' DNA methylation in the peripheral blood and brain tissues, affecting multiple signaling pathways and severely impacting neuronal cell and synaptic functions. This review summarizes the role of DNA methylation in the pathogenesis of AD, aiming to provide a theoretical basis for its early prevention and treatment.
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Affiliation(s)
- Boyi Feng
- Department of Chronic Disease, Longhua District Center for Chronic Disease Control/Mental Health, 510080 Shenzhen, Guangdong, China
- Shenzhen Guangming District People's Hospital, 518107 Shenzhen, Guangdong, China
| | - Junli Zheng
- Department of Chronic Disease, Longhua District Center for Chronic Disease Control/Mental Health, 510080 Shenzhen, Guangdong, China
| | - Ying Cai
- Public Health Service Center, Bao'an District, 518100 Shenzhen, Guangdong, China
| | - Yaguang Han
- First Affiliated Hospital, Heilongjiang University of Chinese Medicine, 150000 Harbin, Heilongjiang, China
| | - Yanhua Han
- First Affiliated Hospital, Heilongjiang University of Chinese Medicine, 150000 Harbin, Heilongjiang, China
| | - Jiaqi Wu
- Department of Chronic Disease, Longhua District Center for Chronic Disease Control/Mental Health, 510080 Shenzhen, Guangdong, China
| | - Jun Feng
- Department of Chronic Disease, Longhua District Center for Chronic Disease Control/Mental Health, 510080 Shenzhen, Guangdong, China
| | - Kai Zheng
- Department of Chronic Disease, Longhua District Center for Chronic Disease Control/Mental Health, 510080 Shenzhen, Guangdong, China
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9
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Zhang C, Liu Z, Sun K, Zhao J, Huang H, Zhang C. Association of serum folic acid levels in response to fasting blood glucose in early pregnancy with the risk of gestational diabetes mellitus: A retrospective cohort study. Nutrition 2024; 122:112383. [PMID: 38422754 DOI: 10.1016/j.nut.2024.112383] [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: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE With increasingly prevalent folic acid consumption in early pregnancy, concerns about its potentially negative effect on maternal metabolism have been raised. Recent findings regarding folic acid levels in the first trimester and the risk of gestational diabetes mellitus have been inconclusive. The aim of this study was to investigate the association of folic acid status in early pregnancy with gestational diabetes mellitus as well as examine whether glucose levels can be modulated by folic acid status during the same first trimester. METHODS This was a retrospective cohort study based on 27 128 Chinese pregnant women who registered during their first prenatal visit from January 2015 to December 2019. Serum folic acid and fasting blood glucose concentrations were measured during the 9th to 13th gestational weeks. Binary logistic regression was applied to estimate the odds ratios of gestational diabetes mellitus by using the serum folic acid levels quartiles with adjustment for major confounders. To investigate the potential effect of modifying key risk factors for gestational diabetes mellitus, we established subgroups, in which analyses were stratified by age (<25, 25-29, 30-34, and ≥35 y), parity (nulliparous and parous), prepregnancy body mass index (< 18.5, 18.5-23.9, and ≥ 24 kg/m2), and family history of diabetes (yes and no). RESULTS The positive association between maternal folate concentrations and fasting blood glucose was observed: the risk for hyperglycemia was higher in those in the middle (Q3) and higher (Q4) quartiles compared with those in Q1 and Q2. A higher risk for gestational diabetes mellitus was found in hyperglycemia of early pregnant women with high folate concentrations (Q3: odds ratio = 5.63; 95% CI, 4.56-6.95, and Q4: odds ratio = 5.57; 95% CI, 4.68-6.64) compared with normal fasting glucose mothers with folate concentrations in Q1 and Q2 after accounting for multiple covariables. Similar patterns were observed for different subgroups. Restricted cubic spline plots had a positive correlation of serum folic acid level with fasting blood glucose concentration as well as risk of gestational diabetes mellitus in a nonlinear pattern, with 32.5 nmol/L as the cutoff point for folic acid level. CONCLUSIONS Our findings underscore the importance of maintaining an appropriate folic acid concentration for preserving a lower risk of gestational diabetes mellitus, especially in women with relatively higher blood glucose in early pregnancy. Additionally, folic acid concentration > 32.5 nmol/L may be considered a risk factor for gestational diabetes mellitus. This research suggested that folic acid levels should be monitored during the first trimester from the first prenatal checkup to prevent adverse effects of excessive folic acid intake.
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Affiliation(s)
- Chenjie Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhaonan Liu
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine
| | - Kuan Sun
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine
| | - Junfei Zhao
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hefeng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Chen Zhang
- Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
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10
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Teng C, Song X, Fan C, Man S, Hu Y, Hou Y, Xin T. Breast cancer clinical outcomes and tumor immune microenvironment: cross-dialogue of multiple epigenetic modification profiles. Aging (Albany NY) 2024; 16:8998-9022. [PMID: 38796789 PMCID: PMC11164499 DOI: 10.18632/aging.205853] [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: 07/27/2023] [Accepted: 02/29/2024] [Indexed: 05/29/2024]
Abstract
The discovery of RNA methylation alterations associated with cancer holds promise for their utilization as potential biomarkers in cancer diagnosis, prognosis, and prediction. RNA methylation has been found to impact the immunological microenvironment of tumors, but the specific role of methylation-related genes (MRGs), particularly in breast cancer (BC), the most common cancer among women globally, within the tumor microenvironment remains unknown. In this study, we obtained data from TCGA and GEO databases to investigate the expression patterns of MRGs in both genomic and transcriptional domains in BC. By analyzing the data, we identified two distinct genetic groupings that were correlated with clinicopathological characteristics, prognosis, degree of TME cell infiltration, and other abnormalities in MRGs among patients. Subsequently, an MRG model was developed to predict overall survival (OS) and its accuracy was evaluated in BC patients. Additionally, a highly precise nomogram was created to enhance the practical usability of the MRG model. In low-risk groups, we observed lower TBM values and higher TIDE scores. We further explored how MRGs influence a patient's prognosis, clinically significant characteristics, response to therapy, and the TME. These risk signatures have the potential to improve treatment strategies for BC patients and could be applied in future clinical settings. Moreover, they may also be utilized to determine prognosis and biological features in these patients.
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Affiliation(s)
- Chong Teng
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaowei Song
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Chengjuan Fan
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Siqi Man
- Oncology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yuanyuan Hu
- Oncology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yifei Hou
- School of Nursing, Harbin Medical University, Harbin, Heilongjiang, China
| | - Tao Xin
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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11
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Tian S, Chen M. Global research progress of gut microbiota and epigenetics: bibliometrics and visualized analysis. Front Immunol 2024; 15:1412640. [PMID: 38803501 PMCID: PMC11128553 DOI: 10.3389/fimmu.2024.1412640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Background Gut microbiota is an important factor affecting host health. With the further study of the mechanism of gut microbiota, significant progress has been made in the study of the link between gut microbiota and epigenetics. This study visualizes the body of knowledge and research priorities between the gut microbiota and epigenetics through bibliometrics. Methods Publications related to gut microbiota and epigenetics were searched in the Web of Science Core Collection (WoSCC) database. Vosviewer 1.6.17 and CiteSpace 6.1.R2 were used for bibliometric analysis. Results WoSCC includes 460 articles from 71 countries. The number of publications on gut microbiota and epigenetics has increased each year since 2011. The USA, PEOPLES R CHINA, and ITALY are at the center of this field of research. The University of California System, Harvard University, and the University of London are the main research institutions. Li, X, Yu, Q, Zhang, S X are the top authors in this research field. We found that current research hotspots and frontiers include short-chain fatty acids (SCFA) play an important role in gut microbiota and epigenetic mechanisms, gut microbiota and epigenetics play an important role in host obesity, diet, and metabolism. Gut microbiota and epigenetics are closely related to colorectal cancer, breast cancer, and inflammatory bowel disease. At the same time, we found that gut microbiota regulates epigenetics through the gut-brain axis and has an impact on psychiatric diseases. Therefore, probiotics can regulate gut microbiota, improve lifestyle, and reduce the occurrence and development of diseases. Conclusion This is the first comprehensive and in-depth bibliometric study of trends and developments in the field of gut microbiota and epigenetics research. This study helps to guide the direction of research scholars in their current field of study.
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Affiliation(s)
- Siyu Tian
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine (TCM), Chengdu, China
| | - Min Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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12
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Faienza MF, Urbano F, Anaclerio F, Moscogiuri LA, Konstantinidou F, Stuppia L, Gatta V. Exploring Maternal Diet-Epigenetic-Gut Microbiome Crosstalk as an Intervention Strategy to Counter Early Obesity Programming. Curr Issues Mol Biol 2024; 46:4358-4378. [PMID: 38785533 PMCID: PMC11119222 DOI: 10.3390/cimb46050265] [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: 03/28/2024] [Revised: 04/21/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Alterations in a mother's metabolism and endocrine system, due to unbalanced nutrition, may increase the risk of both metabolic and non-metabolic disorders in the offspring's childhood and adulthood. The risk of obesity in the offspring can be determined by the interplay between maternal nutrition and lifestyle, intrauterine environment, epigenetic modifications, and early postnatal factors. Several studies have indicated that the fetal bowel begins to colonize before birth and that, during birth and nursing, the gut microbiota continues to change. The mother's gut microbiota is primarily transferred to the fetus through maternal nutrition and the environment. In this way, it is able to impact the establishment of the early fetal and neonatal microbiome, resulting in epigenetic signatures that can possibly predispose the offspring to the development of obesity in later life. However, antioxidants and exercise in the mother have been shown to improve the offspring's metabolism, with improvements in leptin, triglycerides, adiponectin, and insulin resistance, as well as in the fetal birth weight through epigenetic mechanisms. Therefore, in this extensive literature review, we aimed to investigate the relationship between maternal diet, epigenetics, and gut microbiota in order to expand on current knowledge and identify novel potential preventative strategies for lowering the risk of obesity in children and adults.
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Affiliation(s)
- Maria Felicia Faienza
- Pediatric Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “A. Moro”, 70124 Bari, Italy
| | - Flavia Urbano
- Giovanni XXIII Pediatric Hospital, 70126 Bari, Italy; (F.U.); (L.A.M.)
| | - Federico Anaclerio
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (F.K.); (L.S.); (V.G.)
- Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | | | - Fani Konstantinidou
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (F.K.); (L.S.); (V.G.)
- Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Liborio Stuppia
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (F.K.); (L.S.); (V.G.)
- Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Valentina Gatta
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (F.K.); (L.S.); (V.G.)
- Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
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Su X, Liu J, Tu Z, Ji Q, Li J, Liu F. DNMT3A promotes glioma growth and malignancy via TNF-α/NF-κB signaling pathway. Transl Cancer Res 2024; 13:1786-1806. [PMID: 38737693 PMCID: PMC11082822 DOI: 10.21037/tcr-23-1943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/22/2024] [Indexed: 05/14/2024]
Abstract
Background DNMT3A is the main molecule responsible for DNA methylation in cells. DNMT3A affects the progression of inflammation, degenerative diseases, and malignant tumors, and exhibits significant aberrantly expression in tumor tissues. Methods Transcriptome data and relevant clinical information were downloaded from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and Gene Expression Omnibus (GEO) datasets. Differential expression analysis and prognostic analysis were conducted based on above statistics. We constructed a clinical prognostic model and identified DNMT3A as an independent prognostic factor to accurately predict patient prognosis. Differential gene enrichment analysis revealed that DNMT3A affects the progression of glioma through multiple pathways, among which the tumor necrosis factor-α (TNF-α)/nuclear factor-kappa B (NF-κB) pathway shows a strong correlation. Immunological analysis also revealed a certain correlation between DNMT3A and tumor immunity. We demonstrated through gene editing that DNMT3A can affect the release of TNF-α in cells, thereby affecting the progression of glioma. Functional experiments have also demonstrated that DNMT3A plays a crucial role in tumors. Results RNA-sequencing and survival analyses of lower-grade glioma (LGG) patients in TCGA, CGGA, and GEO cohorts showed that high DNMT3A expression correlated with poor prognosis of LGG patients. Univariate and multivariate Cox regression analyses showed that DNMT3A expression was an independent prognostic indicator in LGG. The prognosis prediction nomogram with age, World Health Organization (WHO) grading, and DNMT3A expression showed reliable performance in predicting the 1-, 3-, and 5-year overall survival (OS) of LGG patients. Functional enrichment analysis, gene set enrichment analysis (GSEA), and ESTIMATE algorithm analyses showed that DNMT3A expression was associated with the tumor infiltration of immune cells and predicted response to immunotherapy in two immunotherapy cohorts of pan-cancer patients. Furthermore, short hairpin RNA (shRNA)-mediated knockdown of DNMT3A in the LGG cell lines suppressed proliferation, migration, and invasion of LGG cells by downregulating the TNF-α/NF-κB signaling pathway. Conclusions Our data showed that DNMT3A was a potential prognostic biomarker in glioma. DNMT3A promoted proliferation and malignancy of LGG cells through the TNF-α/NF-κB signaling pathway. DNMT3A is a promising therapeutic target for treating patients with LGG.
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Affiliation(s)
- Xiaoyan Su
- Department of Pathology, the 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Junzhe Liu
- Department of Neurosurgery, the 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
| | - Zewei Tu
- Department of Neurosurgery, the 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
| | - Qiankun Ji
- Department of Neurosurgery, Zhoukou Central Hospital, Zhoukou, China
| | - Jingying Li
- Department of Comprehensive Intensive Care Unit, the 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Fanrong Liu
- Department of Pathology, the 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
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14
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Agudelo MC, Agudelo S, Lorincz A, Ramírez AT, Castañeda KM, Garcés-Palacio I, Zea AH, Piyathilake C, Sanchez GI. Folate deficiency modifies the risk of CIN3+ associated with DNA methylation levels: a nested case-control study from the ASCUS-COL trial. Eur J Nutr 2024; 63:563-572. [PMID: 38129362 PMCID: PMC10899296 DOI: 10.1007/s00394-023-03289-4] [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: 07/17/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE To our knowledge, there are very few studies evaluating if the levels of folate modify the risk of cervical intraepithelial neoplasia grade 2 and higher (CIN2+ and CIN3+) associated with the levels of HPV genome methylation, two cofactors related to single carbon metabolism and independently associated with cervical cancer in previous studies. We conducted a case-control study nested in a three-arm randomized clinical pragmatic trial (ASCUS-COL trial) to evaluate the risk of CIN3+ associated with methylation levels according to serum folate concentrations. METHODS Cases (n = 155) were women with histologically confirmed CIN2+ (113 CIN2, 38 CIN3, and 4 SCC) and controls were age and follow-up time at diagnosis-matched women with histologically confirmed ≤ CIN1 (n = 155), selected from the 1122 hrHPV + women of this trial. The concentrations of serum folate were determined by the radioimmunoassay SimulTRAC-SNB-VitaminB12/Folate-RIAKit and the methylation levels by the S5 classifier. Stepwise logistic regression models were used to estimate the association between folate or methylation levels and CIN2+ or CIN3+. The joint effect of folate levels and methylation on the risk of CIN3+ was estimated using combinations of categorical stratifications. RESULTS Folate levels were significantly lower in women with CIN3+ than in other diagnostic groups (p = 0.019). The risk of CIN3+ was eight times higher (OR 8.9, 95% CI 3.4-24.9) in women with folate deficiency and high methylation levels than in women with normal folate and high methylation levels (OR 1.4, 95% CI 0.4-4.6). CONCLUSION High methylation and deficient folate independently increased the risk of CIN3+ while deficient folate combined with high methylation was associated with a substantially elevated risk of CIN3+.
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Affiliation(s)
- María C Agudelo
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Samuel Agudelo
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Attila Lorincz
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Arianis Tatiana Ramírez
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
- Postdoctoral Fellow at the Prevention and Implementation Group, International Agency for Research On Cancer/World Health Organization, Lyon, France
| | - Kelly Melisa Castañeda
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Isabel Garcés-Palacio
- Epidemiology Group, School of Public Health, Universidad de Antioquia, Medellín, Colombia
| | - Arnold H Zea
- Stanley S. Scott Cancer Center, Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, USA
| | - Chandrika Piyathilake
- Department of Nutrition Sciences, The University of Alabama at Birmingham, Birmingham, USA
| | - Gloria Ines Sanchez
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia.
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15
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Mendoza-Martínez GD, Orzuna-Orzuna JF, Roque-Jiménez JA, Gloria-Trujillo A, Martínez-García JA, Sánchez-López N, Hernández-García PA, Lee-Rangel HA. A Polyherbal Mixture with Nutraceutical Properties for Ruminants: A Meta-Analysis and Review of BioCholine Powder. Animals (Basel) 2024; 14:667. [PMID: 38473052 PMCID: PMC11154432 DOI: 10.3390/ani14050667] [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: 01/03/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
BioCholine Powder is a polyherbal feed additive composed of Achyrantes aspera, Trachyspermum ammi, Azadirachta indica, and Citrullus colocynthis. The objective of this study was to analyze published results that support the hypothesis that the polyherbal product BioCholine Powder has rumen bypass choline metabolites through a meta-analysis and effect size analysis (ES). Using Scopus, Web of Science, ScienceDirect, PubMed, and university dissertation databases, a systematic search was conducted for experiments published in scientific documents that evaluated the effects of BioCholine supplementation on the variables of interest. The analyzed data were extracted from twenty-one publications (fifteen scientific articles, three abstracts, and three graduate dissertations available in institutional libraries). The studies included lamb growing-finishing, lactating ewes and goats, calves, and dairy cows. The effects of BioCholine were analyzed using random effects statistical models to compare the weighted mean difference (WMD) between BioCholine-supplemented ruminants and controls (no BioCholine). Heterogeneity was explored, and three subgroup analyses were performed for doses [(4 (or 5 g/d), 8 (10 g/d)], supplementation in gestating and lactating ewes (pre- and postpartum supplementation), and blood metabolites by species and physiological state (lactating goats, calves, lambs, ewes). Supplementation with BioCholine in sheep increased the average daily lamb gain (p < 0.05), final body weight (p < 0.01), and daily milk yield (p < 0.05) without effects on intake or feed conversion. Milk yield was improved in small ruminants with BioCholine prepartum supplementation (p < 0.10). BioCholine supplementation decreased blood urea (p < 0.01) and increased levels of the liver enzymes alanine transaminase (ALT; p < 0.10) and albumin (p < 0.001). BioCholine doses over 8 g/d increased blood glucose, albumin (p < 0.10), cholesterol, total protein, and globulin (p < 0.05). The ES values of BioCholine in retained energy over the control in growing lambs were +7.15% NEm (p < 0.10) and +9.25% NEg (p < 0.10). In conclusion, adding BioCholine Powder to domestic ruminants' diets improves productive performance, blood metabolite indicators of protein metabolism, and liver health, showing its nutraceutical properties where phosphatidylcholine prevails as an alternative that can meet the choline requirements in ruminants.
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Affiliation(s)
- Germán David Mendoza-Martínez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | | | - José Alejandro Roque-Jiménez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Ejido Nuevo León, Mexicali 21705, Mexico
| | - Adrián Gloria-Trujillo
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | - José Antonio Martínez-García
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | - Nallely Sánchez-López
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | | | - Héctor Aaron Lee-Rangel
- Facultad de Agronomía y Veterinaria, Centro de Biociencias, Instituto de Investigaciones en Zonas Desérticas, Universidad Autónoma de San Luis Potosí, S.L.P., Soledad de Graciano Sánchez 78000, Mexico;
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16
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Song YF, Bai ZY, Luo Z, Wang LJ, Zheng H. Choline-mediated hepatic lipid homoeostasis in yellow catfish: unravelling choline's lipotropic and methyl donor functions and significance of ire-1α signalling pathway. Br J Nutr 2024; 131:202-213. [PMID: 37642130 DOI: 10.1017/s000711452300185x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Choline plays a crucial role in hepatic lipid homeostasis by acting as a major methyl-group donor. However, despite this well-accepted fact, no study has yet explored how choline's methyl-donor function contributes to preventing hepatic lipid dysregulation. Moreover, the potential regulatory role of Ire-1α, an ER-transmembrane transducer for the unfolded protein response (UPRer), in choline-mediated hepatic lipid homeostasis remains unexplored. Thus, this study investigated the mechanism by which choline prevents hepatic lipid dysregulation, focusing on its role as a methyl-donor and the involvement of Ire-1α in this process. To this end, a model animal for lipid metabolism, yellow catfish (Pelteobagrus fulvidraco) were fed two different diets (adequate or deficient choline diets) in vivo for 10 weeks. The key findings of studies are as follows: 1. Dietary choline, upregulated selected lipolytic and fatty acid β-oxidation transcripts promoting hepatic lipid homeostasis. 2. Dietary choline ameliorated UPRer and prevented hepatic lipid dysregulation mainly through ire-1α signalling, not perk or atf-6α signalling. 3. Choline inhibited the transcriptional expression level of ire-1α by activating site-specific DNA methylations in the promoter of ire-1α. 4. Choline-mediated ire-1α methylations reduced Ire-1α/Fas interactions, thereby further inhibiting Fas activity and reducing lipid droplet deposition. These results offer a novel insight into the direct and indirect regulation of choline on lipid metabolism genes and suggests a potential crosstalk between ire-1α signalling and choline-deficiency-induced hepatic lipid dysregulation, highlighting the critical contribution of choline as a methyl-donor in maintaining hepatic lipid homeostasis.
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Affiliation(s)
- Yu-Feng Song
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan430070, People's Republic of China
| | - Zhen-Yu Bai
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan430070, People's Republic of China
| | - Zhi Luo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan430070, People's Republic of China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, People's Republic of China
| | - Ling-Jiao Wang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan430070, People's Republic of China
| | - Hua Zheng
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan430070, People's Republic of China
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17
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Hellbach F, Freuer D, Meisinger C, Peters A, Winkelmann J, Costeira R, Hauner H, Baumeister SE, Bell JT, Waldenberger M, Linseisen J. Usual dietary intake and change in DNA methylation over years: EWAS in KORA FF4 and KORA fit. Front Nutr 2024; 10:1295078. [PMID: 38249614 PMCID: PMC10799384 DOI: 10.3389/fnut.2023.1295078] [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: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Changes in DNA methylation can increase or suppress the expression of health-relevant genes. We investigated for the first time the relationship between habitual food consumption and changes in DNA methylation. Methods The German KORA FF4 and KORA Fit studies were used to study the change in methylation over a median follow-up of 4 years. Only subjects participating in both surveys and with available dietary and methylation data were included in the analysis (n = 465). DNA methylation was measured using the Infinium MethylationEPIC BeadChip (Illumina), resulting in 735,527 shared CpGs across both studies. Generalized estimating equation models with an interaction term of exposure and time point were used to analyze the association of 34 food groups, folic acid, and two dietary patterns with changes in DNA methylation over time. Results The results were corrected for genomic inflation. Significant interaction terms indicate different effects between both time points. We observed only a few significant associations between food intake and change in DNA methylation, except for cream and spirit consumption. The annotated genes include CLN3, PROM1, DLEU7, TLL2, and UGT1A10. Discussion We identified weak associations between food consumption and DNA methylation change. The differential results for cream and spirits, both consumed in low quantities, require replication in independent studies.
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Affiliation(s)
- Fabian Hellbach
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
| | - Dennis Freuer
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Christa Meisinger
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Annette Peters
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Technical University of Munich, Institute of Human Genetics, Klinikum Rechts der Isar, Munich, Germany
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- School of Medicine, Institute of Nutritional Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian-Edgar Baumeister
- Medical Faculty, Institute of Health Services Research in Dentistry, University of Münster, Münster, Germany
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Jakob Linseisen
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
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18
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Bou Ghanem A, Hussayni Y, Kadbey R, Ratel Y, Yehya S, Khouzami L, Ghadieh HE, Kanaan A, Azar S, Harb F. Exploring the complexities of 1C metabolism: implications in aging and neurodegenerative diseases. Front Aging Neurosci 2024; 15:1322419. [PMID: 38239489 PMCID: PMC10794399 DOI: 10.3389/fnagi.2023.1322419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
The intricate interplay of one-carbon metabolism (OCM) with various cellular processes has garnered substantial attention due to its fundamental implications in several biological processes. OCM serves as a pivotal hub for methyl group donation in vital biochemical reactions, influencing DNA methylation, protein synthesis, and redox balance. In the context of aging, OCM dysregulation can contribute to epigenetic modifications and aberrant redox states, accentuating cellular senescence and age-associated pathologies. Furthermore, OCM's intricate involvement in cancer progression is evident through its capacity to provide essential one-carbon units crucial for nucleotide synthesis and DNA methylation, thereby fueling uncontrolled cell proliferation and tumor development. In neurodegenerative disorders like Alzheimer's and Parkinson's, perturbations in OCM pathways are implicated in the dysregulation of neurotransmitter synthesis and mitochondrial dysfunction, contributing to disease pathophysiology. This review underscores the profound impact of OCM in diverse disease contexts, reinforcing the need for a comprehensive understanding of its molecular complexities to pave the way for targeted therapeutic interventions across inflammation, aging and neurodegenerative disorders.
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Affiliation(s)
- Ayman Bou Ghanem
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Yaman Hussayni
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Raghid Kadbey
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Yara Ratel
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Shereen Yehya
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Lara Khouzami
- College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
- AUB Diabetes, American University of Beirut Medical Center, Beirut, Lebanon
| | - Amjad Kanaan
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Frederic Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
- AUB Diabetes, American University of Beirut Medical Center, Beirut, Lebanon
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19
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Wang J, Chen Y, Xiao Z, Liu X, Liu C, Huang K, Chen H. Phase Separation of Chromatin Structure-related Biomolecules: A Driving Force for Epigenetic Regulations. Curr Protein Pept Sci 2024; 25:553-566. [PMID: 38551058 DOI: 10.2174/0113892037296216240301074253] [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: 01/03/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 07/25/2024]
Abstract
Intracellularly, membrane-less organelles are formed by spontaneous fusion and fission of macro-molecules in a process called phase separation, which plays an essential role in cellular activities. In certain disease states, such as cancers and neurodegenerative diseases, aberrant phase separations take place and participate in disease progression. Chromatin structure-related proteins, based on their characteristics and upon external stimuli, phase separate to exert functions like genome assembly, transcription regulation, and signal transduction. Moreover, many chromatin structure-related proteins, such as histones, histone-modifying enzymes, DNA-modifying enzymes, and DNA methylation binding proteins, are involved in epigenetic regulations through phase separation. This review introduces phase separation and how phase separation affects epigenetics with a focus on chromatin structure-related molecules.
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Affiliation(s)
- Jiao Wang
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zixuan Xiao
- ISA Wenhua Wuhan High School, Fenglin Road, Junshan New Town, Wuhan Economics & Technological Development Zone, Wuhan, Hubei 430119, China
| | - Xikai Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chengyu Liu
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hong Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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20
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Bakulski KM, Blostein F, London SJ. Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:126001. [PMID: 38048101 PMCID: PMC10695268 DOI: 10.1289/ehp12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND The prenatal environment influences lifetime health; epigenetic mechanisms likely predominate. In 2016, the first international consortium paper on cigarette smoking during pregnancy and offspring DNA methylation identified extensive, reproducible exposure signals. This finding raised expectations for epigenome-wide association studies (EWAS) of other exposures. OBJECTIVE We review the current state-of-the-science for DNA methylation associations across prenatal exposures in humans and provide future recommendations. METHODS We reviewed 134 prenatal environmental EWAS of DNA methylation in newborns, focusing on 51 epidemiological studies with meta-analysis or replication testing. Exposures spanned cigarette smoking, alcohol consumption, air pollution, dietary factors, psychosocial stress, metals, other chemicals, and other exogenous factors. Of the reproducible DNA methylation signatures, we examined implementation as exposure biomarkers. RESULTS Only 19 (14%) of these prenatal EWAS were conducted in cohorts of 1,000 or more individuals, reflecting the still early stage of the field. To date, the largest perinatal EWAS sample size was 6,685 participants. For comparison, the most recent genome-wide association study for birth weight included more than 300,000 individuals. Replication, at some level, was successful with exposures to cigarette smoking, folate, dietary glycemic index, particulate matter with aerodynamic diameter < 10 μ m and < 2.5 μ m , nitrogen dioxide, mercury, cadmium, arsenic, electronic waste, PFAS, and DDT. Reproducible effects of a more limited set of prenatal exposures (smoking, folate) enabled robust methylation biomarker creation. DISCUSSION Current evidence demonstrates the scientific premise for reproducible DNA methylation exposure signatures. Better powered EWAS could identify signatures across many exposures and enable comprehensive biomarker development. Whether methylation biomarkers of exposures themselves cause health effects remains unclear. We expect that larger EWAS with enhanced coverage of epigenome and exposome, along with improved single-cell technologies and evolving methods for integrative multi-omics analyses and causal inference, will expand mechanistic understanding of causal links between environmental exposures, the epigenome, and health outcomes throughout the life course. https://doi.org/10.1289/EHP12956.
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Affiliation(s)
| | - Freida Blostein
- University of Michigan, Ann Arbor, Michigan, USA
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephanie J. London
- National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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21
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Martín-Fernández-de-Labastida S, Alegria-Lertxundi I, de Pancorbo MM, Arroyo-Izaga M. Association between nutrient intake related to the one-carbon metabolism and colorectal cancer risk: a case-control study in the Basque Country. Eur J Nutr 2023; 62:3181-3191. [PMID: 37543963 PMCID: PMC10611602 DOI: 10.1007/s00394-023-03229-2] [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: 01/31/2023] [Accepted: 07/27/2023] [Indexed: 08/08/2023]
Abstract
PURPOSE Epidemiologic evidence for the association between methyl-donor nutrient intake and colorectal cancer (CRC) risk remains inconclusive. We aimed to examine the relationship between intake of vitamins of the B group, methionine, total choline and betaine and CRC risk, in a population from the CRC screening programme in the Basque Country. DESIGN This observational study included 308 patients with CRC and 308 age- and sex-matched subjects as controls. During recruitment, dietary, anthropometric, lifestyle, socioeconomic, demographic, and health status information was collected. Conditional logistic regression was used to estimate the odds ratios (ORs) for CRC risk. RESULTS The adjusted ORs for CRC risk decreased with higher intakes of choline and betaine (p < 0.05). After further adjustment for folate, high intake of choline and betaine remained associated with a reduced CRC risk (adjusted model for choline, OR third tertile vs first tertile = 0.45, 95% CI 0.26-0.80, p = 0.006; for betaine, OR third tertile vs first tertile = 0.27, 95% CI 0.16-0.47, p < 0.001). Regarding the other nutrients, our findings indicated a non-significant decrease in CRC risk with the high level of intake. CONCLUSIONS Our data suggest that choline and betaine intake influence CRC risk in the studied population.
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Grants
- 2011111153 Osasun Saila, Eusko Jaurlaritzako
- S-PE12UN058 Ekonomiaren Garapen eta Lehiakortasun Saila, Eusko Jaurlaritza
- IT1633-22 Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza
- PRE_2014_1_161 Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza
- PRE_2015_2_0084 Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza
- EP_2016_1_0098 Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza
- PRE_2017_2_0006 Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza
- Universidad del País Vasco
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Affiliation(s)
- Silvia Martín-Fernández-de-Labastida
- Department of Pharmacy and Food Sciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Araba/Álava, Spain
| | - Iker Alegria-Lertxundi
- Department of Pharmacy and Food Sciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Araba/Álava, Spain
| | - Marian M de Pancorbo
- Department of Z. and Cellular Biology A., Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Araba/Álava, Spain
- BIOMICs Research Group, Microfluidics & BIOMICs Cluster, Lascaray Research Center, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Araba/Álava, Spain
- Bioaraba, BA04.03, Vitoria-Gasteiz, Araba/Álava, Spain
| | - Marta Arroyo-Izaga
- Department of Pharmacy and Food Sciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Araba/Álava, Spain.
- BIOMICs Research Group, Microfluidics & BIOMICs Cluster, Lascaray Research Center, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Araba/Álava, Spain.
- Bioaraba, BA04.03, Vitoria-Gasteiz, Araba/Álava, Spain.
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22
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Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
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Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
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23
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D'Alessandro A, Lukens JR, Zimring JC. The role of PIMT in Alzheimer's disease pathogenesis: A novel hypothesis. Alzheimers Dement 2023; 19:5296-5302. [PMID: 37157118 DOI: 10.1002/alz.13115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/11/2023] [Indexed: 05/10/2023]
Abstract
There are multiple theories of Alzheimer's disease pathogenesis. One major theory is that oxidation of amyloid beta (Aβ) promotes plaque deposition that directly contributes to pathology. A competing theory is that hypomethylation of DNA (due to altered one carbon metabolism) results in pathology through altered gene regulation. Herein, we propose a novel hypothesis involving L-isoaspartyl methyltransferase (PIMT) that unifies the Aβ and DNA hypomethylation hypotheses into a single model. Importantly, the proposed model allows bidirectional regulation of Aβ oxidation and DNA hypomethylation. The proposed hypothesis does not exclude simultaneous contributions by other mechanisms (e.g., neurofibrillary tangles). The new hypothesis is formulated to encompass oxidative stress, fibrillation, DNA hypomethylation, and metabolic perturbations in one carbon metabolism (i.e., methionine and folate cycles). In addition, deductive predictions of the hypothesis are presented both to guide empirical testing of the hypothesis and to provide candidate strategies for therapeutic intervention and/or nutritional modification. HIGHLIGHTS: PIMT repairs L-isoaspartyl groups on amyloid beta and decreases fibrillation. SAM is a common methyl donor for PIMT and DNA methyltransferases. Increased PIMT activity competes with DNA methylation and vice versa. The PIMT hypothesis bridges a gap between plaque and DNA methylation hypotheses.
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Affiliation(s)
- Angelo D'Alessandro
- University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado, USA
| | - John R Lukens
- Carter Immunology Center and Center for Brain Immunology and Glia, University of Virginia Departments of Pathology and Neuroscience, Charlottesville, Virginia, USA
| | - James C Zimring
- Carter Immunology Center and Center for Brain Immunology and Glia, University of Virginia Departments of Pathology and Neuroscience, Charlottesville, Virginia, USA
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24
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Mirisola MG. The Nutriepigenome. Genes (Basel) 2023; 14:1997. [PMID: 38002940 PMCID: PMC10671240 DOI: 10.3390/genes14111997] [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: 07/31/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Unlike genetic changes, epigenetics modulates gene expression without stable modification of the genome. Even though all cells, including sperm and egg, have an epigenome pattern, most of these modifications occur during lifetime and interestingly, some of them, are reversible. Lifestyle and especially nutrients as well as diet regimens are presently gaining importance due to their ability to affect the epigenome. On the other hand, since the epigenome profoundly affects gene expression profile it can be speculated that the epigenome could modulate individual response to nutrients. Recent years have thus seen growing interest on nutrients, macronutrients ratio and diet regimens capable to affect the epigenetic pattern. In fact, while genetic alterations are mostly detrimental at the individual level, reshaping the epigenome may be a feasible strategy to positively counteract the detrimental effect of aging. Here, I review nutrient consumption and diet regimens as a possible strategy to counteract aging-driven epigenome derangement.
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Affiliation(s)
- Mario G Mirisola
- STeBiCeF Department, Università di Palermo, Building 16, Viale delle Scienze, 90128 Palermo, Italy
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25
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Huang Y, Hu Q, Wei Z, Chen L, Luo Y, Li X, Li C. Influence of MTHFR polymorphism, alone or in combination with smoking and alcohol consumption, on cancer susceptibility. Open Life Sci 2023; 18:20220680. [PMID: 37772262 PMCID: PMC10523282 DOI: 10.1515/biol-2022-0680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/17/2023] [Accepted: 07/18/2023] [Indexed: 09/30/2023] Open
Abstract
5,10-methylenetetrahydrofolate reductase (MTHFR) mutations play a significant role in various types of cancers, serving as crucial regulators of folate levels in this process. Several studies have examined the effects of smoking and drinking on MTHFR-related cancers, yielding inconsistent results. Therefore, the objective of this study was to evaluate the magnitude of the effects of gene-smoking or gene-drinking interactions on cancer development. We conducted a comprehensive literature search in PubMed, Web of Science, CNKI, and Wan Fang databases up until May 10th, 2022, to identify relevant articles that met our inclusion criteria. The extracted data from these studies were used to calculate the overall odds ratio (OR) and corresponding 95% confidence interval (95% CI) using either a fixed-effect or random-effect model in Stata version 11.2. Stratified analyses were performed based on ethnicity, control group origin, and cancer classification to assess the risk of cancers associated with gene-smoking or gene-drinking interactions. Sensitivity analyses were conducted to investigate potential sources of heterogeneity, and publication bias was assessed using the Begg's test and Egger's test. Additionally, regression analysis was employed to explore the influence of relevant variables on heterogeneity. To evaluate the statistical correlations, analytical methods such as the false-positive report probability and the Bayesian false discovery probability were applied to assess the reliability of the findings. In our meta-analysis, a total of 47 articles were included, comprising 13,701 cases and 21,995 controls for the C677T polymorphism and 5,149 cases and 8,450 controls for the A1298C polymorphism. The results indicated a significant association between C677T polymorphism and cancer risks when combined with smoking (CT + TT vs CC, OR [95% CI] = 1.225 [1.009-1.487], p = 0.041). Stratified analysis further revealed a significant increase in liver cancer risk for individuals with the C677T when combined with smoking (liver cancer: CT + TT vs CC, OR [95% CI] = 1.564 [1.014-2.413], p = 0.043), particularly among Asian smokers (CT + TT vs CC, OR [95% CI] = 1.292 [1.007-1.658], p = 0.044). Regarding the A1298C polymorphism, an elevated risk of cancer was observed in mixed populations alone (CC + AC vs AA, OR [95% CI] = 1.609 [1.087-2.381], p = 0.018), as well as when combined with smoking (CC + AC vs AA, OR [95% CI] = 1.531 [1.127-2.080], p = 0.006). In non-drinkers, C677T polymorphism was found to be associated with esophageal cancer risk (C677T: CT + TT vs CC, OR [95% CI] = 1.544 [1.011-2.359], p = 0.044) and colon cancer risk (CC + AC vs AA, OR [95% CI] = 1.877 [1.166-3.054], p = 0.010), but there was no clear link between this polymorphism and cancer risk among drinkers. The association between the C677T polymorphism and cancer risk among smokers was found to be significant, suggesting that the combination of tobacco and the C677T polymorphism may enhance the carcinogenic process, particularly in liver cancer. However, no similar relationship was observed for the A1298C polymorphism. Interestingly, significantly increased cancer risk was observed in individuals with C677T genetic variants who were nondrinkers, but not among drinkers. These findings highlight the potential role of the C677T polymorphism in modifying cancer risk in specific contexts, such as smoking and alcohol consumption.
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Affiliation(s)
- Yonghui Huang
- Department of Prosthodontics, The Affiliated Stomatology Hospital of Guangxi Medical University, Nanning530021, P. R. China
| | - Qiurui Hu
- Department of Prosthodontics, The Affiliated Stomatology Hospital of Guangxi Medical University, Nanning530021, P. R. China
| | - Zhenxia Wei
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatology Hospital of Guangxi Medical University, Nanning530021, P. R. China
| | - Li Chen
- Department of Prosthodontics, The Affiliated Stomatology Hospital of Guangxi Medical University, Nanning530021, P. R. China
| | - Ying Luo
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Nanning 530021, P. R. China
| | - Xiaojie Li
- Department of Prosthodontics, The Affiliated Stomatology Hospital of Guangxi Medical University, Nanning530021, P. R. China
- Medical Scientific Research Center, College of Stomatology, Guangxi Medical University, Nanning530021, P. R. China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Nanning 530021, P. R. China
| | - Cuiping Li
- Medical Scientific Research Center, College of Stomatology, Guangxi Medical University, Nanning530021, P. R. China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Nanning 530021, P. R. China
- Department of Experiment, The Affiliated Stomatology Hospital of Guangxi Medical University, Nanning530021, P. R. China
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26
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Meng ZY, Fan YC, Zhang CS, Zhang LL, Wu T, Nong MY, Wang T, Chen C, Jiang LH. EXOSC10 is a novel hepatocellular carcinoma prognostic biomarker: a comprehensive bioinformatics analysis and experiment verification. PeerJ 2023; 11:e15860. [PMID: 37701829 PMCID: PMC10494838 DOI: 10.7717/peerj.15860] [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: 01/13/2023] [Accepted: 07/17/2023] [Indexed: 09/14/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a common malignant tumor. There are few studies on EXOSC10 (exosome component 10) in HCC; however, the importance of EXOSC10 for HCC remains unclear. Methods In the study, the prognosis value of EXOSC10 and the immune correlation were explored by bioinformatics. The expression of EXOSC10 was verified by tissue samples from clinical patients and in vitro experiment (liver cancer cell lines HepG2, MHCC97H and Huh-7; normal human liver cell line LO2). Immunohistochemistry (IHC) was used to detect EXOSC10 protein expression in clinical tissue from HCC. Huh-7 cells with siEXOSC10 were constructed using lipofectamine 3000. Cell counting kit 8 (CCK-8) and colony formation were used to test cell proliferation. The wound healing and transwell were used to analyze the cell migration capacity. Mitochondrial membrane potential, Hoechst 33342 dye, and flow cytometer were used to detect the change in cell apoptosis, respectively. Differential expression genes (DEGs) analysis and gene set enrichment analysis (GSEA) were used to investigate the potential mechanism of EXOSC10 and were verified by western blotting. Results EXOSC10 was highly expressed in tissues from patients with HCC and was an independent prognostic factor for overall survival (OS) in HCC. Increased expression of EXOSC10 was significantly related to histological grade, T stage, and pathological stage. Multivariate analysis indicated that the high expression level of EXOSC10 was correlated with poor overall survival (OS) in HCC. GO and GSEA analysis showed enrichment of the cell cycle and p53-related signaling pathway. Immune analysis showed that EXOSC10 expression was a significant positive correlation with immune infiltration in HCC. In vitro experiments, cell proliferation and migration were inhibited by the elimination of EXOSC10. Furthermore, the elimination of EXOSC10 induced cell apoptosis, suppressed PARP, N-cadherin and Bcl-2 protein expression levels, while increasing Bax, p21, p53, p-p53, and E-cadherin protein expression levels. Conclusions EXOSC10 had a predictive value for the prognosis of HCC and may regulate the progression of HCC through the p53-related signaling pathway.
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Affiliation(s)
- Zhi-Yong Meng
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Nanning, China
- First Clinical Medical College, Guangxi University of Traditional Chinese Medicine, Nanning, China
| | - Yu-Chun Fan
- Medical College, Guangxi University, Nanning, China
| | - Chao-Sheng Zhang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Nanning, China
| | - Lin-Li Zhang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Nanning, China
| | - Tong Wu
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Nanning, China
| | - Min-Yu Nong
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Nanning, China
| | - Tian Wang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Nanning, China
| | - Chuang Chen
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Li-He Jiang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Nanning, China
- Medical College, Guangxi University, Nanning, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province,Taizhou, Zhejiang, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province (Zunyi Medical University), Guizhou, China
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Liu D, Aziz NA, Landstra EN, Breteler MMB. The lipidomic correlates of epigenetic aging across the adult lifespan: A population-based study. Aging Cell 2023; 22:e13934. [PMID: 37496173 PMCID: PMC10497837 DOI: 10.1111/acel.13934] [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: 04/03/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
Lipid signaling is involved in longevity regulation, but which specific lipid molecular species affect human biological aging remains largely unknown. We investigated the relation between complex lipids and DNA methylation-based metrics of biological aging among 4181 participants (mean age 55.1 years (range 30.0-95.0)) from the Rhineland Study, an ongoing population-based cohort study in Bonn, Germany. The absolute concentration of 14 lipid classes, covering 964 molecular species and 267 fatty acid composites, was measured by Metabolon Complex Lipid Panel. DNA methylation-based metrics of biological aging (AgeAccelPheno and AgeAccelGrim) were calculated based on published algorithms. Epigenome-wide association analyses (EWAS) of biological aging-associated lipids and pathway analysis were performed to gain biological insights into the mechanisms underlying the effects of lipidomics on biological aging. We found that higher levels of molecular species belonging to neutral lipids, phosphatidylethanolamines, phosphatidylinositols, and dihydroceramides were associated with faster biological aging, whereas higher levels of lysophosphatidylcholine, hexosylceramide, and lactosylceramide species were associated with slower biological aging. Ceramide, phosphatidylcholine, and lysophosphatidylethanolamine species with odd-numbered fatty acid tail lengths were associated with slower biological aging, whereas those with even-numbered chain lengths were associated with faster biological aging. EWAS combined with functional pathway analysis revealed several complex lipids associated with biological aging as important regulators of known longevity and aging-related pathways.
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Affiliation(s)
- Dan Liu
- Population Health SciencesGerman Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - N. Ahmad Aziz
- Population Health SciencesGerman Center for Neurodegenerative Diseases (DZNE)BonnGermany
- Department of Neurology, Faculty of MedicineUniversity of BonnBonnGermany
| | - Elvire Nadieh Landstra
- Population Health SciencesGerman Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Monique M. B. Breteler
- Population Health SciencesGerman Center for Neurodegenerative Diseases (DZNE)BonnGermany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of MedicineUniversity of BonnBonnGermany
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Rossi M, Khalifeh M, Fiori F, Parpinel M, Serraino D, Pelucchi C, Negri E, Giacosa A, Crispo A, Collatuzzo G, Hannun Y, Luberto C, La Vecchia C, Boffetta P. Dietary choline and sphingomyelin choline moiety intake and risk of colorectal cancer: a case-control study. Eur J Clin Nutr 2023; 77:905-910. [PMID: 37479807 DOI: 10.1038/s41430-023-01298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 05/03/2023] [Accepted: 06/05/2023] [Indexed: 07/23/2023]
Abstract
INTRODUCTION Phospholipids are possible favorable agents for colorectal cancer (CRC). Choline has been inversely related to CRC risk but findings are inconsistent. We assessed the effect of dietary sphingomyelin (SM) choline moiety and total choline intake on risk of CRC. METHOD This analysis is based on a multicenter case-control study conducted between 1992 and 1996 in Italy. A total of 6107 subjects were enrolled, including 1225 colon cancer cases, 728 rectal cancer cases and 4154 hospital-based controls. We applied data on the composition of foods in terms of SM choline moiety and choline intake on dietary information collected through a validated food-frequency questionnaire. Odds ratio (OR) for energy-adjusted tertiles of SM choline moiety and choline were estimated through logistic regression models adjusted for sex, age, center, education, alcohol consumption, body mass index, family history of CRC, and physical activity. RESULTS Choline was inversely related to CRC risk (OR for the highest versus the lowest tertile: 0.85; 95% confidence interval [CI]: 0.73-0.99), with a significant trend in risk. The OR for an increment of one standard deviation of energy-adjusted choline intake was 0.93 (95% CI: 0.88-0.98). The association was consistent in colon and rectal cancer and also across colon subsites. SM choline moiety was not associated with CRC risk (OR for the highest versus the lowest tertile: 0.96, 95% CI 0.84-1.11). CONCLUSION This study shows an inverse association between choline intake and CRC but not with SM choline moiety.
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Affiliation(s)
- Marta Rossi
- Department of Clinical Sciences and Community Health, University of Milan, 20133, Milan, Italy
| | - Malak Khalifeh
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Federica Fiori
- Department of Medicine, University of Udine, 33100, Udine, Italy
| | - Maria Parpinel
- Department of Medicine, University of Udine, 33100, Udine, Italy
| | - Diego Serraino
- Unit of Cancer Epidemiology, Centro di Riferimento Oncologico, National Cancer Institute IRCCS, 33108, Aviano, Italy
| | - Claudio Pelucchi
- Department of Clinical Sciences and Community Health, University of Milan, 20133, Milan, Italy
| | - Eva Negri
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Attilio Giacosa
- Department of Gastroenterology and Clinical Nutrition, Policlinico di Monza, 20900, Monza, Italy
| | - Anna Crispo
- Epidemiology and Biostatistics Unit, Istituto Nazionale dei Tumori IRCCS, Fondazione G. Pascale, 80131, Naples, Italy
| | | | - Yusuf Hannun
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Chiara Luberto
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Carlo La Vecchia
- Department of Clinical Sciences and Community Health, University of Milan, 20133, Milan, Italy
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA.
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy.
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Li Q, Cheng Y, Chen W, Wang Y, Dai R, Yang X. Pan-cancer analysis of the PDE4DIP gene with potential prognostic and immunotherapeutic values in multiple cancers including acute myeloid leukemia. Open Med (Wars) 2023; 18:20230782. [PMID: 37663233 PMCID: PMC10473463 DOI: 10.1515/med-2023-0782] [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: 05/03/2023] [Revised: 07/07/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Phosphodiesterase 4D interacting protein (PDE4DIP) interacts with cAMP-specific phosphodiesterase 4D and its abnormal expression promotes the development of hematological malignancies, breast cancer, and pineal cell carcinoma. However, there is currently no systematic pan-cancer analysis of the association between PDE4DIP and various cancers. Thus, this study aimed to elucidate the potential functions of PDE4DIP in various cancers. Based on the multiple public databases and online websites, we conducted comprehensive analyses for PDE4DIP in various cancers, including differential expression, prognosis, genetic variation, DNA methylation, and immunity. We thoroughly analyzed the specific role of PDE4DIP in acute myeloid leukemia (LAML). The results indicated that there were differences in PDE4DIP expression in cancers, and in kidney chromophobe, LAML, pheochromocytoma and paraganglioma, thymoma, and uveal melanoma, PDE4DIP had potential prognostic value. PDE4DIP expression was also correlated with genetic variation, DNA methylation, immune cell infiltration, and immune-related genes in cancers. Functional enrichment analysis showed that PDE4DIP was mainly related to immune-related pathways in cancers, and in LAML, PDE4DIP was mainly related to immunoglobulin complexes, T-cell receptor complexes, and immune response regulatory signaling pathways. Our study systematically revealed for the first time the potential prognostic and immunotherapeutic value of PDE4DIP in various cancers, including LAML.
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Affiliation(s)
- Qi Li
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province – The Affiliated Hospital of Kunming University of Science and Technology, 650032Kunming, Yunnan, China
| | - Yujing Cheng
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province – The Affiliated Hospital of Kunming University of Science and Technology, 650032Kunming, Yunnan, China
| | - Wanlu Chen
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province – The Affiliated Hospital of Kunming University of Science and Technology, 650032Kunming, Yunnan, China
| | - Ying Wang
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province – The Affiliated Hospital of Kunming University of Science and Technology, 650032Kunming, Yunnan, China
| | - Run Dai
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province – The Affiliated Hospital of Kunming University of Science and Technology, 650032Kunming, Yunnan, China
| | - Xin Yang
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province – The Affiliated Hospital of Kunming University of Science and Technology, 650032Kunming, Yunnan, China
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30
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Liu F, Zhou H, Peng Y, Qiao Y, Wang P, Si C, Wang X, Gong J, Chen K, Song F. Plasma One-Carbon Metabolism-Related Micronutrients and the Risk of Breast Cancer: Involvement of DNA Methylation. Nutrients 2023; 15:3621. [PMID: 37630812 PMCID: PMC10458034 DOI: 10.3390/nu15163621] [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: 06/30/2023] [Revised: 08/05/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Findings of epidemiologic studies focusing on the association between one-carbon metabolism-related micronutrients and breast cancer risk, along with the involvement of DNA methylation, have been inconsistent and incomprehensive. We conducted a case-control study in China including 107 paired participants and comprehensively detected 12 plasma one-carbon metabolism-related micronutrients. Genomic DNA methylation was measured using an 850 K chip and differential methylation probes (DMPs) were identified. Multivariate logistic regression was performed to estimate the associations between plasma micronutrients and the odds of breast cancer. The mediation of selected DMPs in micronutrient breast cancer associations was examined using mediation analyses. An inverse association of plasma folate, methionine cycling-related micronutrients (methionine, S-adenosylmethionine, and S-adenosylhomocysteine), and all micronutrients in the choline metabolism and enzymatic factor groups, and a positive association of methionine cycling-related cysteine with breast cancer risk were observed. Nine micronutrients (methionine, cysteine, SAM, folate, choline, betaine, P5P, vitamins B2, and B12) were related to global or probe-specific methylation levels (p < 0.05). The selected DMPs mediated the micronutrient breast cancer associations with an average mediation proportion of 36.43%. This study depicted comprehensive associations between circulating one-carbon metabolism-related micronutrients and breast cancer risk mediated by DNA methylation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Major Diseases in the Population, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China; (F.L.); (H.Z.); (Y.P.); (Y.Q.); (P.W.); (C.S.); (X.W.); (J.G.)
| | - Fangfang Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Major Diseases in the Population, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China; (F.L.); (H.Z.); (Y.P.); (Y.Q.); (P.W.); (C.S.); (X.W.); (J.G.)
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31
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Nohesara S, Abdolmaleky HM, Thiagalingam S. Epigenetic Aberrations in Major Psychiatric Diseases Related to Diet and Gut Microbiome Alterations. Genes (Basel) 2023; 14:1506. [PMID: 37510410 PMCID: PMC10379841 DOI: 10.3390/genes14071506] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Nutrition and metabolism modify epigenetic signatures like histone acetylation and DNA methylation. Histone acetylation and DNA methylation in the central nervous system (CNS) can be altered by bioactive nutrients and gut microbiome via the gut-brain axis, which in turn modulate neuronal activity and behavior. Notably, the gut microbiome, with more than 1000 bacterial species, collectively contains almost three million functional genes whose products interact with millions of human epigenetic marks and 30,000 genes in a dynamic manner. However, genetic makeup shapes gut microbiome composition, food/nutrient metabolism, and epigenetic landscape, as well. Here, we first discuss the effect of changes in the microbial structure and composition in shaping specific epigenetic alterations in the brain and their role in the onset and progression of major mental disorders. Afterward, potential interactions among maternal diet/environmental factors, nutrition, and gastrointestinal microbiome, and their roles in accelerating or delaying the onset of severe mental illnesses via epigenetic changes will be discussed. We also provide an overview of the association between the gut microbiome, oxidative stress, and inflammation through epigenetic mechanisms. Finally, we present some underlying mechanisms involved in mediating the influence of the gut microbiome and probiotics on mental health via epigenetic modifications.
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Affiliation(s)
- Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
| | - Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boson, MA 02215, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA 02218, USA
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32
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Patel P, Selvaraju V, Babu JR, Geetha T. Association of the DNA Methylation of Obesity-Related Genes with the Dietary Nutrient Intake in Children. Nutrients 2023; 15:2840. [PMID: 37447167 DOI: 10.3390/nu15132840] [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: 05/24/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
The occurrence of obesity stems from both genetic and external influences. Despite thorough research and attempts to address it through various means such as dietary changes, physical activity, education, and medications, a lasting solution to this widespread problem remains elusive. Nutrients play a crucial role in various cellular processes, including the regulation of gene expression. One of the mechanisms by which nutrients can affect gene expression is through DNA methylation. This modification can alter the accessibility of DNA to transcription factors and other regulatory proteins, thereby influencing gene expression. Nutrients such as folate and vitamin B12 are involved in the one-carbon metabolism pathway, which provides the methyl groups necessary for DNA methylation. Studies have shown that the inadequate intake of these nutrients can lead to alterations in DNA methylation patterns. For this study, we aim to understand the differences in the association of the dietary intake between normal weight and overweight/obese children and between European American and African American children with the DNA methylation of the three genes NRF1, FTO, and LEPR. The research discovered a significant association between the nutritional intake of 6-10-years-old children, particularly the methyl donors present in their diet, and the methylation of the NRF1, FTO, and LEPR genes. Additionally, the study emphasizes the significance of considering health inequalities, particularly family income and maternal education, when investigating the epigenetic impact of methyl donors in diet and gene methylation.
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Affiliation(s)
- Priyadarshni Patel
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
| | | | - Jeganathan Ramesh Babu
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
| | - Thangiah Geetha
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
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Wu J, Yu X, Zhu H, Chen P, Liu T, Yin R, Qiang Y, Xu L. RelB is a potential molecular biomarker for immunotherapy in human pan-cancer. Front Mol Biosci 2023; 10:1178446. [PMID: 37388242 PMCID: PMC10303125 DOI: 10.3389/fmolb.2023.1178446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction: The nuclear factor kB (NF-κB) pathway emerges as a critical regulator of immune responses and is often dysregulated in human cancers. It consists of a family of transcription factors involved in many biological responses. Activated NF-κB subunits results in the nuclear translocation and activation of transcription, and the NF-κB pathway is known to influence the transcription of many genes. Noncanonical NF-κB and its components have been shown to have effects, usually protumorigenic, in many different cancer types. Besides, NF-κB signaling had diverse and complicated roles in cancer with studies that NF-κB could both contribute to tumor promotion and suppression of oncogenesis relying on the cellular context. RelB, a member of noncanonical NF-κB was abnormally regulated in most cancer types, however the molecular features and clinical signature of RelB expression, as well as its role in cancer immunity in human pan-cancer remains to be elucidated. Methods: We used the open databases to explore RelB expression, clinical features and the association with tumor-infiltration cells in human pan-cancer. In this study, we investigated the aberration expression and prognostic significance of RelB, and the correlation with clinicopathological characters and immune cells infiltration in various cancers. The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were used to analyze the mRNA expression level in different cancer types. Kaplan-Meier analysis and Cox regression were used to explore the prognostic significance of RelB in human pan-cancer. Then we took advantage of the TCGA database to analyze the relationship between RelB expression and DNA methylation, the infiltration of immune cells, immune checkpoint genes, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MSS). Results: Higher expression of RelB was significantly detected in human cancer tissues and a high level of RelB expression was significantly linked with a worse outcome in LGG, KIPAN, ACC, UVM, LUAD,THYM, GBM, LIHC and TGCT but associated with a favorable overall survival (OS) in SARC, SKCM and BRCA. According to the Human Protein Altas database, RelB was considered as an independent factor in breast cancer and renal cancer prognosis. GSEA results revealed that RelB was involved in many oncogenesisrelated processes and immunity-related pathways. RelB was significantly correlated with DNA methylation in 13 types of cancer. Meanwhile, RelB expression was associated with TMB in 5 types of cancer and MSI in 8 types of cancer. In the final, we analyzed the relationship between RelB expression and immune-infiltration cells in human pan-cancer, which suggested RelB could be a promising therapeutic target for cancer immunotherapy. Discussion: Our study further provided insights into a deeper understanding of RelB as a prognostic biomarker.
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Affiliation(s)
- Jintao Wu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Xinyu Yu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Hongyu Zhu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Peng Chen
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Tongyan Liu
- Department of Science and Technology, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Department of Science and Technology, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Biobank of Lung Cancer, Jiangsu Biobank of Clinical Resources, Nanjing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yan Qiang
- Department of Intensive Care Unit, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Lin Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
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Strandvik B, Qureshi AR, Painer J, Backman-Johansson C, Engvall M, Fröbert O, Kindberg J, Stenvinkel P, Giroud S. Elevated plasma phospholipid n-3 docosapentaenoic acid concentrations during hibernation. PLoS One 2023; 18:e0285782. [PMID: 37294822 PMCID: PMC10256182 DOI: 10.1371/journal.pone.0285782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/28/2023] [Indexed: 06/11/2023] Open
Abstract
Factors for initiating hibernation are unknown, but the condition shares some metabolic similarities with consciousness/sleep, which has been associated with n-3 fatty acids in humans. We investigated plasma phospholipid fatty acid profiles during hibernation and summer in free-ranging brown bears (Ursus arctos) and in captive garden dormice (Eliomys quercinus) contrasting in their hibernation patterns. The dormice received three different dietary fatty acid concentrations of linoleic acid (LA) (19%, 36% and 53%), with correspondingly decreased alpha-linolenic acid (ALA) (32%, 17% and 1.4%). Saturated and monounsaturated fatty acids showed small differences between summer and hibernation in both species. The dormice diet influenced n-6 fatty acids and eicosapentaenoic acid (EPA) concentrations in plasma phospholipids. Consistent differences between summer and hibernation in bears and dormice were decreased ALA and EPA and marked increase of n-3 docosapentaenoic acid and a minor increase of docosahexaenoic acid in parallel with several hundred percent increase of the activity index of elongase ELOVL2 transforming C20-22 fatty acids. The highest LA supply was unexpectantly associated with the highest transformation of the n-3 fatty acids. Similar fatty acid patterns in two contrasting hibernating species indicates a link to the hibernation phenotype and requires further studies in relation to consciousness and metabolism.
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Affiliation(s)
- Birgitta Strandvik
- Department of Biosciences and Nutrition, Karolinska Institutet NEO, Stockholm, Sweden
| | | | - Johanna Painer
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, Austria
| | | | - Martin Engvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ole Fröbert
- Department of Cardiology, Faculty of Health, Örebro University, Örebro, Sweden
- Department of Clinical Medicine, Aarhus University Health, Aarhus, Denmark
- Department of Clinical Pharmacology, Aarhus University Hospital, Aarhus, Denmark
- StenoDiabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jonas Kindberg
- Department of Wildlife, Fish and Environmental Studies, University of Agricultural Sciences, Umeå, Sweden
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Peter Stenvinkel
- Division of Renal Medicine, CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - Sylvain Giroud
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, Austria
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35
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Han X, Fang F, Cui W, Liu Y, Liu Y. Effect of Ethanol-Induced Methyl Donors Consumption on the State of Hypomethylation in Cervical Cancer. Int J Mol Sci 2023; 24:ijms24097729. [PMID: 37175434 PMCID: PMC10178338 DOI: 10.3390/ijms24097729] [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: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Cervical cancer causes malignant tumors in females and threatens the physical and mental health of women. Current research shows that persistent infection of high-risk HPV is the main cause of cervical cancer. However, not all cervical cancer is caused by HPV infection, which may also be related to other factors, such as nutritional status and lifestyle. This study focuses on the effect of alcohol consumption on the methylation status of cervical cancer from the perspective of methyl donors. We established a mouse tumor-bearing model with cervical cancer SiHa cells, and at the same time, we cultured SiHa cells in vitro. Different concentrations of ethanol were administered to the model mice and SiHa cells. Then, we detected the levels of the methyl-donor folate and methionine and their metabolite homocysteine levels in mice serum, tumor tissues, and SiHa cells. Furthermore, we determined the expression of the members of the DNA methyltransferase family (DNMT1, DNMT3a, and DNMT3b) in tumor tissue by immunohistochemistry. qRT-PCR and Western blotting analysis were used to detect the mRNA and protein levels of members of the DNA methyltransferase family in cervical cancer SiHa cells. Our results show that the levels of the methyl donor (folate and methionine) decreased with the increase of ethanol concentration (p < 0.05), and the homocysteine level increased significantly (p < 0.05). In SiHa cells, the mRNA and protein levels of the DNMT family members and their receptors were significantly higher than those in the control group (p < 0.05). Collectively, these results suggest that ethanol could influence DNMT expression by inducing methyl donor consumption, thereby causing cervical cancer cells to exhibit genome-wide hypomethylation.
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Affiliation(s)
- Xiao Han
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Fang Fang
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Weiwei Cui
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Ya Liu
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Yuxin Liu
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
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Hellbach F, Sinke L, Costeira R, Baumeister SE, Beekman M, Louca P, Leeming ER, Mompeo O, Berry S, Wilson R, Wawro N, Freuer D, Hauner H, Peters A, Winkelmann J, Koenig W, Meisinger C, Waldenberger M, Heijmans BT, Slagboom PE, Bell JT, Linseisen J. Pooled analysis of epigenome-wide association studies of food consumption in KORA, TwinsUK and LLS. Eur J Nutr 2023; 62:1357-1375. [PMID: 36571600 PMCID: PMC10030421 DOI: 10.1007/s00394-022-03074-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/12/2022] [Indexed: 12/27/2022]
Abstract
PURPOSE Examining epigenetic patterns is a crucial step in identifying molecular changes of disease pathophysiology, with DNA methylation as the most accessible epigenetic measure. Diet is suggested to affect metabolism and health via epigenetic modifications. Thus, our aim was to explore the association between food consumption and DNA methylation. METHODS Epigenome-wide association studies were conducted in three cohorts: KORA FF4, TwinsUK, and Leiden Longevity Study, and 37 dietary exposures were evaluated. Food group definition was harmonized across the three cohorts. DNA methylation was measured using Infinium MethylationEPIC BeadChip in KORA and Infinium HumanMethylation450 BeadChip in the Leiden study and the TwinsUK study. Overall, data from 2293 middle-aged men and women were included. A fixed-effects meta-analysis pooled study-specific estimates. The significance threshold was set at 0.05 for false-discovery rate-adjusted p values per food group. RESULTS We identified significant associations between the methylation level of CpG sites and the consumption of onions and garlic (2), nuts and seeds (18), milk (1), cream (11), plant oils (4), butter (13), and alcoholic beverages (27). The signals targeted genes of metabolic health relevance, for example, GLI1, RPTOR, and DIO1, among others. CONCLUSION This EWAS is unique with its focus on food groups that are part of a Western diet. Significant findings were mostly related to food groups with a high-fat content.
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Affiliation(s)
- Fabian Hellbach
- Institute for Medical Information Processing, Biometry, and Epidemiology, Medical Faculty, Ludwig-Maximilian University Munich, Marchioninistr. 15, 81377, Munich, Germany.
- Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Stenglinstraße 2, 86156, Augsburg, Germany.
| | - Lucy Sinke
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, England, UK
| | - Sebastian-Edgar Baumeister
- Institute of Health Services Research in Dentistry, Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Panayiotis Louca
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, England, UK
| | - Emily R Leeming
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, England, UK
| | - Olatz Mompeo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, England, UK
| | - Sarah Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Rory Wilson
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Nina Wawro
- Institute for Medical Information Processing, Biometry, and Epidemiology, Medical Faculty, Ludwig-Maximilian University Munich, Marchioninistr. 15, 81377, Munich, Germany
- Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Stenglinstraße 2, 86156, Augsburg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Dennis Freuer
- Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Stenglinstraße 2, 86156, Augsburg, Germany
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Georg-Brauchle-Ring 62, 80992, Munich, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD E.V.), Ingolstädter Landstr. 1, 85764, Munich-Neuherberg, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (HmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Wolfgang Koenig
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Pettenkoferstr. 8A & 9, 80336, Munich, Germany
- German Heart Centre Munich, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Helmholtzstr. 22, 89081, Ulm, Germany
| | - Christa Meisinger
- Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Stenglinstraße 2, 86156, Augsburg, Germany
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD E.V.), Ingolstädter Landstr. 1, 85764, Munich-Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Pettenkoferstr. 8A & 9, 80336, Munich, Germany
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, England, UK
| | - Jakob Linseisen
- Institute for Medical Information Processing, Biometry, and Epidemiology, Medical Faculty, Ludwig-Maximilian University Munich, Marchioninistr. 15, 81377, Munich, Germany
- Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Stenglinstraße 2, 86156, Augsburg, Germany
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Heredia-Mendez AJ, Sánchez-Sánchez G, López-Camarillo C. Reprogramming of the Genome-Wide DNA Methylation Landscape in Three-Dimensional Cancer Cell Cultures. Cancers (Basel) 2023; 15:cancers15071991. [PMID: 37046652 PMCID: PMC10093594 DOI: 10.3390/cancers15071991] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 03/19/2023] [Indexed: 03/29/2023] Open
Abstract
During the last century, 2D cell cultures have been the tool most widely used to study cancer biology, drug discovery, genomics, and the regulation of gene expression at genetic/epigenetic levels. However, this experimental approach has limitations in faithfully recreating the microenvironment and cellular processes occurring in tumors. For these reasons, 3D cell cultures have recently been implemented to optimize the conditions that better recreate the biological and molecular features of tumors, including cell–cell and cell–extracellular matrix (ECM) interactions, growth kinetics, metabolic activities, and the development of gradients in the cellular microenvironment affecting the availability of oxygen and nutrients. In this sense, tumor cells receive stimuli from the local environment, resulting in significant changes in their signaling pathways, gene expression, and transcriptional and epigenetic patterns. In this review, we discuss how different types of 3D cell culture models can be applied to characterize the epigenetic footprints of cancer cell lines, emphasizing that DNA methylation patterns play an essential role in the emergence and development of cancer. However, how 3D cancer cell cultures remodel the epigenetic programs is poorly understood, with very few studies in this emerging topic. Here, we have summarized the studies on the reprogramming of the epigenetic landscape of DNA methylation during tumorigenesis and discuss how it may be affected by microenvironmental factors, specifically in 3D cell cultures.
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Salas-Perez F, Assmann TS, Ramos-Lopez O, Martínez JA, Riezu-Boj JI, Milagro FI. Crosstalk between Gut Microbiota and Epigenetic Markers in Obesity Development: Relationship between Ruminococcus, BMI, and MACROD2/ SEL1L2 Methylation. Nutrients 2023; 15:nu15071550. [PMID: 37049393 PMCID: PMC10097304 DOI: 10.3390/nu15071550] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Changes in gut microbiota composition and in epigenetic mechanisms have been proposed to play important roles in energy homeostasis, and the onset and development of obesity. However, the crosstalk between epigenetic markers and the gut microbiome in obesity remains unclear. The main objective of this study was to establish a link between the gut microbiota and DNA methylation patterns in subjects with obesity by identifying differentially methylated DNA regions (DMRs) that could be potentially regulated by the gut microbiota. DNA methylation and bacterial DNA sequencing analysis were performed on 342 subjects with a BMI between 18 and 40 kg/m2. DNA methylation analyses identified a total of 2648 DMRs associated with BMI, while ten bacterial genera were associated with BMI. Interestingly, only the abundance of Ruminococcus was associated with one BMI-related DMR, which is located between the MACROD2/SEL1L2 genes. The Ruminococcus abundance negatively correlated with BMI, while the hypermethylated DMR was associated with reduced MACROD2 protein levels in serum. Additionally, the mediation test showed that 19% of the effect of Ruminococcus abundance on BMI is mediated by the methylation of the MACROD2/SEL1L2 DMR. These findings support the hypothesis that a crosstalk between gut microbiota and epigenetic markers may be contributing to obesity development.
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Affiliation(s)
| | - Taís Silveira Assmann
- Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Federal University of do Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana 22390, Mexico
| | - J Alfredo Martínez
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Department of Nutrition, Food Science and Physiology, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBERobn), Carlos III Health Institute, 28029 Madrid, Spain
| | - Jose Ignacio Riezu-Boj
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Fermín I Milagro
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Department of Nutrition, Food Science and Physiology, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBERobn), Carlos III Health Institute, 28029 Madrid, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
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Beyond Antioxidant Activity: Redox Properties of Catechins May Affect Changes in the DNA Methylation Profile—The Example of SRXN1 Gene. Antioxidants (Basel) 2023; 12:antiox12030754. [PMID: 36979004 PMCID: PMC10045509 DOI: 10.3390/antiox12030754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
The role of catechins in the epigenetic regulation of gene expression has been widely studied; however, if and how this phenomenon relates to the redox properties of these polyphenols remains unknown. Our earlier study demonstrated that exposure of the human colon adenocarcinoma HT29 cell line to these antioxidants affects the expression of redox-related genes. In particular, treatment with (−)-epigallocatechin (EGC) downregulated transcription of gene encoding sulfiredoxin-1 (SRXN1), the peroxidase involved in the protection of cells against hydrogen peroxide-induced oxidative stress. The aim of this study was to investigate whether the observed SRXN1 downregulation was accompanied by changes in the DNA methylation level of its promoter and, if so, whether it was correlated with the redox properties of catechins. The impact on DNA methylation profile in HT29 cells treated with different concentrations of five catechins, varying in chemical structures and standard reduction potentials as well as susceptibility to oxidation, was monitored by a methylation-sensitive high-resolution melting technique employing the SRXN1 promoter region as a model target. We demonstrated that catechins, indeed, are able to modulate DNA methylation of the SRXN1 gene in a redox-related manner. The nonlinear method in the statistical analysis made it possible to fish out two parameters (charge transfer in oxidation process Qox and time of electron transfer t), whose strong interactions correlated with observed modulation of DNA methylation by catechins. Based on these findings, we present a proof-of-concept that DNA methylation, which limits SRXN1 expression and thus restricts the multidirectional antioxidant action of SRXN1, may represent a mechanism protecting cells against reductive stress caused by particularly fast-reacting reductants such as EGC and (−)-epicatechin gallate (ECG) in our study.
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Huang CY, Chen WJ, Lee HL, Lin YC, Huang YL, Shiue HS, Pu YS, Hsueh YM. Possible Combined Effects of Plasma Folate Levels, Global DNA Methylation, and Blood Cadmium Concentrations on Renal Cell Carcinoma. Nutrients 2023; 15:nu15040937. [PMID: 36839294 PMCID: PMC9959822 DOI: 10.3390/nu15040937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Epigenetic effects of environmental pollutants may be related to carcinogenesis. This study aimed to explore the association between the global DNA methylation marker: 5-methyl-2-deoxycytidine (5mdC) and renal cell carcinoma (RCC), and further investigated whether plasma folate and vitamin B12 levels and 5mdC modified the association between blood cadmium concentrations and RCC. We recruited 174 RCC patients and 673 non-RCC controls. Blood cadmium concentrations, plasma folate and vitamin B12 levels were measured. The amount of 5mdC in the DNA sample was expressed as percentages of the total cytosine content. An increase of 5mdC (%) and plasma folate and vitamin B12 levels were associated with decreasing odds ratio (OR) of RCC. Although plasma folate levels were not directly associated with 5mdC (%), a combined effect was observed with the odds of low plasma folate levels and low 5mdC (%) were greater among RCC patients compared to controls (OR (95% confidence interval, CI) = 11.86 (5.27-26.65)). Additionally, we observed that the odds of low plasma folate and high blood cadmium levels were greater among RCC patients than in controls (OR (95% CI): 8.15 (1.39-7.13)). This study provides suggestive evidence that plasma folate levels may modify the associations between 5mdC (%) or blood cadmium concentrations and RCC.
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Affiliation(s)
- Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, College of Medicine National Taiwan University, Taipei City 110, Taiwan
| | - Wei-Jen Chen
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hui-Ling Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Ying-Chin Lin
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City 110, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 110, Taiwan
- Department of Occupational Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City 110, Taiwan
| | - Ya-Li Huang
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 110, Taiwan
| | - Horng-Sheng Shiue
- Department of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan
| | - Yeong-Shiau Pu
- Department of Urology, National Taiwan University Hospital, College of Medicine National Taiwan University, Taipei City 110, Taiwan
| | - Yu-Mei Hsueh
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City 110, Taiwan
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 110, Taiwan
- Correspondence: ; Tel.: +886-2736-1661 (ext. 6513)
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Restoring Epigenetic Reprogramming with Diet and Exercise to Improve Health-Related Metabolic Diseases. Biomolecules 2023; 13:biom13020318. [PMID: 36830687 PMCID: PMC9953584 DOI: 10.3390/biom13020318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Epigenetic reprogramming predicts the long-term functional health effects of health-related metabolic disease. This epigenetic reprogramming is activated by exogenous or endogenous insults, leading to altered healthy and different disease states. The epigenetic and environmental changes involve a roadmap of epigenetic networking, such as dietary components and exercise on epigenetic imprinting and restoring epigenome patterns laid down during embryonic development, which are paramount to establishing youthful cell type and health. Nutrition and exercise are among the most well-known environmental epigenetic factors influencing the proper developmental and functional lifestyle, with potential beneficial or detrimental effects on health status. The diet and exercise strategies applied from conception could represent an innovative epigenetic target for preventing and treating human diseases. Here, we describe the potential role of diet and exercise as therapeutic epigenetic strategies for health and diseases, highlighting putative future perspectives in this field.
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Methyl Donor Micronutrients: A Potential Dietary Epigenetic Target in Systemic Lupus Erythematosus Patients. Int J Mol Sci 2023; 24:ijms24043171. [PMID: 36834583 PMCID: PMC9961281 DOI: 10.3390/ijms24043171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by an aberrant immune response and persistent inflammation. Its pathogenesis remains unknown; however, a complex interaction between environmental, genetic, and epigenetic factors has been suggested to cause disease onset. Several studies have demonstrated that epigenetic alterations, such as DNA hypomethylation, miRNA overexpression, and altered histone acetylation, may contribute to SLE onset and the disease's clinical manifestations. Epigenetic changes, especially methylation patterns, are modifiable and susceptible to environmental factors such as diet. It is well known that methyl donor nutrients, such as folate, methionine, choline, and some B vitamins, play a relevant role in DNA methylation by participating as methyl donors or coenzymes in one-carbon metabolism. Based on this knowledge, this critical literature review aimed to integrate the evidence in animal models and humans regarding the role of nutrients in epigenetic homeostasis and their impact on immune system regulation to suggest a potential epigenetic diet that could serve as adjuvant therapy in SLE.
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Long-term variability in physiological measures in relation to mortality and epigenetic aging: prospective studies in the USA and China. BMC Med 2023; 21:20. [PMID: 36647101 PMCID: PMC9843964 DOI: 10.1186/s12916-022-02674-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/21/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Visit-to-visit body weight variability (BWV), pulse rate variability (PRV), and blood pressure variability (BPV) have been respectively linked to multiple health outcomes. The associations of the combination of long-term variability in physiological measures with mortality and epigenetic age acceleration (EAA) remain largely unknown. METHODS We constructed a composite score of physiological variability (0-3) of large variability in BWV, PRV, and BPV (the top tertiles) in 2006/2008-2014/2016 in the Health and Retirement Study (HRS) and 2011-2015 in the China Health and Retirement Longitudinal Study (CHARLS). All-cause mortality was documented through 2018. EAA was calculated using thirteen DNA methylation-based epigenetic clocks among 1047 participants in a substudy of the HRS. We assessed the relation of the composite score to the risk of mortality among 6566 participants in the HRS and 6906 participants in the CHARLS by Cox proportional models and then investigated its association with EAA using linear regression models. RESULTS A higher score of variability was associated with higher mortality risk in both cohorts (pooled hazard ratio [HR] per one-point increment, 1.27; 95% confidence interval [CI], 1.18, 1.39; P-heterogeneity = 0.344), after adjustment for multiple confounders and baseline physiological measures. Specifically, each SD increment in BWV, PRV, and BPV was related to 21% (95% CI: 15%, 28%), 6% (0%, 13%), and 12% (4%, 19%) higher hazard of mortality, respectively. The composite score was significantly related to EAA in second-generation clocks trained on health outcomes (e.g., standardized coefficient = 0.126 in the Levine clock, 95% CI: 0.055, 0.196) but not in most first-generation clocks trained on chronological age. CONCLUSIONS Larger variability in physiological measures was associated with a higher risk of mortality and faster EAA.
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Chen X, Duan X, Chong Q, Li C, Xiao H, Chen S. Genome-Wide DNA Methylation Differences between Bos indicus and Bos taurus. Animals (Basel) 2023; 13:ani13020203. [PMID: 36670743 PMCID: PMC9854497 DOI: 10.3390/ani13020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Disease risk is a persistent problem in domestic cattle farming, while economic traits are the main concern. This study aimed to reveal the epigenetic basis for differences between zebu (Bos indicus) and taurine cattle (Bos taurus) in disease, disease resistance, and economic traits, and provide a theoretical basis for the genetic improvement of domestic cattle. In this study, whole genome bisulfite sequencing (WGBS) was used to analyze the whole-genome methylation of spleen and liver samples from Yunnan zebu and Holstein cattle. In the genome-wide methylation pattern analysis, it was found that the methylation pattern of all samples was dominated by the CG type, which accounted for >94.9%. The DNA methylation levels of different functional regions and transcriptional elements in the CG background varied widely. However, the methylation levels of different samples in the same functional regions or transcriptional elements did not differ significantly. In addition, we identified a large number of differentially methylation region (DMR) in both the spleen and liver groups, of which 4713 and 4663 were annotated to functional elements, and most of them were annotated to the intronic and exonic regions of genes. GO and KEGG functional analysis of the same differentially methylation region (DMG) in the spleen and liver groups revealed that significantly enriched pathways were involved in neurological, disease, and growth functions. As a result of the results of DMR localization, we screened six genes (DNM3, INPP4B, PLD, PCYT1B, KCNN2, and SLIT3) that were tissue-specific candidates for economic traits, disease, and disease resistance in Yunnan zebu. In this study, DNA methylation was used to construct links between genotypes and phenotypes in domestic cattle, providing useful information for further screening of epigenetic molecular markers in zebu and taurine cattle.
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Affiliation(s)
- Xiaona Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Xinyu Duan
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Qingqing Chong
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Heng Xiao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Correspondence: ; Tel.: +86-186-8712-2260
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Ghemrawi M, Tejero NF, Duncan G, McCord B. Pyrosequencing: Current forensic methodology and future applications-a review. Electrophoresis 2023; 44:298-312. [PMID: 36168852 DOI: 10.1002/elps.202200177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Nicole Fernandez Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - George Duncan
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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Cell-free DNA in maternal blood and artificial intelligence: accurate prenatal detection of fetal congenital heart defects. Am J Obstet Gynecol 2023; 228:76.e1-76.e10. [PMID: 35948071 DOI: 10.1016/j.ajog.2022.07.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND DNA cytosine nucleotide methylation (epigenomics and epigenetics) is an important mechanism for controlling gene expression in cardiac development. Combined artificial intelligence and whole-genome epigenomic analysis of circulating cell-free DNA in maternal blood has the potential for the detection of fetal congenital heart defects. OBJECTIVE This study aimed to use genome-wide DNA cytosine methylation and artificial intelligence analyses of circulating cell-free DNA for the minimally invasive detection of fetal congenital heart defects. STUDY DESIGN In this prospective study, whole-genome cytosine nucleotide methylation analysis was performed on circulating cell-free DNA using the Illumina Infinium MethylationEPIC BeadChip array. Multiple artificial intelligence approaches were evaluated for the detection of congenital hearts. The Ingenuity Pathway Analysis program was used to identify gene pathways that were epigenetically altered and important in congenital heart defect pathogenesis to further elucidate the pathogenesis of isolated congenital heart defects. RESULTS There were 12 cases of isolated nonsyndromic congenital heart defects and 26 matched controls. A total of 5918 cytosine nucleotides involving 4976 genes had significantly altered methylation, that is, a P value of <.05 along with ≥5% whole-genome cytosine nucleotide methylation difference, in congenital heart defect cases vs controls. Artificial intelligence analysis of the methylation data achieved excellent congenital heart defect predictive accuracy (areas under the receiver operating characteristic curve, ≥0.92). For example, an artificial intelligence model using a combination of 5 whole-genome cytosine nucleotide markers achieved an area under the receiver operating characteristic curve of 0.97 (95% confidence interval, 0.87-1.0) with 98% sensitivity and 94% specificity. We found epigenetic changes in genes and gene pathways involved in the following important cardiac developmental processes: "cardiovascular system development and function," "cardiac hypertrophy," "congenital heart anomaly," and "cardiovascular disease." This lends biologic plausibility to our findings. CONCLUSION This study reported the feasibility of minimally invasive detection of fetal congenital heart defect using artificial intelligence and DNA methylation analysis of circulating cell-free DNA for the prediction of fetal congenital heart defect. Furthermore, the findings supported an important role of epigenetic changes in congenital heart defect development.
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Methylenetetrahydrofolate reductase (MTHFR) 677C>T polymorphisms in breast cancer: A Filipino preliminary case-control study. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Shen JS, Balaji U, Shigeyasu K, Okugawa Y, Jabbarzadeh-Tabrizi S, Day TS, Arning E, Marshall J, Cheng SH, Gu J, Schiffmann R, Bottiglieri T, Goel A. Dysregulated DNA methylation in the pathogenesis of Fabry disease. Mol Genet Metab Rep 2022; 33:100919. [PMID: 36186841 PMCID: PMC9519376 DOI: 10.1016/j.ymgmr.2022.100919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2022] Open
Abstract
Fabry disease is an X-linked lysosomal storage disorder caused by a deficiency of α-galactosidase A and subsequent accumulation of glycosphingolipids with terminal α-D-galactosyl residues. The molecular process through which this abnormal metabolism of glycosphingolipids causes multisystem dysfunction in Fabry disease is not fully understood. We sought to determine whether dysregulated DNA methylation plays a role in the development of this disease. In the present study, using isogenic cellular models derived from Fabry patient endothelial cells, we tested whether manipulation of α-galactosidase A activity and glycosphingolipid metabolism affects DNA methylation. Bisulfite pyrosequencing revealed that changes in α-galactosidase A activity were associated with significantly altered DNA methylation in the androgen receptor promoter, and this effect was highly CpG loci-specific. Methylation array studies showed that α-galactosidase A activity and glycosphingolipid levels were associated with differential methylation of numerous CpG sites throughout the genome. We identified 15 signaling pathways that may be susceptible to methylation alterations in Fabry disease. By incorporating RNA sequencing data, we identified 21 genes that have both differential mRNA expression and methylation. Upregulated expression of collagen type IV alpha 1 and alpha 2 genes correlated with decreased methylation of these two genes. Methionine levels were elevated in Fabry patient cells and Fabry mouse tissues, suggesting that a perturbed methionine cycle contributes to the observed dysregulated methylation patterns. In conclusion, this study provides evidence that α-galactosidase A deficiency and glycosphingolipid storage may affect DNA methylation homeostasis and highlights the importance of epigenetics in the pathogenesis of Fabry disease and, possibly, of other lysosomal storage disorders.
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Affiliation(s)
- Jin-Song Shen
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, 3434 Live Oak Street, Dallas, TX 75024, United States of America
- Corresponding author at: 4D Molecular Therapeutics, 5858 Horton St., Suite 455, Emeryville, CA 94608, United States of America.
| | - Uthra Balaji
- Baylor Scott & White Research Institute, Biostatistics, Dallas, TX, United States of America
| | - Kunitoshi Shigeyasu
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Dallas, TX, United States of America
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Dallas, TX, United States of America
| | - Siamak Jabbarzadeh-Tabrizi
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, 3434 Live Oak Street, Dallas, TX 75024, United States of America
| | - Taniqua S. Day
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, 3434 Live Oak Street, Dallas, TX 75024, United States of America
| | - Erland Arning
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, 3434 Live Oak Street, Dallas, TX 75024, United States of America
| | - John Marshall
- Sanofi Genzyme, 49 New York Avenue, Framingham, MA 01701, United States of America
| | - Seng H. Cheng
- Sanofi Genzyme, 49 New York Avenue, Framingham, MA 01701, United States of America
| | - Jinghua Gu
- Baylor Scott & White Research Institute, Biostatistics, Dallas, TX, United States of America
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, 3434 Live Oak Street, Dallas, TX 75024, United States of America
| | - Teodoro Bottiglieri
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, 3434 Live Oak Street, Dallas, TX 75024, United States of America
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Dallas, TX, United States of America
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Mukherjee AG, Wanjari UR, Gopalakrishnan AV, Bradu P, Sukumar A, Patil M, Renu K, Dey A, Vellingiri B, George A, Ganesan R. Implications of cancer stem cells in diabetes and pancreatic cancer. Life Sci 2022; 312:121211. [PMID: 36414089 DOI: 10.1016/j.lfs.2022.121211] [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: 08/23/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
This review provides a detailed study of pancreatic cancer (PC) and the implication of different types of cancers concerning diabetes. The combination of anti-diabetic drugs with other anti-cancer drugs and phytochemicals can help prevent and treat this disease. PC cancer stem cells (CSCs) and how they migrate and develop into malignant tumors are discussed. A detailed explanation of the different mechanisms of diabetes development, which can enhance the pancreatic CSCs' proliferation by increasing the IGF factor levels, epigenetic modifications, DNA damage, and the influence of lifestyle factors like obesity, and inflammation, has been discussed. It also explains how cancer due to diabetes is associated with high mortality rates. One of the well-known diabetic drugs, metformin, can be combined with other anti-cancer drugs and prevent the development of PC and has been taken as one of the prime focus in this review. Overall, this paper provides insight into the relationship between diabetes and PC and the methods that can be employed to diagnose this disease at an earlier stage successfully.
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Affiliation(s)
- Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
| | - Pragya Bradu
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Aarthi Sukumar
- Department of Integrative Biology, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Megha Patil
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Kaviyarasi Renu
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, Tamil Nadu, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, 700073, India
| | - Balachandar Vellingiri
- Stem cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab (CUPB), Bathinda - 151401, Punjab, India
| | - Alex George
- Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, 680005, Kerala, India
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, 24252, Republic of Korea
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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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