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DNA methylation immune response

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https://www.readbyqxmd.com/read/29331675/module-analysis-captures-pancancer-genetically-and-epigenetically-deregulated-cancer-driver-genes-for-smoking-and-antiviral-response
#1
Magali Champion, Kevin Brennan, Tom Croonenborghs, Andrew J Gentles, Nathalie Pochet, Olivier Gevaert
The availability of increasing volumes of multi-omics profiles across many cancers promises to improve our understanding of the regulatory mechanisms underlying cancer. The main challenge is to integrate these multiple levels of omics profiles and especially to analyze them across many cancers. Here we present AMARETTO, an algorithm that addresses both challenges in three steps. First, AMARETTO identifies potential cancer driver genes through integration of copy number, DNA methylation and gene expression data...
December 1, 2017: EBioMedicine
https://www.readbyqxmd.com/read/29317916/exposure-to-no2-co-and-pm2-5-is-linked-to-regional-dna-methylation-differences-in-asthma
#2
Mary Prunicki, Laurel Stell, Deendayal Dinakarpandian, Mariangels de Planell-Saguer, Richard W Lucas, S Katharine Hammond, John R Balmes, Xiaoying Zhou, Tara Paglino, Chiara Sabatti, Rachel L Miller, Kari C Nadeau
Background: DNA methylation of CpG sites on genetic loci has been linked to increased risk of asthma in children exposed to elevated ambient air pollutants (AAPs). Further identification of specific CpG sites and the pollutants that are associated with methylation of these CpG sites in immune cells could impact our understanding of asthma pathophysiology. In this study, we sought to identify some CpG sites in specific genes that could be associated with asthma regulation (Foxp3 and IL10) and to identify the different AAPs for which exposure prior to the blood draw is linked to methylation levels at these sites...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29242529/decitabine-a-dna-demethylating-agent-promotes-differentiation-via-notch1-signaling-and-alters-immune-related-pathways-in-muscle-invasive-bladder-cancer
#3
Swathi Ramakrishnan, Qiang Hu, Nithya Krishnan, Dan Wang, Evelyn Smit, Victoria Granger, Monika Rak, Kristopher Attwood, Candace Johnson, Carl Morrison, Roberto Pili, Gurkamal Chatta, Khurshid Guru, Geraldine Gueron, Lacey McNally, Jianmin Wang, Anna Woloszynska-Read
Aberrant DNA methylation observed in cancer can provide survival benefits to cells by silencing genes essential for anti-tumor activity. DNA-demethylating agents such as Decitabine (DAC)/Azacitidine (AZA) activate otherwise silenced tumor suppressor genes, alter immune response and epigenetically reprogram tumor cells. In this study, we show that non-cytotoxic nanomolar DAC concentrations modify the bladder cancer transcriptome to activate NOTCH1 at the mRNA and protein level, increase double-stranded RNA sensors and CK5-dependent differentiation...
December 14, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29240761/microorganisms-in-the-human-placenta-are-associated-with-altered-cpg-methylation-of-immune-and-inflammation-related-genes
#4
Martha Scott Tomlinson, Paige A Bommarito, Elizabeth M Martin, Lisa Smeester, Raina N Fichorova, Andrew B Onderdonk, Karl C K Kuban, T Michael O'Shea, Rebecca C Fry
Microorganisms in the placenta have been linked to adverse pregnancy outcomes as well as neonatal illness. Inflammation in the placenta has been identified as a contributing factor in this association, but the underlying biological mechanisms are not yet fully understood. The placental epigenome may serve as an intermediate between placental microbes and inflammation, contributing to adverse outcomes in the offspring. In the present study, genome-wide DNA methylation (n = 486,428 CpG sites) of 84 placentas was analyzed in relation to 16 species of placental microorganisms using samples collected from the Extremely Low Gestation Age Newborns (ELGAN) cohort...
2017: PloS One
https://www.readbyqxmd.com/read/29229600/genomic-and-epigenomic-signatures-in-ovarian-cancer-associated-with-re-sensitization-to-platinum-drugs
#5
Fang Fang, Horacio Cardenas, Hao Huang, Guanglong Jiang, Susan M Perkins, Chi Zhang, Harold N Keer, Yunlong Liu, Kenneth P Nephew, Daniela Matei
DNA methylation aberrations have been implicated in acquired resistance to platinum drugs in ovarian cancer (OC). In this study, we elucidated an epigenetic signature associated with platinum drug re-sensitization that may offer utility in predicting the outcomes of patients who are co-administered a DNA methyltransferase inhibitror. The OC specimens we analyzed were derived from a recent clinical trial that compared the responses of patients with recurrent platinum-resistant OC who received carboplatin plus the DNA methyltransferase inhibitor guadecitabine or a standard of care chemotherapy regimen selected by the treating physician...
December 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/29229400/tumor-necrosis-factor-producing-t-regulatory-cells-are-associated-with-severe-liver-injury-in-patients-with-acute-hepatitis-a
#6
Yoon Seok Choi, Min Kyung Jung, Jeewon Lee, Seong Jin Choi, Sung Hoon Choi, Hyun Woong Lee, Jong-Joo Lee, Hyung Joon Kim, Sang Hoon Ahn, Dong Hyeon Lee, Won Kim, Su-Hyung Park, Jun R Huh, Hyoung-Pyo Kim, Jun Yong Park, Eui-Cheol Shin
BACKGROUND AND AIMS: CD4+CD25+Foxp3+ T-regulatory (Treg) cells control immune responses and maintain immune homeostasis. However, under inflammatory conditions, Treg cells produce cytokines that promote inflammation. We investigated production of tumor necrosis factor (TNF) by Treg cells in patients with acute hepatitis A (AHA), and examined the characteristics of these cells and association with clinical factors. METHODS: We analyzed blood samples collected from 63 patients with AHA at the time of hospitalization (and some at later time points) and 19 healthy donors in South Korea...
December 8, 2017: Gastroenterology
https://www.readbyqxmd.com/read/29227354/current-views-on-the-pathogenesis-of-sjgren-s-syndrome
#7
Elena Pontarini, Davide Lucchesi, Michele Bombardieri
PURPOSE OF REVIEW: The purpose of this review is to provide an insight into the pathophysiological mechanisms involved in the pathogenesis of primary Sjgren's Syndrome (pSS), highlighting recent findings with potential therapeutic repercussions. RECENT FINDINGS: In the last 2 years, epigenetic analyses provided new insights into pSS pathogenesis. Characterization of DNA methylation patterns, chromatin structures and microRNA confirmed the importance of aberrant interferon and B-cell responses in the development of the disease...
December 8, 2017: Current Opinion in Rheumatology
https://www.readbyqxmd.com/read/29218028/the-folate-cycle-as-a-cause-of-natural-killer-cell-dysfunction-and-viral-etiology-in-type-1-diabetes
#8
Allison L Bayer, Christopher A Fraker
The folate pathway is critical to proper cellular function and metabolism. It is responsible for multiple functions, including energy (ATP) production, methylation reactions for DNA and protein synthesis and the production of immunomodulatory molecules, inosine and adenosine. These play an important role in immune signaling and cytotoxicity. Herein, we hypothesize that defects in the folate pathway in genetically susceptible individuals could lead to immune dysfunction, permissive environments for chronic cyclical latent/lytic viral infection, and, ultimately, the development of unchecked autoimmune responses to infected tissue, in this case islet beta cells...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29201597/current-concepts-of-epigenetics-and-its-role-in-periodontitis
#9
REVIEW
Lena Larsson
Purpose: The focus of this review is to provide an overview of the recent findings on the role of epigenetic mechanisms in periodontal disease, including disease susceptibility, progression, and as potential treatment options. Recent Findings: The findings on the influence of oral pathogens on epigenetic regulation of pathogen recognition receptors, such as Toll-like receptors, as well as pro-inflammatory cytokines suggest an important role for epigenetics in the regulation of the host immune response...
2017: Current Oral Health Reports
https://www.readbyqxmd.com/read/29191170/the-arabidopsis-elp3-elo3-and-elp4-elo1-genes-enhance-disease-resistance-in-fragaria-vesca-l
#10
Katchen Julliany P Silva, Asha M Brunings, Juliana A Pereira, Natalia A Peres, Kevin M Folta, Zhonglin Mou
BACKGROUND: Plant immune response is associated with a large-scale transcriptional reprogramming, which is regulated by numerous transcription regulators such as the Elongator complex. Elongator is a multitasking protein complex involved in diverse cellular processes, including histone modification, DNA methylation, and tRNA modification. In recent years, Elongator is emerging as a key regulator of plant immune responses. However, characterization of Elongator's function in plant immunity has been conducted only in the model plant Arabidopsis thaliana...
December 1, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29167521/dna-methylation-in-silkworm-genome-may-provide-insights-into-epigenetic-regulation-of-response-to-bombyx-mori-cypovirus-infection
#11
Ping Wu, Wencai Jie, Qi Shang, Enoch Annan, Xiaoxu Jiang, Chenxiang Hou, Tao Chen, Xijie Guo
DNA methylation is an important epigenetic modification that regulates a wide range of biological processes including immune response. However, information on the epigenetics-mediated immune mechanisms in insects is limited. Therefore, in this study, we examined transcriptomes and DNA methylomes in the fat body and midgut tissues of silkworm, Bombyx mori with or without B. mori cytoplasmic polyhedrosis virus (BmCPV) infection. The transcriptional profile and the genomic DNA methylation patterns in the midgut and fat body were tissue-specific and dynamically altered after BmCPV challenge...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29157945/food-allergy-a-review-and-update-on-epidemiology-pathogenesis-diagnosis-prevention-and-management
#12
Scott H Sicherer, Hugh A Sampson
This review provides general information to serve as a primer for those embarking on understanding food allergy and also details advances and updates in epidemiology, pathogenesis, diagnosis and treatment that have occurred over the four years since our last comprehensive review. Although firm prevalence data are lacking, there is a strong impression that food allergy has increased, and rates as high as ∼10% have been documented. Genetic, epigenetic and environmental risk factors are being increasingly elucidated, opening the potential for improved prevention and treatment strategies targeted to those at risk...
November 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29134693/microglia-from-offspring-of-dams-with-allergic-asthma-exhibit-epigenomic-alterations-in-genes-dysregulated-in-autism
#13
Annie Vogel Ciernia, Milo Careaga, Janine M LaSalle, Paul Ashwood
Dysregulation in immune responses during pregnancy increases the risk of a having a child with an autism spectrum disorder (ASD). Asthma is one of the most common chronic diseases among pregnant women, and symptoms often worsen during pregnancy. We recently developed a mouse model of maternal allergic asthma (MAA) that induces changes in sociability, repetitive, and perseverative behaviors in the offspring. Since epigenetic changes help a static genome adapt to the maternal environment, activation of the immune system may epigenetically alter fetal microglia, the brain's resident immune cells...
November 14, 2017: Glia
https://www.readbyqxmd.com/read/29133290/cd137-4-1bb-costimulation-modifies-dna-methylation-in-cd8-t-cell-relevant-genes
#14
M Angela Aznar, Sara Labiano, Angel Diaz-Lagares, Carmen Molina, Saray Garasa, Arantza Azpilicueta, Inaki Etxeberria, Alfonso R Sanchez-Paulete, Alan J Korman, Manel Esteller, Juan Sandoval, Ignacio Melero
CD137 (4-1BB) costimulation imprints long-term changes that instruct the ultimate behavior of T cells that have previously experienced CD137 ligation. Epigenetic changes could provide a suitable mechanism for these long-term consequences. Genome-wide DNA-methylation arrays were carried out on human peripheral blood CD8+ T lymphocytes stimulated with agonist monoclonal antibody to CD137, including urelumab, which is in phase I/II clinical trials for cancer immunotherapy. Several genes showed consistent methylation patterns in response to CD137 costimulation, which were confirmed by pyrosequencing in a series of healthy donors...
November 13, 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/29131380/upregulation-of-prmt6-by-lps-suppresses-klotho-expression-through-interaction-with-nf-%C3%AE%C2%BAb-in-glomerular-mesangial-cells
#15
Kuen-Daw Tsai, Wen-Xi Lee, Wei Chen, Bo-Yu Chen, Kuan-Lin Chen, Tzu-Chia Hsiao, Sue-Hong Wang, Yi-Ju Lee, Shan-Yuan Liang, Jia-Ching Shieh, Ting-Hui Lin
Lipopolysaccharide (LPS) released from gram-negative bacteria stimulates immune responses in infected cells. Epigenetic modifications such as DNA methylation and protein methylation modulate LPS-induced innate immune gene expressions. Expression of the Klotho protein decreased with LPS treatment in rats. In a cellular model, information regarding the effect of LPS on Klotho expression was meager. In the present study, we demonstrated that LPS triggered global DNA and protein methylation in glomerular mesangial MES-13 cells...
November 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29123172/transcriptomic-and-epigenetic-responses-to-short-term-nutrient-exercise-stress-in-humans
#16
R C Laker, C Garde, D M Camera, W J Smiles, J R Zierath, J A Hawley, R Barrès
High fat feeding impairs skeletal muscle metabolic flexibility and induces insulin resistance, whereas exercise training exerts positive effects on substrate handling and improves insulin sensitivity. To identify the genomic mechanisms by which exercise ameliorates some of the deleterious effects of high fat feeding, we investigated the transcriptional and epigenetic response of human skeletal muscle to 9 days of a high-fat diet (HFD) alone (Sed-HFD) or in combination with resistance exercise (Ex-HFD), using genome-wide profiling of gene expression and DNA methylation...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29106553/genome-wide-dna-methylation-changes-associated-with-intermittent-explosive-disorder-a-gene-based-functional-enrichment-analysis
#17
Janitza L Montalvo-Ortiz, Huiping Zhang, Chao Chen, Chunyu Liu, Emil F Coccaro
Background: Intermittent explosive disorder (IED) is defined as a recurrent, problematic, and impulsive aggression that affects 3-4% of the U.S. population. While behavioral genetic studies report a substantial degree of genetic influence on aggression and impulsivity, epigenetic mechanisms underlying aggression and IED is not well known. Methods: The sample included 44 subjects (22 with a DSM-5 diagnosis of IED and 22 comparable subjects without IED). Peripheral blood DNA methylome was profiled using the Illumina Infinium HumanMethylation450 Beadchip...
November 2, 2017: International Journal of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29066321/macrophage-polarization-and-allergic-asthma
#18
REVIEW
Arjun Saradna, Danh C Do, Shruthi Kumar, Qing-Ling Fu, Peisong Gao
Allergic asthma is associated with airway inflammation and airway hyperresponsiveness. Macrophage polarization has been shown to have a profound impact on asthma pathogenesis. On exposure to local microenvironments, recruited macrophages can be polarized into either classically activated (or M1) or alternatively activated (or M2) phenotypes. Macrophage polarization has been heavily associated with development of asthma. The process of regulation of macrophage polarization involves an intricate interplay between various cytokines, chemokines, transcriptional factors, and immune-regulatory cells...
October 7, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/29059104/transfusion-strategies-are-associated-with-epigenetic-changes-following-blunt-trauma
#19
Martin Sillesen, Yongqing Li, Hasan B Alam
INTRODUCTION: Epigenetics has been identified in multiple diseases. The effect of transfusion strategy on epigenetics is unknown. We hypothesized that expression of epigenetic regulating genes would be associated with resuscitation strategy following blunt trauma. METHODS: Retrospective study using the inflammation in host response to injury (glue grant) dataset. Volume transfused over 24 hours of packed red blood cells (PRBC), Fresh Frozen Plasma(FFP), Platelets(PLT) as well as crystalloids was extracted along with leucocyte microarray data of genes with known epigenetic modulating activity from day 1 after injury...
October 20, 2017: Shock
https://www.readbyqxmd.com/read/29048607/the-arabidopsis-chromatin-remodeling-factor-chr5-regulates-plant-immune-responses-and-nucleosome-occupancy
#20
Baohong Zou, Qi Sun, Wenli Zhang, Yuan Ding, Dong-Lei Yang, Jian Hua
ATP-dependent chromatin remodeling factors use the energy of ATP hydrolysis to alter the structure of chromatin and are important regulators of eukaryotic gene expression. One such factor CHR5 (Chromatin Remodeling Factor 5) in Arabidopsis (Arabidopsis thaliana) was previously found to be involved in growth and development regulation. Here we show that CHR5 is required for the upregulation of the intracellular immune receptor gene SNC1 (SUPPRESSOR OF npr1-1, CONSTITUTIVE1) and consequently the autoimmunity induced by SNC1 upregulation...
October 17, 2017: Plant & Cell Physiology
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