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Effects of Dietary Interventions on DNA Methylation during Lifecycle

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A special issue of Nutrients (ISSN 2072-6643). This special issue belongs to the section "Nutrigenetics and Nutrigenomics".

Deadline for manuscript submissions: closed (20 December 2021) | Viewed by 28567

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Special Issue Editors

Prof. Dr. Dina Bellizzi

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Guest Editor

Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
Interests: microbiota; microbiome; epigenetics; epigenetic biomarkers; DNA methylation modifications; mitochondrial DNA methylation; aging; nutrition; multi-drug resistance
Special Issues, Collections and Topics in MDPI journals

Dr. Patrizia D'Aquila

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Dear Colleagues,

Epigenetic modifications have emerged as newsworthy features given their peculiar plasticity to undergo more or less consistent changes during lifecycle in response to a wide range of environmental changes, including lifestyle and dietary habits (nutrients, foods, and dietary patterns). In the last few decades alone, in fact, a wide variety of studies has reported the epigenetic effects of diet on phenotype, susceptibility to diseases, and life expectancy. In particular, considering their function as substrates or cofactors for epigenetic enzymes, nutrients and their metabolites have been recognized as responsible for global rearrangements of DNA methylation profiles and for regulating life extension. Furthermore, a fetal epigenetic adaptation, eliciting long-lasting effects in adult life, has been demonstrated in response to maternal and paternal nutritional status at both ends of the spectrum, under- and over-nutrition and micro- and macro-nutrient imbalance.

We would like to propose this Special Issue including original research articles, reviews, and comments to provide a comprehensive overview of recent advances in the impact of diet on DNA methylation pattern during lifecycle and to move the nutritional epigenetics field forward.

Disentangling the epigenetic signature triggered by food components appears particularly attractive because it might shift the clinical approaches for population-based strategies toward easy-to-use personalized nutritional interventions in both health and disease.

Prof. Dr. Dina Bellizzi
Dr. Patrizia D'Aquila
Guest Editors

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Keywords

Nutrition
DNA methylation
Diet
Epigenetic modifications

Published Papers (6 papers)

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Research

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13 pages, 1262 KiB

Open AccessArticle

Impact of Nutrition on Age-Related Epigenetic RNA Modifications in Rats

by Patrizia D’Aquila, Francesco De Rango, Ersilia Paparazzo, Maurizio Mandalà, Dina Bellizzi and Giuseppe Passarino

Nutrients 2022, 14(6), 1232; https://0-doi-org.brum.beds.ac.uk/10.3390/nu14061232 - 15 Mar 2022

Cited by 5 | Viewed by 2326

Abstract

Nutrition plastically modulates the epigenetic landscape in various tissues of an organism during life via epigenetic changes. In the present study, to clarify whether this modulation involves RNA methylation, we evaluated global RNA methylation profiles and the expression of writer, reader, and eraser genes, encoding for enzymes involved in the RNA methylation. The study was carried out in the heart, liver, and kidney samples from rats of different ages in response to a low-calorie diet. We found that, although each tissue showed peculiar RNA methylation levels, a general increase in these levels was observed throughout the lifespan as well as in response to the six-month diet. Similarly, a prominent remodeling of the expression of writer, reader, and eraser genes emerged. Our data provide a comprehensive overview of the role exerted by diet on the tissue-specific epigenetic plasticity of RNA according to aging in rats, providing the first evidence that methylation of RNA, similarly to DNA methylation, can represent an effective biomarker of aging. What is more, the fact that it is regulated by nutrition provides the basis for the development of targeted approaches capable of guaranteeing the maintenance of a state of good health. Full article

(This article belongs to the Special Issue Effects of Dietary Interventions on DNA Methylation during Lifecycle)

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13 pages, 543 KiB

Open AccessArticle

Antibacterial Activity and Epigenetic Remodeling of Essential Oils from Calabrian Aromatic Plants

by Patrizia D’Aquila, Ersilia Paparazzo, Michele Crudo, Sonia Bonacci, Antonio Procopio, Giuseppe Passarino and Dina Bellizzi

Nutrients 2022, 14(2), 391; https://0-doi-org.brum.beds.ac.uk/10.3390/nu14020391 - 17 Jan 2022

Cited by 12 | Viewed by 2706

Abstract

Natural compounds have historically had a wide application in nutrition. Recently, a fundamental role has been identified for essential oils extracted from aromatic plants for their nutritional, antimicrobial, and antioxidant properties, and as food preservatives. In the present study, essential oils (EOs) from ten aromatic plants grown in Calabria (Italy), used routinely to impart aroma and taste to food, were evaluated for their antibacterial activity. This activity was investigated against Escherichia coli strain JM109, and its derived antibiotic-resistant cells selected by growing the strain at low concentrations of ampicillin, ciprofloxacin, and gentamicin by measuring the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC). Although all the essential oils showed bactericidal activity, those from Clinopodium nepeta, Origanum vulgare, and Foeniculum vulgare displayed the greatest inhibitory effects on the bacterial growth of all cell lines. It is plausible that the antibacterial activity is mediated by epigenetic modifications since the tested essential oils induce methylation both at adenine and cytosine residues in the genomes of most cell lines. This study contributes to a further characterization of the properties of essential oils by shedding new light on the molecular mechanisms that mediate these properties. Full article

(This article belongs to the Special Issue Effects of Dietary Interventions on DNA Methylation during Lifecycle)

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13 pages, 563 KiB

Open AccessArticle

Genomics of Postprandial Lipidomics in the Genetics of Lipid-Lowering Drugs and Diet Network Study

by Marguerite R. Irvin, May E. Montasser, Tobias Kind, Sili Fan, Dinesh K. Barupal, Amit Patki, Rikki M. Tanner, Nicole D. Armstrong, Kathleen A. Ryan, Steven A. Claas, Jeffrey R. O’Connell, Hemant K. Tiwari and Donna K. Arnett

Nutrients 2021, 13(11), 4000; https://0-doi-org.brum.beds.ac.uk/10.3390/nu13114000 - 10 Nov 2021

Cited by 2 | Viewed by 2378

Abstract

Postprandial lipemia (PPL) is an important risk factor for cardiovascular disease. Inter-individual variation in the dietary response to a meal is known to be influenced by genetic factors, yet genes that dictate variation in postprandial lipids are not completely characterized. Genetic studies of the plasma lipidome can help to better understand postprandial metabolism by isolating lipid molecular species which are more closely related to the genome. We measured the plasma lipidome at fasting and 6 h after a standardized high-fat meal in 668 participants from the Genetics of Lipid-Lowering Drugs and Diet Network study (GOLDN) using ultra-performance liquid chromatography coupled to (quadrupole) time-of-flight mass spectrometry. A total of 413 unique lipids were identified. Heritable and responsive lipid species were examined for association with single-nucleotide polymorphisms (SNPs) genotyped on the Affymetrix 6.0 array. The most statistically significant SNP findings were replicated in the Amish Heredity and Phenotype Intervention (HAPI) Heart Study. We further followed up findings from GOLDN with a regional analysis of cytosine-phosphate-guanine (CpGs) sites measured on the Illumina HumanMethylation450 array. A total of 132 lipids were both responsive to the meal challenge and heritable in the GOLDN study. After correction for multiple testing of 132 lipids (α = 5 × 10⁻⁸/132 = 4 × 10⁻¹⁰), no SNP was statistically significantly associated with any lipid response. Four SNPs in the region of a known lipid locus (fatty acid desaturase 1 and 2/FADS1 and FADS2) on chromosome 11 had p < 8.0 × 10⁻⁷ for arachidonic acid FA(20:4). Those SNPs replicated in HAPI Heart with p < 3.3 × 10⁻³. CpGs around the FADS1/2 region were associated with arachidonic acid and the relationship of one SNP was partially mediated by a CpG (p = 0.005). Both SNPs and CpGs from the fatty acid desaturase region on chromosome 11 contribute jointly and independently to the diet response to a high-fat meal. Full article

(This article belongs to the Special Issue Effects of Dietary Interventions on DNA Methylation during Lifecycle)

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19 pages, 2244 KiB

Open AccessArticle

Therapeutic Effects of Dietary Soybean Genistein on Triple-Negative Breast Cancer via Regulation of Epigenetic Mechanisms

by Manvi Sharma, Itika Arora, Min Chen, Huixin Wu, Michael R. Crowley, Trygve O. Tollefsbol and Yuanyuan Li

Nutrients 2021, 13(11), 3944; https://0-doi-org.brum.beds.ac.uk/10.3390/nu13113944 - 04 Nov 2021

Cited by 11 | Viewed by 3480

Abstract

Consumption of dietary natural components such as genistein (GE) found in soy-rich sources is strongly associated with a lower risk of breast cancer. However, bioactive dietary component-based therapeutic strategies are largely understudied in breast cancer treatment. Our investigation sought to elucidate the potential mechanisms linking bioactive dietary GE to its breast cancer chemotherapeutic potential in a special subtype of aggressive breast cancer—triple-negative breast cancer (TNBC)—by utilizing two preclinical patient-derived xenograft (PDX) orthotopic mouse models: BCM-3204 and TM00091. Our study revealed that administration of GE resulted in a delay of tumor growth in both PDX models. With transcriptomics analyses in TNBC tumors isolated from BCM-3204 PDXs, we found that dietary soybean GE significantly influenced multiple tumor-regulated gene expressions. Further validation assessment of six candidate differentially expressed genes (DEGs)—Cd74, Lpl, Ifi44, Fzd9, Sat1 and Wwc1—demonstrated a similar trend at gene transcriptional and protein levels as observed in RNA-sequencing results. Mechanistically, GE treatment-induced Cd74 downregulation regulated the NF-κB/Bcl-xL/TAp63 signal pathway, which may contribute to soybean GE-mediated therapeutic effects on TNBC tumors. Additionally, our findings revealed that GE can modify expression levels of key epigenetic-associated genes such as DNA methyltransferases (Dnmt3b), ten-eleven translocation (Tet3) methylcytosine dioxygenases and histone deacetyltransferase (Hdac2), and their enzymatic activities as well as genomic DNA methylation and histone methylation (H3K9) levels. Collectively, our investigation shows high significance for potential development of a novel therapeutic approach by using bioactive soybean GE for TNBC patients who have few treatment options. Full article

(This article belongs to the Special Issue Effects of Dietary Interventions on DNA Methylation during Lifecycle)

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Review

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28 pages, 1187 KiB

Open AccessReview

Targeting DNA Methylation in the Adult Brain through Diet

by Joseph Allison, Aleksandra Kaliszewska, Sara Uceda, Manuel Reiriz and Natalia Arias

Nutrients 2021, 13(11), 3979; https://0-doi-org.brum.beds.ac.uk/10.3390/nu13113979 - 08 Nov 2021

Cited by 22 | Viewed by 9331

Abstract

Metabolism and nutrition have a significant role in epigenetic modifications such as DNA methylation, which can influence gene expression. Recently, it has been suggested that bioactive nutrients and gut microbiota can alter DNA methylation in the central nervous system (CNS) through the gut–brain axis, playing a crucial role in modulating CNS functions and, finally, behavior. Here, we will focus on the effect of metabolic signals in shaping brain DNA methylation during adulthood. We will provide an overview of potential interactions among diet, gastrointestinal microbiome and epigenetic alterations on brain methylation and behavior. In addition, the impact of different diet challenges on cytosine methylation dynamics in the adult brain will be discussed. Finally, we will explore new ways to modulate DNA hydroxymethylation, which is particularly abundant in neural tissue, through diet. Full article

(This article belongs to the Special Issue Effects of Dietary Interventions on DNA Methylation during Lifecycle)

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17 pages, 711 KiB

Open AccessReview

Early Life Nutrition and Mental Health: The Role of DNA Methylation

by Rola A Bekdash

Nutrients 2021, 13(9), 3111; https://0-doi-org.brum.beds.ac.uk/10.3390/nu13093111 - 04 Sep 2021

Cited by 28 | Viewed by 7268

Abstract

Does the quality of our diet during early life impact our long-term mental health? Accumulating evidence suggests that nutrition interacts with our genes and that there is a strong association between the quality of diet and mental health throughout life. Environmental influences such as maternal diet during pregnancy or offspring diet have been shown to cause epigenetic changes during critical periods of development, such as chemical modifications of DNA or histones by methylation for the regulation of gene expression. One-carbon metabolism, which consists of the folate and methionine cycles, is influenced by the diet and generates S-Adenosylmethinoine (SAM), the main methyl donor for methylation reactions such as DNA and histone methylation. This review provides current knowledge on how the levels of one-carbon metabolism associated micronutrients such as choline, betaine, folate, methionine and B vitamins that play a role in brain function can impact our well-being and mental health across the lifespan. Micronutrients that act as methyl donors for SAM formation could affect global or gene methylation, altering gene expression and phenotype. Strategies should then be adopted to better understand how these nutrients work and their impact at different stages of development to provide individualized dietary recommendations for better mental health outcomes. Full article

(This article belongs to the Special Issue Effects of Dietary Interventions on DNA Methylation during Lifecycle)

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