scholarly journals Epigenetic Studies of Atopic Dermatitis

2020 ◽  
Author(s):  
Vladimir Sobolev ◽  
Elizaveta Bystritskaya ◽  
Oxana Svitich
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Atopic Dermatitis ◽  
Nucleotide Sequence ◽  
T Lymphocyte ◽  
Population Genetic ◽  
Regulatory Mechanisms ◽  
Adaptive Immune ◽  
Epigenetic Regulator ◽  
Activity Of Enzymes

Since the pathogenesis of atopic dermatitis could not be explained only by a population genetic and phenotypic profiles, epigenetic regulator factors have been considered. Epigenetics is the study of inherited changes in gene expression that are not related to changes in its nucleotide sequence. One of the main classical regulatory mechanisms in human cells is DNA methylation. It is not clear how permanent modifications caused by this process are and whether it is possible to affect them by changing the activity of enzymes that trigger remodeling reactions. In this chapter we analyze all recent studies in this field. We focus more on methylation of innate and adaptive immune factors, with an emphasis on T-lymphocyte genes such as CD3, CD4, and CD8.

scholarly journals Molecular Mechanisms Underlying the Link between Diet and DNA Methylation

2018 ◽  
Vol 19 (12) ◽  
pp. 4055 ◽  
Author(s):  
Fatma Zehra Kadayifci ◽  
Shasha Zheng ◽  
Yuan-Xiang Pan
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Dna Demethylation ◽  
Direct Role ◽  
Large Numbers ◽  
Modifiable Factors ◽  
Activity Of Enzymes ◽  
Biochemical Mechanisms ◽  
The One

DNA methylation is a vital modification process in the control of genetic information, which contributes to the epigenetics by regulating gene expression without changing the DNA sequence. Abnormal DNA methylation—both hypomethylation and hypermethylation—has been associated with improper gene expression, leading to several disorders. Two types of risk factors can alter the epigenetic regulation of methylation pathways: genetic factors and modifiable factors. Nutrition is one of the strongest modifiable factors, which plays a direct role in DNA methylation pathways. Large numbers of studies have investigated the effects of nutrition on DNA methylation pathways, but relatively few have focused on the biochemical mechanisms. Understanding the biological mechanisms is essential for clarifying how nutrients function in epigenetics. It is believed that nutrition affects the epigenetic regulations of DNA methylation in several possible epigenetic pathways: mainly, by altering the substrates and cofactors that are necessary for proper DNA methylation; additionally, by changing the activity of enzymes regulating the one-carbon cycle; and, lastly, through there being an epigenetic role in several possible mechanisms related to DNA demethylation activity. The aim of this article is to review the potential underlying biochemical mechanisms that are related to diet modifications in DNA methylation and demethylation.

scholarly journals Resveratrol, EGCG and Vitamins Modulate Activated T Lymphocytes

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5600
Author(s):  
Joseph Schwager ◽  
Nicole Seifert ◽  
Albine Bompard ◽  
Daniel Raederstorff ◽  
Igor Bendik
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
T Lymphocytes ◽  
T Lymphocyte ◽  
Adaptive Immune Response ◽  
Marginal Effect ◽  
Th2 Response ◽  
T Lymphocyte Subsets ◽  
Adaptive Immune ◽  
T Lymphocyte Proliferation

Vitamins and bioactives, which are constituents of the food chain, modulate T lymphocyte proliferation and differentiation, antibody production, and prevent inflammation and autoimmunity. We investigated the effects of vitamins (vitamin A (VA), D (VD), E (VE)) and bioactives (i.e., resveratrol (Res), epigallocatechin-3-gallate (EGCG)) on the adaptive immune response, as well as their synergistic or antagonistic interactions. Freshly isolated T lymphocytes from healthy individuals were activated with anti-CD3/CD28 antibodies for 4–5 days in the presence of bioactives and were analyzed by cytofluorometry. Interleukins, cytokines, and chemokines were measured by multiple ELISA. Gene expression was measured by quantitative RT-PCR. Res and EGCG increased CD4 surface intensity. EGCG led to an increased proportion of CD8+ lymphocytes. Anti-CD3/CD28 activation induced exuberant secretion of interleukins and cytokines by T lymphocyte subsets. VD strongly enhanced Th2 cytokines (e.g., IL-5, IL-13), whereas Res and EGCG favored secretion of Th1 cytokines (e.g., IL-2, INF-γ). Res and VD mutually influenced cytokine production, but VD dominated the cytokine secretion pattern. The substances changed gene expression of interleukins and cytokines in a similar way as they did secretion. Collectively, VD strongly modulated cytokine and interleukin production and favored Th2 functions. Resveratrol and EGCG promoted the Th1 response. VA and VE had only a marginal effect, but they altered both Th1 and Th2 response. In vivo, bioactives might therefore interact with vitamins and support the outcome and extent of the adaptive immune response.

Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation

2019 ◽  
Vol 60 (8) ◽  
pp. 1702-1721 ◽  
Author(s):  
Libo Xing ◽  
Youmei Li ◽  
Siyan Qi ◽  
Chenguang Zhang ◽  
Wenchun Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Regulatory Mechanisms ◽  
Gene Body ◽  
Flower Bud ◽  
Transcriptional Responses ◽  
Global Methylation ◽  
Bud Formation ◽  
Body Regions ◽  
Flower Bud Formation

Abstract In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because ‘Fuji’ apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.

Nitric oxide is an epigenetic regulator of gene expression by directly controlling DNA methylation patterns

2018 ◽  
Vol 120 ◽  
pp. S114 ◽  
Author(s):  
Rhea Bovee ◽  
Vy Pham ◽  
Jenna Fernandez ◽  
Natalia Tretyakova ◽  
Douglas D. Thomas
Keyword(s):  
Gene Expression ◽  
Nitric Oxide ◽  
Dna Methylation ◽  
Epigenetic Regulator ◽  
Methylation Patterns

scholarly journals Distinct DNA Methylation Patterns of Subependymal Giant Cell Astrocytomas in Tuberous Sclerosis Complex

2021 ◽  
Author(s):  
Anika Bongaarts ◽  
Caroline Mijnsbergen ◽  
Jasper J. Anink ◽  
Floor E. Jansen ◽  
Wim G. M. Spliet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Immune Response ◽  
Extracellular Matrix ◽  
Immune System ◽  
Mapk Pathway ◽  
Adaptive Immune Response ◽  
Methylation Profile ◽  
Adaptive Immune ◽  
Matrix Organization

AbstractTuberous sclerosis complex (TSC) is a monogenic disorder caused by mutations in either the TSC1 or TSC2 gene, two key regulators of the mechanistic target of the rapamycin complex pathway. Phenotypically, this leads to growth and formation of hamartomas in several organs, including the brain. Subependymal giant cell astrocytomas (SEGAs) are low-grade brain tumors commonly associated with TSC. Recently, gene expression studies provided evidence that the immune system, the MAPK pathway and extracellular matrix organization play an important role in SEGA development. However, the precise mechanisms behind the gene expression changes in SEGA are still largely unknown, providing a potential role for DNA methylation. We investigated the methylation profile of SEGAs using the Illumina Infinium HumanMethylation450 BeadChip (SEGAs n = 42, periventricular control n = 8). The SEGA methylation profile was enriched for the adaptive immune system, T cell activation, leukocyte mediated immunity, extracellular structure organization and the ERK1 & ERK2 cascade. More interestingly, we identified two subgroups in the SEGA methylation data and show that the differentially expressed genes between the two subgroups are related to the MAPK cascade and adaptive immune response. Overall, this study shows that the immune system, the MAPK pathway and extracellular matrix organization are also affected on DNA methylation level, suggesting that therapeutic intervention on DNA level could be useful for these specific pathways in SEGA. Moreover, we identified two subgroups in SEGA that seem to be driven by changes in the adaptive immune response and MAPK pathway and could potentially hold predictive information on target treatment response.

scholarly journals Distinct DNA Methylation Patterns of Subependymal Giant Cell Astrocytomas in Tuberous Sclerosis Complex

2021 ◽  
Author(s):  
Anika Bongaarts ◽  
Caroline Mijnsbergen ◽  
Jasper J. Anink ◽  
Floor E. Jansen ◽  
Wim G.M. Spliet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Immune Response ◽  
Extracellular Matrix ◽  
Immune System ◽  
Mapk Pathway ◽  
Adaptive Immune Response ◽  
Methylation Profile ◽  
Adaptive Immune ◽  
Matrix Organization

Abstract Tuberous sclerosis complex (TSC) is a monogenic disorder caused by mutations in either the TSC1 or TSC2 gene, two key regulators of the mechanistic target of the rapamycin complex pathway. Phenotypically, this leads to growth and formation of hamartomas in several organs, including the brain. Subependymal giant cell astrocytomas (SEGAs) are low-grade brain tumors commonly associated with TSC. Recently, gene expression studies provided evidence that the immune system, the MAPK pathway and extracellular matrix organization play an important role in SEGA development. However, the precise mechanisms behind the gene expression changes in SEGA are still largely unknown, providing a potential role for DNA methylation. We investigated the methylation profile of SEGAs using the Illumina Infinium HumanMethylation450 BeadChip (SEGAs n = 42, periventricular control n = 8). The SEGA methylation profile was enriched for the adaptive immune system, T cell activation, leukocyte mediated immunity, extracellular structure organization and the ERK1 & ERK2 cascade. More interestingly, we identified two subgroups in the SEGA methylation data and show that the differentially expressed genes between the two subgroups are related to the MAPK cascade and adaptive immune response. Overall, this study shows that the immune system, the MAPK pathway and extracellular matrix organization are also affected on DNA methylation level, suggesting that therapeutic intervention on DNA level could be useful for these specific pathways in SEGA. Moreover, we identified two subgroups in SEGA that seem to be driven by changes in the adaptive immune response and MAPK pathway and could potentially hold predictive information on target treatment response.

scholarly journals DNA methylation during human adipogenesis and the impact of fructose

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Giulia Tini ◽  
Vijayalakshmi Varma ◽  
Rosario Lombardo ◽  
Greg T. Nolen ◽  
Gregory Lefebvre ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Differentially Expressed Genes ◽  
Time Dependent ◽  
Regulatory Mechanisms ◽  
Differentially Methylated Regions ◽  
Genome Wide ◽  
A Genome ◽  
Final Maturation ◽  
The Impact

Abstract Background Increased adipogenesis and altered adipocyte function contribute to the development of obesity and associated comorbidities. Fructose modified adipocyte metabolism compared to glucose, but the regulatory mechanisms and consequences for obesity are unknown. Genome-wide methylation and global transcriptomics in SGBS pre-adipocytes exposed to 0, 2.5, 5, and 10 mM fructose, added to a 5-mM glucose-containing medium, were analyzed at 0, 24, 48, 96, 192, and 384 h following the induction of adipogenesis. Results Time-dependent changes in DNA methylation compared to baseline (0 h) occurred during the final maturation of adipocytes, between 192 and 384 h. Larger percentages (0.1% at 192 h, 3.2% at 384 h) of differentially methylated regions (DMRs) were found in adipocytes differentiated in the glucose-containing control media compared to adipocytes differentiated in fructose-supplemented media (0.0006% for 10 mM, 0.001% for 5 mM, and 0.005% for 2.5 mM at 384 h). A total of 1437 DMRs were identified in 5237 differentially expressed genes at 384 h post-induction in glucose-containing (5 mM) control media. The majority of them inversely correlated with the gene expression, but 666 regions were positively correlated to the gene expression. Conclusions Our studies demonstrate that DNA methylation regulates or marks the transformation of morphologically differentiating adipocytes (seen at 192 h), to the more mature and metabolically robust adipocytes (as seen at 384 h) in a genome-wide manner. Lower (2.5 mM) concentrations of fructose have the most robust effects on methylation compared to higher concentrations (5 and 10 mM), suggesting that fructose may be playing a signaling/regulatory role at lower concentrations of fructose and as a substrate at higher concentrations.

scholarly journals Epigenetics and sarcoidosis

2021 ◽  
Vol 30 (160) ◽  
pp. 210076
Author(s):  
Iain R. Konigsberg ◽  
Lisa A. Maier ◽  
Ivana V. Yang
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Lung Disease ◽  
Histone Modifications ◽  
Genetic Variants ◽  
Lung Diseases ◽  
Hypersensitivity Pneumonitis ◽  
Epigenetic Modifications ◽  
Regulatory Mechanisms ◽  
Beryllium Disease

Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis.

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