scholarly journals A Differential DNA Methylome Signature of Pulmonary Immune Cells from Individuals Converting to Latent Tuberculosis Infection

2021 ◽  
Author(s):  
Lovisa Karlsson ◽  
Jyotirmoy Das ◽  
Moa Nilsson ◽  
Amanda Tyren ◽  
Isabelle Pehrson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Immune Cells ◽  
Methylation Status ◽  
Latent Tuberculosis ◽  
Dna Methylome ◽  
T Cell Migration ◽  
Increased Risk ◽  
Before And After ◽  
Methylome Analysis ◽  
Latent Tb

Tuberculosis (TB), caused by Mycobacterium tuberculosis, spreads via aerosols and the first encounter with the immune system is with the pulmonary resident immune cells. The role of epigenetic regulations through DNA methylation in the immune cells is emerging. We have previously shown that capacity to kill M. tuberculosis is reflected in the DNA methylome. The aim of this study was to investigate epigenetic modifications in the pulmonary immune cells in a cohort of medical students with a previously documented increased risk of TB exposure, longitudinally. Sputum samples containing alveolar macrophages (AMs) and T cells were collected before and after study subjects worked in hospital departments with a high-risk of TB exposure. DNA methylome analysis revealed that a unique DNA methylation profile was present already at inclusion in subjects who developed latent TB during the study. The profile was both reflected in different overall DNA methylation distribution as well as more profound alterations in the methylation status of a unique set of CpG-sites. Over-representation analysis of the DMGs showed enrichment in pathways related to metabolic reprograming of macrophages and T cell migration and IFN-γ production. In conclusion, we identified a unique DNA methylation signature in individuals, while still IGRA-negative and who later developed latent TB. Epigenetic regulation was found in pathways that have previously been reported to be important in TB. Together the study suggests that DNA methylation status of pulmonary immune cells can predict IGRA conversion.

scholarly journals A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lovisa Karlsson ◽  
Jyotirmoy Das ◽  
Moa Nilsson ◽  
Amanda Tyrén ◽  
Isabelle Pehrson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Immune Cells ◽  
Methylation Status ◽  
Latent Tuberculosis ◽  
Metabolic Reprogramming ◽  
Dna Methylome ◽  
Differentially Methylated Genes ◽  
Increased Risk ◽  
Latent Tb ◽  
Latent Tb Infection

AbstractTuberculosis (TB), caused by Mycobacterium tuberculosis, spreads via aerosols and the first encounter with the immune system is with the pulmonary-resident immune cells. The role of epigenetic regulations in the immune cells is emerging and we have previously shown that macrophages capacity to kill M. tuberculosis is reflected in the DNA methylome. The aim of this study was to investigate epigenetic modifications in alveolar macrophages and T cells in a cohort of medical students with an increased risk of TB exposure, longitudinally. DNA methylome analysis revealed that a unique DNA methylation profile was present in healthy subjects who later developed latent TB during the study. The profile was reflected in a different overall DNA methylation distribution as well as a distinct set of differentially methylated genes (DMGs). The DMGs were over-represented in pathways related to metabolic reprogramming of macrophages and T cell migration and IFN-γ production, pathways previously reported important in TB control. In conclusion, we identified a unique DNA methylation signature in individuals, with no peripheral immune response to M. tuberculosis antigen who later developed latent TB. Together the study suggests that the DNA methylation status of pulmonary immune cells can reveal who will develop latent TB infection.

scholarly journals DNA methylome signatures of prenatal exposure to synthetic glucocorticoids in hippocampus and peripheral whole blood of female guinea pigs in early life

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aya Sasaki ◽  
Margaret E. Eng ◽  
Abigail H. Lee ◽  
Alisa Kostaki ◽  
Stephen G. Matthews
Keyword(s):  
Dna Methylation ◽  
Whole Blood ◽  
Guinea Pigs ◽  
Critical Role ◽  
Methylation Status ◽  
Peripheral Tissues ◽  
Epigenetic Biomarkers ◽  
Differentially Methylated Genes ◽  
Increased Risk ◽  
Synthetic Glucocorticoids

AbstractSynthetic glucocorticoids (sGC) are administered to women at risk of preterm delivery, approximately 10% of all pregnancies. In animal models, offspring exposed to elevated glucocorticoids, either by administration of sGC or endogenous glucocorticoids as a result of maternal stress, show increased risk of developing behavioral, endocrine, and metabolic dysregulation. DNA methylation may play a critical role in long-lasting programming of gene regulation underlying these phenotypes. However, peripheral tissues such as blood are often the only accessible source of DNA for epigenetic analyses in humans. Here, we examined the hypothesis that prenatal sGC administration alters DNA methylation signatures in guinea pig offspring hippocampus and whole blood. We compared these signatures across the two tissue types to assess epigenetic biomarkers of common molecular pathways affected by sGC exposure. Guinea pigs were treated with sGC or saline in late gestation. Genome-wide modifications of DNA methylation were analyzed at single nucleotide resolution using reduced representation bisulfite sequencing in juvenile female offspring. Results indicate that there are tissue-specific as well as common methylation signatures of prenatal sGC exposure. Over 90% of the common methylation signatures associated with sGC exposure showed the same directionality of change in methylation. Among differentially methylated genes, 134 were modified in both hippocampus and blood, of which 61 showed methylation changes at identical CpG sites. Gene pathway analyses indicated that prenatal sGC exposure alters the methylation status of gene clusters involved in brain development. These data indicate concordance across tissues of epigenetic programming in response to alterations in glucocorticoid signaling.

Hepatic IGF1 DNA methylation is influenced by gender but not by intrauterine growth restriction in the young lamb

2015 ◽  
Vol 6 (6) ◽  
pp. 558-572 ◽  
Author(s):  
D. J. Carr ◽  
J. S. Milne ◽  
R. P. Aitken ◽  
C. L. Adam ◽  
J. M. Wallace
Keyword(s):  
Dna Methylation ◽  
Growth Hormone ◽  
Sexual Dimorphism ◽  
Mrna Expression ◽  
Intrauterine Growth Restriction ◽  
Messenger Rna ◽  
Methylation Status ◽  
Growth Restriction ◽  
Intrauterine Growth ◽  
Increased Risk

Intrauterine growth restriction (IUGR) and postnatal catch-up growth confer an increased risk of adult-onset disease. Overnourishment of adolescent ewes generates IUGR in ∼50% of lambs, which subsequently exhibit increased fractional growth rates. We investigated putative epigenetic changes underlying this early postnatal phenotype by quantifying gene-specific methylation at cytosine:guanine (CpG) dinucleotides. Hepatic DNA/RNA was extracted from IUGR [eight male (M)/nine female (F)] and normal birth weight (12 M/9 F) lambs. Polymerase chain reaction was performed using primers targeting CpG islands in 10 genes: insulin, growth hormone, insulin-like growth factor (IGF)1, IGF2, H19, insulin receptor, growth hormone receptor, IGF receptors 1 and 2, and the glucocorticoid receptor. Using pyrosequencing, methylation status was determined by quantifying cytosine:thymine ratios at 57 CpG sites. Messenger RNA (mRNA) expression of IGF system genes and plasma IGF1/insulin were determined. DNA methylation was independent of IUGR status but sexual dimorphism in IGF1 methylation was evident (M<F, P=0.008). IGF1 mRNA:18S and plasma IGF1 were M>F (both P<0.001). IGF1 mRNA expression correlated negatively with IGF1 methylation (r=−0.507, P=0.002) and positively with plasma IGF1 (r=0.884, P<0.001). Carcass and empty body weights were greater in males (P=0.002–0.014) and this gender difference in early body conformation was mirrored by sexual dimorphism in hepatic IGF1 DNA methylation, mRNA expression and plasma IGF1 concentrations.

scholarly journals Persistent DNA Hyper-methylation Dampens Host Anti-Mycobacterial Immunity

2019 ◽  
Author(s):  
Andrew R. DiNardo ◽  
Kimal Rajapakshe ◽  
Tomoki Nishiguchi ◽  
Godwin Mtetwa ◽  
Qiniso Dlamini ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Immune Cells ◽  
Methylation Status ◽  
Host Immunity ◽  
Immune Responsiveness ◽  
Chronic Infections ◽  
Household Contacts ◽  
Full Complement ◽  
Ifn Γ ◽  
Specific Immune Responsiveness

AbstractMycobacterium tuberculosis (Mtb) has co-evolved with humans for millennia and developed multiple mechanisms to evade host immunity. Restoring host immunity in order to shorten existing therapy and improve outcomes will require identifying the full complement by which host immunity is inhibited. Perturbing host DNA methylation is a mechanism induced by chronic infections such as HIV, HPV, LCMV and schistosomiasis to evade host immunity. Here, we evaluated the DNA methylation status of TB patients and their asymptomatic household contacts demonstrating that TB patients have DNA hyper-methylation of the IL-2-STAT5, TNF-NF-ϰB and IFN-γ signaling pathways. By MSRE-qPCR, multiple genes of the IL-12-IFN-γ signaling pathway (IL12B, IL12RB2, TYK2, IFNGR1, JAK1 and JAK2) were hyper-methylated in TB patients. The DNA hyper-methylation of these pathways is associated with decreased immune responsiveness with decreased mitogen induced upregulation of IFN-γ, TNF, IL-6 and IL-1β production. The DNA hyper-methylation of the IL-12-IFN-γ pathway was associated with decreased IFN-γ induced gene expression and decreased IL-12 inducible up-regulation of IFN-γ. This work demonstrates that immune cells from TB patients are characterized by DNA hyper-methylation of genes critical to mycobacterial immunity resulting in decreased mycobacteria-specific and non-specific immune responsiveness.

scholarly journals DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands

Epigenomics ◽  
2016 ◽  
Vol 8 (10) ◽  
pp. 1367-1387 ◽  
Author(s):  
Per Wahlberg ◽  
Anders Lundmark ◽  
Jessica Nordlund ◽  
Stephan Busche ◽  
Amanda Raine ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
De Novo ◽  
Lymphoblastic Leukemia ◽  
Cpg Islands ◽  
Leukemia Cells ◽  
Dna Methylome ◽  
Methylome Analysis

scholarly journals Faulty homocysteine recycling in diabetic retinopathy

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Renu A. Kowluru ◽  
Ghulam Mohammad ◽  
Nikhil Sahajpal
Keyword(s):  
Dna Methylation ◽  
Diabetic Retinopathy ◽  
Methylenetetrahydrofolate Reductase ◽  
Epigenetic Modification ◽  
Mitochondrial Dynamics ◽  
Methylation Status ◽  
Mitochondrial Damage ◽  
Diabetic Patients ◽  
Retinal Microvasculature ◽  
Increased Risk

Abstract Background Although hyperglycemia is the main instigator in the development of diabetic retinopathy, elevated circulating levels of a non-protein amino acid, homocysteine, are also associated with an increased risk of retinopathy. Homocysteine is recycled back to methionine by methylenetetrahydrofolate reductase (MTHFR) and/or transsulfurated by cystathionine β-synthase (CBS) to form cysteine. CBS and other transsulfuration enzyme cystathionine-γ-lyase (CSE), through desulfuration, generates H2S. Methionine cycle also regulates DNA methylation, an epigenetic modification associated with the gene suppression. The aim of this study was to investigate homocysteine and its metabolism in diabetic retinopathy. Methods Homocysteine and H2S levels were analyzed in the retina, and CBS, CSE and MTHFR in the retinal microvasculature from human donors with established diabetic retinopathy. Mitochondrial damage was evaluated in retinal microvessels by quantifying enzymes responsible for maintaining mitochondrial dynamics (fission-fusion-mitophagy). DNA methylation status of CBS and MTHFR promoters was examined using methylated DNA immunoprecipitation technique. The direct effect of homocysteine on mitochondrial damage was confirmed in human retinal endothelial cells (HRECs) incubated with 100 μM L-homocysteine. Results Compared to age-matched nondiabetic control human donors, retina from donors with established diabetic retinopathy had ~ 3-fold higher homocysteine levels and ~ 50% lower H2S levels. The enzymes important for both transsulfuration and remethylation of homocysteine including CBS, CSE and MTHFR, were 40–60% lower in the retinal microvasculature from diabetic retinopathy donors. While the mitochondrial fission protein, dynamin related protein 1, and mitophagy markers optineurin and microtubule-associated protein 1A/1B-light chain 3 (LC3), were upregulated, the fusion protein mitofusin 2 was downregulated. In the same retinal microvessel preparations from donors with diabetic retinopathy, DNA at the promoters of CBS and MTHFR were hypermethylated. Incubation of HRECs with homocysteine increased reactive oxygen species and decreased transcripts of mtDNA-encoded CYTB. Conclusions Compromised transsulfuration and remethylation processes play an important role in the poor removal of retinal homocysteine in diabetic patients. Thus, regulation of their homocysteine levels should ameliorate retinal mitochondrial damage, and by regulating DNA methylation status of the enzymes responsible for homocysteine transsulfuration and remethylation, should prevent excess accumulation of homocysteine.

scholarly journals Molecular tumor classification using DNA methylome analysis

2020 ◽  
Vol 29 (R2) ◽  
pp. R205-R213 ◽  
Author(s):  
Martin Sill ◽  
Christoph Plass ◽  
Stefan M Pfister ◽  
Daniel B Lipka
Keyword(s):  
Dna Methylation ◽  
Genetic Diagnostics ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Liquid Biopsies ◽  
Dna Methylome ◽  
Hematopoietic Malignancies ◽  
Methylome Analysis ◽  
Molecular Patterns ◽  
Molecular Tumor Classification

Abstract Tumor classifiers based on molecular patterns promise to define and reliably classify tumor entities. The high tissue- and cell type-specificity of DNA methylation, as well as its high stability, makes DNA methylation an ideal choice for the development of tumor classifiers. Herein, we review existing tumor classifiers using DNA methylome analysis and will provide an overview on their emerging impact on cancer classification, the detection of novel cancer subentities and patient stratification with a focus on brain tumors, sarcomas and hematopoietic malignancies. Furthermore, we provide an outlook on the enormous potential of DNA methylome analysis to complement classical histopathological and genetic diagnostics, including the emerging field of epigenomic analysis in liquid biopsies.

scholarly journals A DNA methylome biosignature in alveolar macrophages from TB-exposed individuals predicts exposure to mycobacteria

2021 ◽  
Author(s):  
Maria Lerm ◽  
Jyotirmoy Das ◽  
Jakob Paues ◽  
Nina Idh ◽  
Isabelle Pehrson
Keyword(s):  
Dna Methylation ◽  
Immune Cells ◽  
Contact Tracing ◽  
Clinical Use ◽  
Strongly Correlated ◽  
Epigenetic Changes ◽  
Dna Methylome ◽  
Hla Dr ◽  
Lung Compartment ◽  
Unsupervised Cluster Analysis

Several studies have identified biomarkers for tuberculosis (TB) diagnosis based on blood cell transcriptomics. Here, we instead studied epigenomics in the lung compartment by obtaining induced sputum from subjects included in a TB contact tracing. CD3- and HLA-DR-positive cells were isolated from the collected sputum and DNA methylome analyses performed. Unsupervised cluster analysis revealed that DNA methylomes of cells from TB-exposed individuals and controls appeared as separate clusters and the numerous genes that were differentially methylated were functionally connected. The enriched pathways were strongly correlated to data from published work on protective heterologous immunity to TB. Taken together, our results demonstrate that epigenetic changes related to trained immunity occurs in the pulmonary immune cells of TB-exposed individuals and that a DNA methylation signature can be derived from the DNA methylome. Such a signature can be further developed for clinical use as a marker of TB exposure.

The impact of DNA methylation on the identification of recurrent prostate cancer

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 21086-21086
Author(s):  
J. J. Alumkal ◽  
Z. Zhang ◽  
E. B. Humphreys ◽  
C. Bennett ◽  
L. A. Mangold ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Dna Methylation ◽  
Radical Prostatectomy ◽  
Biochemical Recurrence ◽  
Methylation Status ◽  
Surgical Margin ◽  
Multivariable Logistic Regression Analysis ◽  
Tissue Samples ◽  
Increased Risk ◽  
The Impact

21086 Purpose: Biochemical (PSA) recurrence of prostate cancer following radical prostatectomy remains a major problem. Better biomarkers are needed to identify high and low-risk patients. DNA methylation of promoter regions leads to gene silencing in many cancers. In this study, we assessed the impact of changes in DNA methylation on biochemical recurrence in men with prostate cancer. Methods: We examined the methylation status of fifteen genes using MSP (Methylation Specific PCR) on tissue samples from 151 patients with clinically localized prostate cancer for whom at least five years of follow-up after prostatectomy was available. Results: In a multivariable logistic regression analysis, extra capsular penetration, high Gleason score, and involvement of the lymph nodes, seminal vesicles, or surgical margin were associated with an increased risk of recurrence. In addition, samples with methylation of 2 specific genes involved in cell-cell adhesion and apoptosis were associated with biochemical recurrence with an odds ratio of 5.64 (95% CI=1.47–21.7, p=0.012) compared to samples without methylation of both of these genes. The methylation status of these 2 genes had a higher sensitivity (72.3%; 95% CI=57–84.4%) for detecting recurrences than all the clinico-pathological variables (p<0.02) except extra-capsular penetration (p=0.346). The methylation status of these 2 genes had a similar negative predictive value (79.0%; 95% CI=66.8–88.3%) as the individual clinico-pathological variables examined. Conclusion: DNA Methylation of specific genes is independently associated with an increased risk of biochemical recurrence after radical prostatectomy even one considers the prognostic clinico-pathologic variables used in the clinic today. Our findings should be validated on another larger group of patients with prostate cancer who have undergone radical prosatetectomies. No significant financial relationships to disclose.

P1052EXPANDED HEMODIALYSIS (HDX) DOES NOT AFFECT EPIGENETIC INTERCELLULAR SIGNALS INVOLVED IN INFLAMMATION AND CARDIOVASCULAR DISEASE

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Carmen Vida ◽  
Matilde Alique ◽  
Patricia De Sequera Ortiz ◽  
Guillermo Bodega ◽  
Carlos Oliva ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Status ◽  
Control Group ◽  
Dialysis Session ◽  
Plasma Dna ◽  
Methylated Dna ◽  
Dna And Rna ◽  
Before And After ◽  
Dialysis Membranes ◽  
And Control

Abstract Background and Aims Epigenetic signals play a principal role in homeostasis, but also may promote diseases including cardiovascular diseases (CVDs) when are altered. Extracellular vesicles (EVs) or plasma circulating DNA and RNA may have relevant functions in both physiological and pathophysiological contexts related to the epigenetic intercellular communication. Thus, changes in the endothelial or platelet EVs, or the plasma circulating methylated DNA may contribute to the chronic inflammation and the subsequent CVDs in chronic kidney disease patients, particularly when are in hemodialysis (HD). Dialysis membranes do not usually allow the passage of molecules larger than 30-40 kDa. However, the new system of expanded hemodialysis (HDx) with a medium-cut-off membrane (MCO), due to its characteristics, could alter the plasma content of these EVs and DNA methylation, and thereby, promote the development of CVDs. Therefore, our study evaluates whether global plasma DNA methylation and EVs content are modified during an HDx session. Method For this study, we selected 12 dialysis patients: HDx patients (n=6; dialyzed with MCO) and control group (n=6; dialyzed with other HD membranes). Before and after a dialysis session, plasma samples were obtained. EVs were isolated by ultracentrifugation, and the total number of EVs and platelet and endothelial-derived EVs were characterized and quantified by flow cytometry. RNA and DNA extraction and quantification were carried out using different kits and NanoDrop spectrophotometer. DNA methylation was assessed with a 5-methyl cytosine (5-mC) DNA assay kit. Results As shown in the figure, after a dialysis session with the HDx, no significant differences were observed in the total number of EVs, as well in the number of platelet- and endothelial-derived EVs, in comparison to those observed in HDx patients before the dialysis session. By contrast, patients dialyzed with other HD membranes presented differences in the number of total EVs and platelet and endothelial EVs, which decreased significantly (p&lt;0.05) after the dialysis session. Concerning DNA methylation, no statistically significant changes in total DNA 5-mC (%) were observed in both HDx and control patients after the dialysis session. However, a slight tendency to decrease methylated DNA was observed with the HDx compared to other HD membranes (control). Moreover, no significant changes in DNA and RNA % were observed after dialysis session in both HDx and control group. Conclusion To our knowledge, this is the first study to investigate the influence of the HDx technique on the content of plasma cellular EVs and DNA methylation status. HDx does not affect EVs levels, although it shows a tendency to purify plasma methylated DNA. Although this study was not designed to analyze the comparative effectiveness between different membranes, interestingly this effect in epigenetic signals was not observed with other HD membranes, where patients showed a marked reduction of EVs content. The differential activity of HDx about other HD membranes deserves further investigation. Funding (PI17/01029; PI19/00240; ISCIII-FEDER). Santander/UCM PR41/17-20964. Spanish Society of Nephrology 2018. UAH-GP2018-4

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