Journal articles: 'Peripheral blood mononuclear cells methylation'

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Zhu, Hong, Long-Fei Wu, Xing-Bo Mo, Xin Lu, Hui Tang, Xiao-Wei Zhu, Wei Xia, et al. "Rheumatoid arthritis–associated DNA methylation sites in peripheral blood mononuclear cells." Annals of the Rheumatic Diseases 78, no. 1 (October 8, 2018): 36–42. http://dx.doi.org/10.1136/annrheumdis-2018-213970.

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ObjectivesTo identify novel DNA methylation sites significant for rheumatoid arthritis (RA) and comprehensively understand their underlying pathological mechanism.MethodsWe performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood mononuclear cells from RA patients and health controls; (2) correlation analysis and causal inference tests for DNA methylation and mRNA expression data; (3) differential methylation genes regulatory network construction; (4) validation tests of 10 differential methylation positions (DMPs) of interest and corresponding gene expressions; (5) correlation between PARP9 methylation and its mRNA expression level in Jurkat cells and T cells from patients with RA; (6) testing the pathological functions of PARP9 in Jurkat cells.ResultsA total of 1046 DNA methylation positions were associated with RA. The identified DMPs have regulatory effects on mRNA expressions. Causal inference tests identified six DNA methylation–mRNA–RA regulatory chains (eg, cg00959259-PARP9-RA). The identified DMPs and genes formed an interferon-inducible gene interaction network (eg, MX1, IFI44L, DTX3L and PARP9). Key DMPs and corresponding genes were validated their differences in additional samples. Methylation of PARP9 was correlated with mRNA level in Jurkat cells and T lymphocytes isolated from patients with RA. The PARP9 gene exerted significant effects on Jurkat cells (eg, cell cycle, cell proliferation, cell activation and expression of inflammatory factor IL-2).ConclusionsThis multistage study identified an interferon-inducible gene interaction network associated with RA and highlighted the importance of PARP9 gene in RA pathogenesis. The results enhanced our understanding of the important role of DNA methylation in pathology of RA.

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Zhao, M., F. Gao, X. Wu, J. Tang, and Q. Lu. "Abnormal DNA methylation in peripheral blood mononuclear cells from patients with vitiligo." British Journal of Dermatology 163, no. 4 (June 19, 2010): 736–42. http://dx.doi.org/10.1111/j.1365-2133.2010.09919.x.

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Di Francesco, Andrea, Beatrice Arosio, Anastasia Falconi, Maria Vittoria Micioni Di Bonaventura, Mohsen Karimi, Daniela Mari, Martina Casati, Mauro Maccarrone, and Claudio D’Addario. "Global changes in DNA methylation in Alzheimer’s disease peripheral blood mononuclear cells." Brain, Behavior, and Immunity 45 (March 2015): 139–44. http://dx.doi.org/10.1016/j.bbi.2014.11.002.

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Kitkumthorn, Nakarin, Time Tuangsintanakul, Prakasit Rattanatanyong, Danai Tiwawech, and Apiwat Mutirangura. "LINE-1 methylation in the peripheral blood mononuclear cells of cancer patients." Clinica Chimica Acta 413, no. 9-10 (May 2012): 869–74. http://dx.doi.org/10.1016/j.cca.2012.01.024.

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Delgado-Cruzata, Lissette, Neomi Vin-Raviv, Parisa Tehranifar, Julie Flom, Diane Reynolds, Karina Gonzalez, Regina M. Santella, and Mary Beth Terry. "Correlations in global DNA methylation measures in peripheral blood mononuclear cells and granulocytes." Epigenetics 9, no. 11 (November 2, 2014): 1504–10. http://dx.doi.org/10.4161/15592294.2014.983364.

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Tseng, Lin, Lin, Li, Yen, Chan, Tsai, et al. "Next-Generation Sequencing Profiles of the Methylome and Transcriptome in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis." Journal of Clinical Medicine 8, no. 9 (August 22, 2019): 1284. http://dx.doi.org/10.3390/jcm8091284.

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Using next-generation sequencing to decipher methylome and transcriptome and underlying molecular mechanisms contributing to rheumatoid arthritis (RA) for improving future therapies, we performed methyl-seq and RNA-seq on peripheral blood mononuclear cells (PBMCs) from RA subjects and normal donors. Principal component analysis and hierarchical clustering revealed distinct methylation signatures in RA with methylation aberrations noted across chromosomes. Methylation alterations varied with CpG features and genic characteristics. Typically, CpG islands and CpG shores were hypermethylated and displayed the greatest methylation variance. Promoters were hypermethylated and enhancers/gene bodies were hypomethylated, with methylation variance associated with expression variance. RA genetically associated genes preferentially displayed differential methylation and differential expression or interacted with differentially methylated and differentially expressed genes. These differentially methylated and differentially expressed genes were enriched with several signaling pathways and disease categories. 10 genes (CD86, RAB20, XAF1, FOLR3, LTBR, KCNH8, DOK7, PDGFA, PITPNM2, CELSR1) with concomitantly differential methylation in enhancers/promoters/gene bodies and differential expression in B cells were validated. This integrated analysis of methylome and transcriptome identified novel epigenetic signatures associated with RA and highlighted the interaction between genetics and epigenetics in RA. These findings help our understanding of the pathogenesis of RA and advance epigenetic studies in regards to the disease.

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Calabrese, Roberta, Michele Zampieri, Rosella Mechelli, Viviana Annibali, Tiziana Guastafierro, Fabio Ciccarone, Giulia Coarelli, Renato Umeton, Marco Salvetti, and Paola Caiafa. "Methylation-dependent PAD2 upregulation in multiple sclerosis peripheral blood." Multiple Sclerosis Journal 18, no. 3 (August 30, 2011): 299–304. http://dx.doi.org/10.1177/1352458511421055.

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Background: Peptidylarginine deiminase 2 (PAD2) and peptidylarginine deiminase 4 (PAD4) are two members of PAD family which are over-expressed in the multiple sclerosis (MS) brain. Through its enzymatic activity PAD2 converts myelin basic protein (MBP) arginines into citrullines – an event that may favour autoimmunity – while peptidylarginine deiminase 4 (PAD4) is involved in chromatin remodelling. Objectives: Our aim was to verify whether an altered epigenetic control of PAD2, as already shown in the MS brain, can be observed in peripheral blood mononuclear cells (PBMCs) of patients with MS since some of these cells also synthesize MBP. Methods: The expression of most suitable reference genes and of PAD2 and PAD4 was assessed by qPCR. Analysis of DNA methylation was performed by bisulfite method. Results: The comparison of PAD2 expression level in PBMCs from patients with MS vs. healthy donors showed that, as well as in the white matter of MS patients, the enzyme is significantly upregulated in affected subjects. Methylation pattern analysis of a CpG island located in the PAD2 promoter showed that over-expression is associated with promoter demethylation. Conclusion: Defective regulation of PAD2 in the periphery, without the immunological shelter of the blood–brain barrier, may contribute to the development of the autoimmune responses in MS.

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Mahurkar, S., C. Polytarchou, D. Iliopoulos, C. Pothoulakis, E. A. Mayer, and L. Chang. "Genome-wide DNA methylation profiling of peripheral blood mononuclear cells in irritable bowel syndrome." Neurogastroenterology & Motility 28, no. 3 (December 16, 2015): 410–22. http://dx.doi.org/10.1111/nmo.12741.

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Lu, Yi‐Hua, Bing‐Hua Wang, Fei Jiang, Xing‐Bo Mo, Long‐Fei Wu, Pei He, Xin Lu, Fei‐Yan Deng, and Shu‐Feng Lei. "Multi‐omics integrative analysis identified SNP‐methylation‐mRNA: Interaction in peripheral blood mononuclear cells." Journal of Cellular and Molecular Medicine 23, no. 7 (May 20, 2019): 4601–10. http://dx.doi.org/10.1111/jcmm.14315.

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Kulakova, O. G., M. R. Kabilov, L. V. Danilova, E. V. Popova, O. A. Baturina, E. Yu Tsareva, N. M. Baulina, et al. "Whole-Genome DNA Methylation Analysis of Peripheral Blood Mononuclear Cells in Multiple Sclerosis Patients with Different Disease Courses." Acta Naturae 8, no. 3 (September 15, 2016): 103–10. http://dx.doi.org/10.32607/20758251-2016-8-3-103-110.

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Multiple sclerosis (MS) is a severe neurodegenerative disease of polygenic etiology affecting the central nervous system. In addition to genetic factors, epigenetic mechanisms, primarily DNA methylation, which regulate gene expression, play an important role in MS development and progression. In this study, we have performed the first whole-genome DNA methylation profiling of peripheral blood mononuclear cells in relapsing-remitting MS (RRMS) and primary-progressive MS (PPMS) patients and compared them to those of healthy individuals in order to identify the differentially methylated CpG-sites (DMSs) associated with these common clinical disease courses. In addition, we have performed a pairwise comparison of DNA methylation profiles in RRMS and PPMS patients. All three pairwise comparisons showed significant differences in methylation profiles. Hierarchical clustering of the identified DMS methylation levels and principal component analysis for data visualization demonstrated a clearly defined aggregation of DNA samples of the compared groups into separate clusters. Compared with the control, more DMSs were identified in PPMS patients than in RRMS patients (67 and 30, respectively). More than half of DMSs are located in genes, exceeding the expected number for random distribution of DMSs between probes. RRMS patients mostly have hypomethylated DMSs, while in PPMS patients DMSs are mostly hypermethylated. CpG-islands and CpG-shores contain 60% of DMSs, identified by pairwise comparison of RRMS and control groups, and 79% of those identified by pairwise comparison of PPMS and control groups. Pairwise comparison of patients with two clinical MS courses revealed 51 DMSs, 82% of which are hypermethylated in PPMS. Overall, it was demonstrated that there are more changes in the DNA methylation profiles in PPMS than in RRMS. The data confirm the role of DNA methylation in MS development. We have shown, for the first time, that DNA methylation as an epigenetic mechanism is involved in the formation of two distinct clinical courses of MS: namely, RRMS and PPMS.

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GONCHAROVA, T. G., D. R. KAIDAROVA, R. E. KADYRBAYEVA, M. G. ORAZGALIEVA, D. G. ADILBAY, D. CHEISHVILI, F. VAISHEVA, and M. SZYF. "Early diagnostic of lung cancer based on methylation of mononuclear cell fraction: Method development." Oncologia i radiologia Kazakhstana 57, no. 3 (September 30, 2020): 11–16. http://dx.doi.org/10.52532/2663-4864-2020-3-57-11-16.

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Relevance: According to the International Agency for Research on Cancer (IARС), lung cancer (LC) today ranks first in cancer incidence worldwide [1]. In the Republic of Kazakhstan, about 3800 new cases of LC and more than 2000 deaths from LC are registered each year (one-year mortality exceeds 49.4%) [2]. This supports the relevance of early LC diagnostics. The study of DNA methylation in human peripheral blood mononuclear cells (PBMC) suggests its use as an early diagnostic and prognostic marker for LC before detecting a malignant neoplasm by visual diagnostic methods. The purpose of the study was to find specific diagnostic and prognostic markers by DNA methylation profiling of PBMC in patients with LC. Results: Methylation markers of blood mononuclear fraction were detected in CG islets associated with genes ICAM5, mir138, SYNE1, and KLK4 in 97% of plasma samples from patients with LC and were absent in healthy people. The usability of these markers to differentiate LC from 16 other cancers using NCBI GEO and TCGA methylation data was demonstrated with a specificity level of 0.96 and a sensitivity of 0.84. Conclusion: The specificity and sensitivity of the method of LC early diagnostics and prognosis based on the methylation of blood mononuclear cells (detection of methylation of CG islets associated with the ICAM5, mir138, SYNE1, and KLK4 genes in PBMC) are enough to use it in screening for LC.

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Hasselbalch, Hans Carl, Helene Myrtue Nielsen, Fazila Asmar, Christen Lykkegaard Andersen, Lasse Sommer Kristensen, Kruse A. Torben, Mads Thomassen, et al. "DNA Methylation Profiling of Sorted Cells from Myelofibrosis Patients reveals Aberrant Epigenetic Regulation of Immune Pathways and identifies Early MPN Driver Genes." Blood 124, no. 21 (December 6, 2014): 4576. http://dx.doi.org/10.1182/blood.v124.21.4576.4576.

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Abstract Introduction: Primary myelofibrosis (PMF) belongs to the heterogeneous group of chronic myeloproliferative neoplasms (MPN) together with essential thrombocytosis (ET) and polycythemia vera (PV). It has been suggested that these neoplasms represent a biological continuum from early cancer stage (ET,PV) to advanced MF. Multiple studies report frequent mutations in epigenetic regulators. However, the association to epigenetic changes and the role of epigenetic aberrations in different cell populations is still unknown. We therefore performed DNA methylation profiling of sorted cells from MF patients to unravel pathways contributing to disease phenotype and gain insight into MF pathogenesis. As an aberrant DNA methylation pattern may be an early event in tumorigenesis and may be crucial for progression of the malignant clone towards the more aggressive forms of MPN, we further aimed to identify methylated candidate driver genes. Material and methods: Peripheral blood samples from 16 MF patients were together with BM (bone marrow) and peripheral blood from 3 healthy age matched controls sorted in CD34+ cells, granulocytes and mononuclear cells, and analysed for differential methylated regions using Illumina Infinium HumanMethylation 450K BeadChip. Candidate genes were validated by pyrosequencing in a second cohort of 30 MF patients. To identify potential driver genes the DNA methylation status of candidate genes were likewise analyzed in a larger cohort consisting of 60 ET and PV patients. Results: The number of differential methylated CpG sites between MF cells and the healthy counterparts differed extensively among the three cell populations analyzed. In MF CD34+ cells 1628 CpG sites were differential methylated compared to normal CD34+ cells, and 519 and 213 differential methylated CpG sites were observed in MF granulocytes and MF mononuclear cells, respectively (Δβ was set to 0.2 with an adjusted p-value < 0.05, T-test). Differentially methylated genes were mainly involved in cancer and embryogenic pathways in both the MF CD34+ and mononuclear cells, while mononuclear cells also showed aberrant methylation of genes involved in the inflammatory disease pathways. MF granulocytes showed significant aberrations in pathways involving immunological diseases, cell death and survival. Candidate genes have been identified and validation is ongoing. Interestingly, a gradual increase of the DNA methylation level of TRIM59 was observed from the healthy controls (31%) over ET (53%) to PV (64%) and MF (65%). ET patients could be distinguished from both healthy controls (P= 0.0004, Mann-Whitney test) and from the more progressed stages PV and MF (P=0.0132, Mann-Whitney test) based on the TRIM59 DNA methylation level. TRIM59 promoter methylation could, however, not discriminate between PV and MF (P=0.4721, Mann-Whitney test). Conclusion: Genome-wide DNA methylation profiling of sorted MF blood cells provided an exclusive insight into which pathways that are contributing to MF disease phenotype at a cell specific level. The MF CD34+ cells had the highest number of differential methylated CpG sites (n=1628) when comparing to granulocytes (n=519) and mononuclear cells (n=213) and should be cells of choice when exploring new treatment strategies. Interestingly, the mononuclear compartment show aberrant methylation of inflammatory genes supporting a role of aberrant immune regulation in the pathogenesis of MPN. Earlier studies have failed to identify aberrant methylation in early ET and PV, however, the preliminary data on the methylation of individual genes (TRIM59 promoter methylation) shows that it might be possible to identify early driver genes, and that it may be possible to select a panel of genes that can discriminate early MPN from the late MF stage. Disclosures No relevant conflicts of interest to declare.

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Feng, Wen, Lei Zhou, Haifei Wang, Zhengzheng Hu, Xiaomei Wang, Jianlian Fu, Aiguo Wang, and Jian‐Feng Liu. "Functional analysis of DNA methylation of the PACSIN1 promoter in pig peripheral blood mononuclear cells." Journal of Cellular Biochemistry 120, no. 6 (December 9, 2018): 10118–27. http://dx.doi.org/10.1002/jcb.28295.

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Deguchi, Yasahiro, Shigeru Negoro, and Susumu Kishimoto. "Methylation of c-myc gene changes in human lymphoproliferative diseases." Bioscience Reports 7, no. 8 (August 1, 1987): 637–43. http://dx.doi.org/10.1007/bf01127676.

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The degree of methylation at the c-myc proto-oncogene was found to change in human lymphoproliferative diseases, when examined using a methylation-sensitive restriction enzyme. In peripheral blood mononuclear cells (PBMC) c-myc DNA showed hypomethylation in human lymphoproliferative diseases, in comparison to normal subjects matched in age and sex. In cases of chronic lymphocytic leukemia (CLL), the change was amplified in the crisis. When the DNA was examined at the actin gene, no significant change was observed. The results suggest that the change in c-myc proto-oncogene methylation might become an important clue in understanding the relationship between levels of gene expression and methylation in human lymphoproliferative diseases.

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Tsuboi, Yoshiki, Hiroya Yamada, Eiji Munetsuna, Ryosuke Fujii, Mirai Yamazaki, Yoshitaka Ando, Genki Mizuno, et al. "Global DNA hypermethylation in peripheral blood mononuclear cells and cardiovascular disease risk: a population-based propensity score-matched cohort study." Journal of Epidemiology and Community Health 75, no. 9 (March 25, 2021): 890–95. http://dx.doi.org/10.1136/jech-2020-215382.

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BackgroundDNA methylation plays an important role in the pathogenesis and progression of cardiovascular disease (CVD) but the prospective association of DNA methylation with CVD has not been evaluated. Here, we conducted a prospective study to examine whether long interspersed nuclear element-1 (LINE-1) DNA methylation is associated with CVD mortality in a Japanese population.MethodsWe targeted 822 Japanese who participated in a health check-up in 1990 and had no clinical history of cancer, stroke or ischaemic heart disease. DNA was extracted from peripheral blood mononuclear cells and LINE-1 DNA methylation at three CpG sites was measured using a pyrosequencing method. We used propensity score (PS) matching to reduce the effect of potential confounding.ResultsDuring 18 118.7 persons-years of follow-up, there were 329 deaths from all-causes and 85 deaths from CVD. In PS-matched analysis, a significantly higher HR for CVD mortality was observed in the hypermethylation group than in the hypomethylation group for elderly participants (HR 2.77; 95% CI 1.55 to 4.93). No significant association between LINE-1 DNA methylation and CVD was observed for middle-aged participants.ConclusionsBased on this prospective study, we suggest that LINE-1 DNA hypermethylation is associated with increased CVD mortality risk in an elderly population.

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Zhao, Ning-Hui, Yu Qian, Chen-Si Wu, Jing-Wen Wang, Yu Fang, Xiao-Peng Fan, Shuai Gao, Yu-Chen Fan, and Kai Wang. "Diagnostic value of NKG2D promoter methylation in hepatitis B virus-associated hepatocellular carcinoma." Biomarkers in Medicine 13, no. 13 (September 2019): 1093–105. http://dx.doi.org/10.2217/bmm-2019-0102.

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Aim: Natural killer cell receptor group 2D (NKG2D) plays an important role in the immune regulation of tumors. We speculate that DNA methylation are involved in the regulation of NKG2D gene. Methods: We investigated the methylation status of the NKG2D promoter in peripheral blood mononuclear cells of hepatocellular carcinoma (HCC) patients, chronic hepatitis B patients and healthy controls by methylation-specific PCR and the mRNA expression level was examined by real-time quantitative PCR. Results: The methylation frequency of NKG2D promoter in HCC patients was higher than that of chronic hepatitis B patients and healthy controls. NKG2D promoter methylation has a good predictive value for HCC diagnosis. Conclusion: NKG2D promoter methylation can be used as a noninvasive marker for detecting HCC.

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Boltz, Valerie F., Cristina Ceriani, Jason W. Rausch, Wei Shao, Michael J. Bale, Brandon F. Keele, Rebecca Hoh, et al. "CpG Methylation Profiles of HIV-1 Proviral DNA in Individuals on ART." Viruses 13, no. 5 (April 29, 2021): 799. http://dx.doi.org/10.3390/v13050799.

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The latent HIV-1 reservoir is comprised of stably integrated and intact proviruses with limited to no viral transcription. It has been proposed that latent infection may be maintained by methylation of pro-viral DNA. Here, for the first time, we investigate the cytosine methylation of a replication competent provirus (AMBI-1) found in a T cell clone in a donor on antiretroviral therapy (ART). Methylation profiles of the AMBI-1 provirus were compared to other proviruses in the same donor and in samples from three other individuals on ART, including proviruses isolated from lymph node mononuclear cells (LNMCs) and peripheral blood mononuclear cells (PBMCs). We also evaluated the apparent methylation of cytosines outside of CpG (i.e., CpH) motifs. We found no evidence for methylation in AMBI-1 or any other provirus tested within the 5′ LTR promoter. In contrast, CpG methylation was observed in the env-tat-rev overlapping reading frame. In addition, we found evidence for differential provirus methylation in cells isolated from LNMCs vs. PBMCs in some individuals, possibly from the expansion of infected cell clones. Finally, we determined that apparent low-level methylation of CpH cytosines is consistent with occasional bisulfite reaction failures. In conclusion, our data do not support the proposition that latent HIV infection is associated with methylation of the HIV 5′ LTR promoter.

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McEwen, Lisa M., Evan G. Gatev, Meaghan J. Jones, Julia L. MacIsaac, Megan M. McAllister, Rebecca E. Goulding, Kenneth M. Madden, Martin G. Dawes, Michael S. Kobor, and Maureen C. Ashe. "DNA methylation signatures in peripheral blood mononuclear cells from a lifestyle intervention for women at midlife: a pilot randomized controlled trial." Applied Physiology, Nutrition, and Metabolism 43, no. 3 (March 2018): 233–39. http://dx.doi.org/10.1139/apnm-2017-0436.

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Physical activity confers many health benefits, but the underlying mechanisms require further exploration. In this pilot randomized controlled trial we tested the association between longitudinal measures of DNA methylation and changes in objective measures, including physical activity, weight loss, and C-reactive protein levels in community-dwelling women aged 55 to 70 years. We assessed DNA methylation from 20 healthy postmenopausal women, who did not have a mobility disability and allocated them to a group-based intervention, Everyday Activity Supports You, or a control group (monthly group-based health-related education sessions). The original randomized controlled trial was 6 months in duration and consisted of nine 2-h sessions that focused on reducing sedentary behaviour for the intervention group, or six 1-h sessions that focused on other topics for the control group. We collected peripheral blood mononuclear cells, both at baseline and 6 months later. Samples were processed using the Illumina 450k Methylation array to quantify DNA methylation at >485 000 CpG sites in the genome. There were no significant associations between DNA methylation and physical activity, but we did observe alterations at epigenetic modifications that correlated with change in percent body weight over a 6-month period at 12 genomic loci, 2 of which were located near the previously reported weight-associated genes RUNX3 and NAMPT. We also generated a potential epigenetic predictor of weight loss using baseline DNA methylation at 5 CpG sites. These exploratory findings suggest a potential biological link between body weight changes and epigenetic processes.

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Jafarpour, Sima, Farideh Saberi, Maryam Yazdi, Reza Nedaeinia, Guilda Amini, Gordon A. Ferns, and Rasoul Salehi. "Association between colorectal cancer and the degree of ITGA4 promoter methylation in peripheral blood mononuclear cells." Gene Reports 27 (June 2022): 101580. http://dx.doi.org/10.1016/j.genrep.2022.101580.

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Dogan, Meeshanthini V., Bridget Shields, Carolyn Cutrona, Long Gao, Frederick X. Gibbons, Ronald Simons, Martha Monick, et al. "The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women." BMC Genomics 15, no. 1 (2014): 151. http://dx.doi.org/10.1186/1471-2164-15-151.

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Kwiatkowska, Marta, Edyta Reszka, Katarzyna Woźniak, Ewa Jabłońska, Jaromir Michałowicz, and Bożena Bukowska. "DNA damage and methylation induced by glyphosate in human peripheral blood mononuclear cells ( in vitro study)." Food and Chemical Toxicology 105 (July 2017): 93–98. http://dx.doi.org/10.1016/j.fct.2017.03.051.

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Li, Yinghua, Hirokazu Nagai, Toshihito Ohno, Masaaki Yuge, Sonoko Hatano, Etsuro Ito, Naoyoshi Mori, Hidehiko Saito, and Tomohiro Kinoshita. "Aberrant DNA methylation ofp57KIP2 gene in the promoter region in lymphoid malignancies of B-cell phenotype." Blood 100, no. 7 (October 1, 2002): 2572–77. http://dx.doi.org/10.1182/blood-2001-11-0026.

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The cyclin-dependent kinase inhibitorp57KIP2 is thought to be a potential tumor suppressor gene (TSG). The present study examines this possibility. We found that the expression ofp57KIP2 gene is absent in various hematological cell lines. Exposing cell lines to the DNA demethylating agent 5-aza-2′-deoxycytidine restoredp57KIP2 gene expression. Bisulfite sequencing analysis of its promoter region showed thatp57KIP2 DNA was completely methylated in cell lines that did not express thep57KIP2 gene. Thus, DNA methylation of its promoter might lead to inactivation of thep57KIP2 gene. DNA methylation of this region is thought to be an aberrant alteration, since DNA was not methylated in normal peripheral blood mononuclear cells or in reactive lymphadenitis. Methylation-specific polymerase chain reaction analysis found frequent DNA methylation of thep57KIP2 gene in primary diffuse large B-cell lymphoma (54.9%) and in follicular lymphoma (44.0%), but methylation was infrequent in myelodysplastic syndrome and adult T-cell leukemia (3.0% and 2.0%, respectively). These findings directly indicate that the profile of the p57KIP2gene corresponds to that of a TSG.

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Chen, Xinchun, JiaLou Zhu, Chuanzhi Zhu, Fei Gao, and Yi Cai. "PGAM1 hypomethylation drives aerobic glycolysis in CD4 T cells to facilitate the host defense against tuberculosis." Journal of Immunology 202, no. 1_Supplement (May 1, 2019): 122.6. http://dx.doi.org/10.4049/jimmunol.202.supp.122.6.

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Abstract Background DNA methylation is important epigenetic mechanism that mediates cellular development and function, but whether DNA methylation is involved in regulating CD4 T cells in the context of tuberculosis (TB) is unclear. Results We used oxidative bisulfite sequencing to measure global DNA methylation levels in isolated CD4 T cells from patients with tuberculous pleuritis (TP), latent TB infection (LTBI) and healthy controls (HC). Compared to peripheral blood mononuclear cells (PBMCs), CD4 T cells from pleural fluid mononuclear cells (PFMCs) showed a significant different global DNA methylation profile, with much lower 5-methylcytosine levels in PFMC. A signature of 376 differentially methylated regions could discriminate between TP PBMC and PFMC T cells, including hypermethylated LAPTM5, FAM134B and FOXP1, and hypomethylated CCL5, TNF and AIM2 in PFMCs. KEGG pathway analysis showed that numerous metabolic pathways, especially ‘Carbon metabolism’, were highly enriched among the differentially methylated genes with lower methylation levels in TP PFMCs. Hypomethylation of the glycolytic enzyme PGAM1 promoted gene expression and increased aerobic glycolysis in CD4 T cells to permit CD4 T-cell proliferation and effector function. Conclusions Diminished DNA methylation levels —especially in genes involved in metabolism —are an important CD4 T-cell signature at the site of infection in TB. DNA hypomethylation of PGAM1is critical mechanism in regulating the CD4 T-cell immune response by enhancing aerobic glycolysis. These findings provide novel insights into the epigenetic regulation of CD4 T-cell responses and identify potential targets for immunotherapy in TB.

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Sung, Wan-Yu, Yuan-Zhao Lin, Daw-Yang Hwang, Chia-Hui Lin, Ruei-Nian Li, Chia-Chun Tseng, Cheng-Chin Wu, Tsan-Teng Ou, and Jeng-Hsien Yen. "Methylation of TET2 Promoter Is Associated with Global Hypomethylation and Hypohydroxymethylation in Peripheral Blood Mononuclear Cells of Systemic Lupus Erythematosus Patients." Diagnostics 12, no. 12 (December 1, 2022): 3006. http://dx.doi.org/10.3390/diagnostics12123006.

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(1) Background: It is widely accepted that aberrant methylation patterns contribute to the development of systemic lupus erythematosus (SLE). Ten–eleven translocation (TET) methylcytosine dioxygenase is an essential enzyme of which there are three members, TET1, 2, and 3, involved in hydroxymethylation, a newly uncovered mechanism of active DNA methylation. The epigenomes of gene transcription are regulated by 5-hydroxymethylcytocine (5-hmC) and TETs, leading to dysregulation of the immune system in SLE. The purpose of this study was to investigate the global hydroxymethylation status in SLE peripheral blood mononuclear cells (PBMCs) and to explore the role of TETs in changing the patterns of methylation. (2) Methods: We collected PBMCs from 101 SLE patients and 100 healthy donors. TaqMan real-time polymerase chain-reaction assay was performed for the detection of 5-methylcytosine (5-mC), 5-hmC, and TET2 mRNA expression and single-nucleotide polymorphism genotyping. The methylation rates in different CpG sites of TET2 promoters were examined using next-generation sequencing-based deep bisulfite sequencing. Putative transcription factors were investigated using the UCSC Genome Browser on the Human Dec. 2013 (GRCh38/hg38) Assembly. (3) Results: 5-mC and 5-hmC were both decreased in SLE. The mRNA expression level of TET2 was notably high and found to be correlated with the levels of immunologic biomarkers that are indicative of SLE disease activity. The analysis of methylation rates in the TET2 promoter revealed that SLE patients had significantly higher and lower rates of methylation in TET2 105146072-154 and TET2 105146218-331, respectively. (4) Conclusions: TET2 may play an important role in 5-mC/5-hmC dynamics in the PBMCs of SLE patients. The epigenetic modification of TET2 promoters could contribute to the pathogenesis of SLE and the intensity of the immunologic reaction.

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Schenk, Alexander, Christine Koliamitra, Claus Jürgen Bauer, Robert Schier, Michal R. Schweiger, Wilhelm Bloch, and Philipp Zimmer. "Impact of Acute Aerobic Exercise on Genome-Wide DNA-Methylation in Natural Killer Cells—A Pilot Study." Genes 10, no. 5 (May 19, 2019): 380. http://dx.doi.org/10.3390/genes10050380.

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Natural Killer (NK-) cells reveal a keen reaction to acute bouts of exercise, including changes of epigenetic modifications. So far, exercise-induced alterations in NK-cell DNA-methylation were shown for single genes only. Studies analyzing genome-wide DNA-methylation have used conglomerates like peripheral blood mononuclear cells (PBMCs) rather than specific subsets of immune cells. Therefore, the aim of this pilot-study was to generate first insights into the influence of a single bout of exercise on genome-wide DNA-methylation in isolated NK-cells to open the field for such analyses. Five healthy women performed an incremental step test and blood samples were taken before and after exercise. DNA was isolated from magnet bead sorted NK-cells and further analyzed for global DNA-methylation using the Infinium MethylationEPIC BeadChip. DNA-methylation was changed at 33 targets after acute exercise. These targets were annotated to 25 genes. Of the targets, 19 showed decreased and 14 increased methylation. The 25 genes with altered DNA-methylation have different roles in cell regulation and differ in their molecular functions. These data give new insights in the exercise induced regulation of NK-cells. By using isolated NK-cells, exercise induced differences in DNA-methylation could be shown. Whether or not these changes lead to functional adaptions needs to be elucidated.

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Esposito, Elisa A., Meaghan J. Jones, Jenalee R. Doom, Julia L. MacIsaac, Megan R. Gunnar, and Michael S. Kobor. "Differential DNA methylation in peripheral blood mononuclear cells in adolescents exposed to significant early but not later childhood adversity." Development and Psychopathology 28, no. 4pt2 (February 5, 2016): 1385–99. http://dx.doi.org/10.1017/s0954579416000055.

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AbstractInternationally adopted adolescents who are adopted as young children from conditions of poverty and deprivation have poorer physical and mental health outcomes than do adolescents conceived, born, and raised in the United States by families similar to those who adopt internationally. Using a sample of Russian and Eastern European adoptees to control for Caucasian race and US birth, and nonadopted offspring of well-educated and well-resourced parents to control for postadoption conditions, we hypothesized that the important differences in environments, conception to adoption, might be reflected in epigenetic patterns between groups, specifically in DNA methylation. Thus, we conducted an epigenome-wide association study to compare DNA methylation profiles at approximately 416,000 individual CpG loci from peripheral blood mononuclear cells of 50 adopted youth and 33 nonadopted youth. Adopted youth averaged 22 months at adoption, and both groups averaged 15 years at testing; thus, roughly 80% of their lives were lived in similar circumstances. Although concurrent physical health did not differ, cell-type composition predicted using the DNA methylation data revealed a striking difference in the white blood cell-type composition of the adopted and nonadopted youth. After correcting for cell type and removing invariant probes, 30 CpG sites in 19 genes were more methylated in the adopted group. We also used an exploratory functional analysis that revealed that 223 gene ontology terms, clustered in neural and developmental categories, were significantly enriched between groups.

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Kraveishvili, Nino, Eka Kvaratskhelia, Sandro Surmava, Merab Kvintradze, Maia Zarandia, Tinatin Gorgiladze, and Elene Abzianidze. "DNA methylation status of interspersed repetitive sequences in patients with migraine." Journal of International Medical Research 51, no. 2 (February 2023): 030006052311521. http://dx.doi.org/10.1177/03000605231152109.

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Objective To analyse the methylation status of the Long Interspersed Nuclear Element-1 (LINE-1) and Short Interspersed Nuclear Element Alu (Alu) of peripheral blood mononuclear cells (PBMCs) from patients with migraine compared with healthy control subjects. Methods This case–control study recruited patients with migraine without aura and age-matched healthy control subjects. PBMCs were purified from peripheral blood samples. Methylation levels and patterns of LINE-1 and Alu sequences were evaluated using combined bisulfite restriction analysis-interspersed repetitive sequences polymerase chain reaction. Results A total of 84 patients with migraine and 82 age-matched healthy controls were enrolled in the study. High levels of unmethylated cytosines in both the LINE-1 and Alu repetitive elements were observed in the migraine group compared with the control subjects. In addition, a significant difference was detected in the methylation level of LINE-1 between TT and CC genotype groups of the methylenetetrahydrofolate reductase gene. Conclusions These results suggest that analysis of epigenetic biomarkers in PBMCs may help to identify patients at a higher risk of migraine development.

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Wang, Chuang-Ming, Chia-Bin Chang, Shiao-Pieng Lee, Michael W-Y Chan, and Shu-Fen Wu. "Differential DNA methylation profiles of peripheral blood mononuclear cells in allergic asthmatic children following dust mite immunotherapy." Journal of Microbiology, Immunology and Infection 53, no. 6 (December 2020): 986–95. http://dx.doi.org/10.1016/j.jmii.2020.06.004.

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Wang, GS, M. Zhang, XP Li, H. Zhang, W. Chen, M. Kan, and YM Wang. "Ultraviolet B exposure of peripheral blood mononuclear cells of patients with systemic lupus erythematosus inhibits DNA methylation." Lupus 18, no. 12 (September 17, 2009): 1037–44. http://dx.doi.org/10.1177/0961203309106181.

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Koos, Björn, Eva Lotta Moderegger, Katharina Rump, Hartmuth Nowak, Katrin Willemsen, Caroline Holtkamp, Patrick Thon, Michael Adamzik, and Tim Rahmel. "LPS-Induced Endotoxemia Evokes Epigenetic Alterations in Mitochondrial DNA That Impacts Inflammatory Response." Cells 9, no. 10 (October 13, 2020): 2282. http://dx.doi.org/10.3390/cells9102282.

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Mitochondrial DNA (mtDNA) plays a vital role as a damage-associated molecular pattern in sepsis being able to shape the immune response. Since pathogen recognition receptors of innate immune cells are activated by demethylated DNA only, we set out to investigate the amount of DNA methyltransferase 1 (DNMT1) in mitochondria and the extent of mtDNA methylation in a human endotoxin model. Peripheral blood mononuclear cells of 20 healthy individuals were isolated from whole blood and stimulated with lipopolysaccharide (LPS) for 48 h. Subsequently, DNMT1 protein abundance was assessed in whole cells and a mitochondrial fraction. At the same time, methylation levels of mtDNA were quantified, and cytokine expression in the supernatant was measured. Despite increased cellular expression of DNMT1 after LPS stimulation, the degree of mtDNA methylation slightly decreased. Strikingly the mitochondrial protein abundance of DNMT1 was reduced by 50% in line with the lower degree of mtDNA methylation. Although only modest alterations were seen in the degree of mtDNA methylation, these strongly correlated with IL-6 and IL-10 expression. Our data may hint at a protein import problem for DNMT1 into the mitochondria under LPS stimulation and suggest a role of demethylated mtDNA in the regulation of the inflammatory immune response.

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Bialek, Katarzyna, Piotr Czarny, Paulina Wigner, Ewelina Synowiec, Lukasz Kolodziej, Michal Bijak, Janusz Szemraj, Mariusz Papp, and Tomasz Sliwinski. "Agomelatine Changed the Expression and Methylation Status of Inflammatory Genes in Blood and Brain Structures of Male Wistar Rats after Chronic Mild Stress Procedure." International Journal of Molecular Sciences 23, no. 16 (August 11, 2022): 8983. http://dx.doi.org/10.3390/ijms23168983.

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The preclinical research conducted so far suggest that depression development may be influenced by the inflammatory pathways both at the periphery and within the central nervous system. Furthermore, inflammation is considered to be strongly connected with antidepressant treatment resistance. Thus, this study explores whether the chronic mild stress (CMS) procedure and agomelatine treatment induce changes in TGFA, TGFB, IRF1, PTGS2 and IKBKB expression and methylation status in peripheral blood mononuclear cells (PBMCs) and in the brain structures of rats. Adult male Wistar rats were subjected to the CMS and further divided into matched subgroups to receive vehicle or agomelatine. TaqMan gene expression assay and methylation-sensitive high-resolution melting (MS-HRM) were used to evaluate the expression of the genes and the methylation status of their promoters, respectively. Our findings confirm that both CMS and antidepressant agomelatine treatment influenced the expression level and methylation status of the promoter region of investigated genes in PBMCs and the brain. What is more, the present study showed that response to either stress stimuli or agomelatine differed between brain structures. Concluding, our results indicate that TGFA, TGFB, PTGS2, IRF1 and IKBKB could be associated with depression and its treatment.

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Treppendahl, Marianne B., Magnus Tobiasson, Anni Aggerholm, Mohsen Karimi, Trine Silkjaer, Lone S. Friis, Mette K. Andersen, et al. "Allelic Methylation Levels of VTRNA2-1 Predict Outcome in Higher Risk MDS Patients Not Treated by Azacytidine." Blood 120, no. 21 (November 16, 2012): 2394. http://dx.doi.org/10.1182/blood.v120.21.2394.2394.

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Abstract Abstract 2394 Introduction: We have recently shown that the allelic methylation level of the non-coding RNA, VTRNA2-1, predict outcome in acute myeloid leukemia (AML) (Treppendahl et al., 2012). VTRNA2-1 is located on chromosome 5q31.1, in the commonly deleted region for higher risk myelodysplastic syndrome (MDS) and de novo AML. Around 75% of the healthy Danish population carries a monoallelically methylated VTRNA2-1 promoter while the rest carries 2 unmethylated promoters. A hypermethylated promoter was only observed in patients. These interindividual differences in the methylation pattern are intriguing, and our data suggest that the gene dosage of this particular type of ncRNA may play an important role in tumor progression or response to therapy, since AML patients with hypomethylation of both alleles of the VTRNA2-1 promoter have a significantly better prognosis, while those with hypermethylation or loss of the second VTRNA2-1 copy have a poorer outcome(Treppendahl et al., 2012). Accordingly, we speculated if the allelic methylation levels of VTRNA2-1 also predict outcome in higher risk MDS patients. Methods: Bone marrow mononuclear cells from primary higher risk MDS patients (IPSS category INT2 and HIGH risk) and peripheral blood mononuclear cells, sampled during treatment with azacytidine, were analyzed for promoter methylation by pyrosequencing and methylation specific melting curve analysis. Results: Bone mononuclear cells from 57 higher risk MDS patients, never treated with azacytidine, were examined for VTRNA2-1 promoter methylation. 18 (32%) cases carried an unmethylated promoter (less than 15% methylation), 31 (54%) cases carried an intermediate methylated promoter (15–41% methylation) and 8 (14%) cases carried a hypermethylated promoter (more than 41% methylation). Patients with hypomethylation of the VTRNA2-1 promoter have a considerable better prognosis than those with intermediate or hypermethylation of the VTRNA2-1 promoter (P=0.026). Interestingly, in an azacytidine treated cohort the survival benefit of having an unmethylated promoter disappeared and a tendency towards a better survival of the methylated cases were observed (N=28, P=0.180).The in vivo effect of azacytidine on VTRNA2-1 methylation were examined in a small cohort of MDS patients (N=6), showing that azacytidine can induce demethylation of the VTRNA2-1 promoter in peripheral blood mononuclear cells. Discussion: Our studies show, that the allelic methylation of VTRNA2-1 can predict outcome, not only in AML patients, but also in higher risk MDS patients not treated with azacytidine. Patients with hypomethylation of the VTRNA2-1 promoter have a considerable better outcome than those with intermediate methylation or hypermethylation of the promoter. Interestingly, in the group of azacytidine treated patients there was no difference in survival between cases with and without methylation of the VTRNA2-1 promoter These data could indicate that patients with methylation of the VTRNA2-1 promoter might have a survival benefit of the azacytidine treatment. Thus we suggest that constitutive interindividual differences in the methylation of VTRNA2-1 potentially can be used as a pretreatment marker for selecting patients who will have a survival benefit of azacytidine treatment. This is to our best knowledge the first study identifying a potential epigenetic marker for selecting patients with benefit of treatment with azacytidine before treatment start. Our study is conducted in a quite heterogeneous and small patient cohort, and it has to be verified in a more homogenously treated larger group of MDS patients, ideally in a prospective clinical trial. Disclosures: No relevant conflicts of interest to declare.

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Li, Quanzhen, Honglin Zhu, Chengsong Zhu, Wentao Mi, Xiaoxia Zuo, and Hui Luo. "Integration of genome-wide transcriptome and DNA methylome uncovered aberrant methylation-regulated genes and pathways in the peripheral blood mononuclear cells of systemic sclerosis." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 45.28. http://dx.doi.org/10.4049/jimmunol.200.supp.45.28.

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Abstract Objectives To delineate the interaction network between gene transcription and DNA methylation in PBMC of systemic sclerosis (SSc) patients and to identify methylation-regulated genes which are involved in the pathogenesis of SSc. Methods Genome-wide transcriptome and DNA methylome were profiled on PBMC from 30 SSc patients and 30 matched normal controls (NC). Differential expressed genes (DEGs) and differential methylated positions (DMPs) were integratively analyzed to identify methylation-regulated genes and associated molecular pathways. Results Transcriptome profiling distinguished 453 DEGs in SSc. Global DNA methylation analysis identified 925 DMPs located on 618 genes. Integration of DEGs and DMPs revealed 20 DEGs containing inversely associated DMPs. These 20 potential methylation-regulated DEGs (MeDEGs), including 12 up-regulated genes (ELANE, CTSG, LTBR, C3AR1, CSTA, SPI1, ODF3B, SAMD4A, PLAUR, NFE2, ZYX and CTSZ) and 8 down-regulated genes (RUNX3, PRF1, PRKCH, PAG1, RASSF5, FYN, CXCR6 and F2R), are predominantly involved in the migration, proliferation, activation and inflammation of immune cells. Unsupervised cluster analysis of the top MeDEGs distinguished SSc from NC with 90% sensitivity and 87% specificity. 4 MeDEGs, F2R, FYN, PAG1 and PRKCH, exhibited significantly progressive decrease in SSc with interstitial lung disease (ILD) compared with SSc without ILD. Conclusion By integration of genome-wide transcriptome and DNA methylome, we identified differential expressed genes associated with aberrant DNA methylation in the PBMC of SSc. The epigenetically dysregulated genes may lead to the abnormal activation of immune regulatory pathways which may contribute to the pathogenesis of SSc.

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Alimam, Samah, William Villiers, Richard Dillon, Michael Simpson, Manohursingh Runglall, Alexander Smith, Prodromos Chatzikyriakou, et al. "Patients with triple-negative, JAK2V617F- and CALR-mutated essential thrombocythemia share a unique gene expression signature." Blood Advances 5, no. 4 (February 18, 2021): 1059–68. http://dx.doi.org/10.1182/bloodadvances.2020003172.

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Abstract Approximately 10% to 15% of patients with essential thrombocythemia (ET) lack the common driver mutations, so-called “triple-negative” (TN) disease. We undertook a systematic approach to investigate for somatic mutations and delineate gene expression signatures in 46 TN patients and compared the results to those with known driver mutations and healthy volunteers. Deep, error-corrected, next-generation sequencing of peripheral blood mononuclear cells using the HaloPlexHS platform and whole-exome sequencing was performed. Using this platform, 10 (22%) of 46 patients had detectable mutations (MPL, n = 6; JAK2V617F, n = 4) with 3 of 10 cases harboring germline MPL mutations. RNA-sequencing and DNA methylation analysis were also performed by using peripheral blood mononuclear cells. Pathway analysis comparing healthy volunteers and ET patients (regardless of mutational status) identified significant enrichment for genes in the tumor necrosis factor, NFκB, and MAPK pathways and upregulation of platelet proliferative drivers such as ITGA2B and ITGB3. Correlation with DNA methylation showed a consistent pattern of hypomethylation at upregulated gene promoters. Interrogation of these promoter regions highlighted enrichment of transcriptional regulators, which were significantly upregulated in patients with ET regardless of mutation status, including CEBPβ and NFκB. For “true” TN ET, patterns of gene expression and DNA methylation were similar to those in ET patients with known driver mutations. These observations suggest that the resultant ET phenotype may, at least in part and regardless of mutation type, be driven by transcriptional misregulation and may propagate downstream via the MAPK, tumor necrosis factor, and NFκB pathways with resultant JAK-STAT activation. These findings identify potential novel mechanisms of disease initiation that require further evaluation.

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Zhu, Honglin, Chengsong Zhu, Wentao Mi, Tao Chen, Hongjun Zhao, Xiaoxia Zuo, Hui Luo, and Quan-Zhen Li. "Integration of Genome-Wide DNA Methylation and Transcription Uncovered Aberrant Methylation-Regulated Genes and Pathways in the Peripheral Blood Mononuclear Cells of Systemic Sclerosis." International Journal of Rheumatology 2018 (September 2, 2018): 1–19. http://dx.doi.org/10.1155/2018/7342472.

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Objective. Systemic sclerosis (SSc) is a systemic connective tissue disease of unknown etiology. Aberrant gene expression and epigenetic modifications in circulating immune cells have been implicated in the pathogenesis of SSc. This study is to delineate the interaction network between gene transcription and DNA methylation in PBMC of SSc patients and to identify methylation-regulated genes which are involved in the pathogenesis of SSc. Methods. Genome-wide mRNA transcription and global DNA methylation analysis were performed on PBMC from 18 SSc patients and 19 matched normal controls (NC) using Illumina BeadChips. Differentially expressed genes (DEGs) and differentially methylated positions (DMPs) were integrative analyzed to identify methylation-regulated genes and associated molecular pathways. Results. Transcriptome analysis distinguished 453 DEGs (269 up- and 184 downregulated) in SSc from NC. Global DNA methylation analysis identified 925 DMPs located on 618 genes. Integration of the two lists revealed only 20 DEGs which harbor inversely correlated DMPs, including 12 upregulated (ELANE, CTSG, LTBR, C3AR1, CSTA, SPI1, ODF3B, SAMD4A, PLAUR, NFE2, ZYX, and CTSZ) and eight downregulated genes (RUNX3, PRF1, PRKCH, PAG1, RASSF5, FYN, CXCR6, and F2R). These potential methylation-regulated DEGs (MeDEGs) are enriched in the pathways related to immune cell migration, proliferation, activation, and inflammation activities. Using a machine learning algorism, we identified six out of the 20 MeDEGs, including F2R, CXCR6, FYN, LTBR, CTSG, and ELANE, which distinguished SSc from NC with 100% accuracy. Four genes (F2R, FYN, PAG1, and PRKCH) differentially expressed in SSc with interstitial lung disease (ILD) compared to SSc without ILD. Conclusion. The identified MeDEGs may represent novel candidate factors which lead to the abnormal activation of immune regulatory pathways in the pathogenesis of SSc. They may also be used as diagnostic biomarkers for SSc and clinical complications.

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Cárdenas, Angélica M., Laura J. Ardila, Rolando Vernal, Samanta Melgar-Rodríguez, and Hernán G. Hernández. "Biomarkers of Periodontitis and Its Differential DNA Methylation and Gene Expression in Immune Cells: A Systematic Review." International Journal of Molecular Sciences 23, no. 19 (October 10, 2022): 12042. http://dx.doi.org/10.3390/ijms231912042.

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The characteristic epigenetic profile of periodontitis found in peripheral leukocytes denotes its impact on systemic immunity. In fact, this profile not only stands for periodontitis as a low-grade inflammatory disease with systemic effects but also as an important source of potentially valuable clinical biomarkers of its systemic effects and susceptibility to other inflammatory conditions. Thus, we aimed to identify relevant genes tested as epigenetic systemic biomarkers in patients with periodontitis, based on the DNA methylation patterns and RNA expression profiles in peripheral immune cells. A detailed protocol was designed following the Preferred Reporting Items for Systematic Review and Meta-analysis -PRISMA guideline. Only cross-sectional and case-control studies that reported potential systemic biomarkers of periodontitis in peripheral immune cell types were included. DNA methylation was analyzed in leukocytes, and gene expression was in polymorphonuclear and mononuclear cells. Hypermethylation was found in TLR regulators genes: MAP3K7, MYD88, IL6R, RIPK2, FADD, IRAK1BP1, and PPARA in early stages of periodontitis, while advanced stages presented hypomethylation of these genes. TGFB1I1, VNN1, HLADRB4, and CXCL8 genes were differentially expressed in lymphocytes and monocytes of subjects with poorly controlled diabetes mellitus, dyslipidemia, and periodontitis in comparison with controls. The DAB2 gene was differentially overexpressed in periodontitis and dyslipidemia. Peripheral blood neutrophils in periodontitis showed differential expression in 163 genes. Periodontitis showed an increase in ceruloplasmin gene expression in polymorphonuclears in comparison with controls. Several genes highlight the role of the epigenetics of peripheral inflammatory cells in periodontitis that could be explored in blood as a source of biomarkers for routine testing.

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FU, Li-Hong. "Methylation status of the IL-10 gene promoter in the peripheral blood mononuclear cells of rheumatoid arthritis patients." HEREDITAS 29, no. 11 (2007): 1357. http://dx.doi.org/10.1360/yc-007-1357.

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Xie, Fang-Fei, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, et al. "Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells." Functional & Integrative Genomics 18, no. 1 (July 22, 2017): 1–10. http://dx.doi.org/10.1007/s10142-017-0568-6.

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Marcon, Francesca, Ester Siniscalchi, Cristina Andreoli, Alessandra Allione, Giovanni Fiorito, Emanuela Medda, Simonetta Guarrera, Giuseppe Matullo, and Riccardo Crebelli. "Telomerase activity, telomere length andhTERTDNA methylation in peripheral blood mononuclear cells from monozygotic twins with discordant smoking habits." Environmental and Molecular Mutagenesis 58, no. 8 (August 26, 2017): 551–59. http://dx.doi.org/10.1002/em.22127.

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Acevedo, Nathalie, Giovanni Scala, Simon Kebede Merid, Paolo Frumento, Sören Bruhn, Anna Andersson, Christoph Ogris, et al. "DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life." International Journal of Molecular Sciences 22, no. 2 (January 14, 2021): 801. http://dx.doi.org/10.3390/ijms22020801.

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DNA methylation changes may predispose becoming IgE-sensitized to allergens. We analyzed whether DNA methylation in peripheral blood mononuclear cells (PBMC) is associated with IgE sensitization at 5 years of age (5Y). DNA methylation was measured in 288 PBMC samples from 74 mother/child pairs from the birth cohort ALADDIN (Assessment of Lifestyle and Allergic Disease During INfancy) using the HumanMethylation450BeadChip (Illumina). PBMCs were obtained from the mothers during pregnancy and from their children in cord blood, at 2 years and 5Y. DNA methylation levels at each time point were compared between children with and without IgE sensitization to allergens at 5Y. For replication, CpG sites associated with IgE sensitization in ALADDIN were evaluated in whole blood DNA of 256 children, 4 years old, from the BAMSE (Swedish abbreviation for Children, Allergy, Milieu, Stockholm, Epidemiology) cohort. We found 34 differentially methylated regions (DMRs) associated with IgE sensitization to airborne allergens and 38 DMRs associated with sensitization to food allergens in children at 5Y (Sidak p ≤ 0.05). Genes associated with airborne sensitization were enriched in the pathway of endocytosis, while genes associated with food sensitization were enriched in focal adhesion, the bacterial invasion of epithelial cells, and leukocyte migration. Furthermore, 25 DMRs in maternal PBMCs were associated with IgE sensitization to airborne allergens in their children at 5Y, which were functionally annotated to the mTOR (mammalian Target of Rapamycin) signaling pathway. This study supports that DNA methylation is associated with IgE sensitization early in life and revealed new candidate genes for atopy. Moreover, our study provides evidence that maternal DNA methylation levels are associated with IgE sensitization in the child supporting early in utero effects on atopy predisposition.

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Xing, Meng, Ying Luo, Le Kuai, Yi Ru, Xiaojie Ding, Xiaoninng Yan, Bin Li, and Xin Li. "DNA Methylation Expression Profile of Blood Heat Syndrome and Blood Stasis Syndrome in TCM Psoriasis." Evidence-Based Complementary and Alternative Medicine 2022 (September 19, 2022): 1–20. http://dx.doi.org/10.1155/2022/9343285.

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Objective. Traditional Chinese medicine (TCM) emphasizes treatment based on syndrome differentiation. This study aimed to clarify the characteristics of DNA methylation expression profiles in peripheral blood mononuclear cells (PBMCs) in patients with psoriasis and analyze the differences in these profiles among different TCM syndromes of psoriasis in order to provide a material basis for the diversity of these syndromes. Methods. Blood samples were collected from 32 participants, including 14 patients with psoriatic blood heat syndrome (BHS), 12 patients with psoriatic blood stasis syndrome (BSS), and 6 healthy controls. PBMCs were extracted and subjected to DNA quality inspection. An Illumina Human Methylation 850k chip was used to sequence each group of samples. According to gene annotation classification together with CpG island annotation classification, the differentially methylated regions between sample groups were screened, while Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were applied to perform functional analyses of DMGs. Finally, the DMGs closely correlating with psoriatic severity were screened using Spearman’s correlation analysis. Results. Compared with normal controls, patients with psoriasis showed an overall trend of hypermethylation. In psoriasis, the differential methylation probes were mainly distributed on gene body region on the genome, while those in CpG regions were mainly distributed in CpG islands. Compared with healthy controls, the overall trends in methylation were similar in psoriatic BHS and BSS patients compared to healthy controls. However, bioinformatic analysis revealed different functions of DMGs. We also found that the methylation levels of TRIM14 and PRDM16 were closely correlated with PASI scores and could serve as potential biomarkers to assess the severity of psoriasis. Conclusions. Our study, for the first time, indicated the possible involvement of DNA methylation in regulating the characteristics of TCM syndromes of psoriasis, providing a new direction for research into TCM psoriatic syndromes.

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Fan, Jun, Asou Norio, and Masao Matsuoka. "Methylation Profile of B-Chronic Lymphocytic Leukemia Cells." Blood 106, no. 11 (November 16, 2005): 2951. http://dx.doi.org/10.1182/blood.v106.11.2951.2951.

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Abstract DNA methylation plays an important role in the development and aging of mammalian cells, and its dysregulation has been frequently observed in cancer cells. The purpose of this study is to investigate the involvement of aberrant DNA methylation in B chronic lymphocytic leukemia (B-CLL) cells. We compared methylation status of B-CLL cells isolated from patients with that of normal CD19+ cells isolated from health donors by methylated CpG island amplification/representative difference analysis method. 5 hypermethylated and 27 hypomethylated DNA regions were identified in B-CLL sample. Among the 27 hypomethylated regions, 5 located on chromosome 9q34, 3 on 10q25-26 and 4 on 19q13. Methylation status was confirmed by sequencing using sodium bisulfite-treated DNA samples. By comparing DNA samples from same patients at different clinical stages, we found that lower methylation density in these regions is linked with disease progression. Expression of 15 genes surrounding hypomethylated regions was studied by RT-PCR. Expression of laminin beta3 gene and melanotransferrin gene was found to be upregulated in all B-CLL cell lines as well as lymphoma cell lines comparing with normal CD19+ peripheral blood mononuclear cells. B-cell CLL/lymphoma 11b gene showed increased expression in only 2 B-CLL cell lines. For other genes, no transcriptional change was found regardless of changed DNA methylation. This study showed the predominance of DNA hypomethylation in B-CLL cells compared with hypermethylation. Hypomethylated regions clustered in a limited number of chromosomes and methylation density appeared to be inversely correlated with disease progress. Figure Figure

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Woźniak, Ewelina, Edyta Reszka, Ewa Jabłońska, Jaromir Michałowicz, Bogumiła Huras, and Bożena Bukowska. "Glyphosate and AMPA Induce Alterations in Expression of Genes Involved in Chromatin Architecture in Human Peripheral Blood Mononuclear Cells (In Vitro)." International Journal of Molecular Sciences 22, no. 6 (March 15, 2021): 2966. http://dx.doi.org/10.3390/ijms22062966.

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We have determined the effect of glyphosate and aminomethylphosphonic acid (AMPA) on expression of genes involved in chromatin architecture in human peripheral blood mononuclear cells (PBMCs). The cells were incubated with glyphosate and AMPA in the concentrations ranging from 0.5 to 100 μM and from 0.5, to 250 μM, respectively. The expression profile of the following genes by quantitative Real-Time PCR was evaluated: Genes involved in the DNA methylation (DNMT1, DNMT3A) and DNA demethylation process (TET3) and those involved in chromatin remodeling: genes involved in the modification of histone methylation (EHMT1, EHMT2) and genes involved in the modification of histone deacetylation (HDAC3, HDAC5). Gene profiling showed that glyphosate changed the expression of DNMT1, DMNT3A, and HDAC3, while AMPA changed the expression of DNMT1 and HDAC3. The results also revealed that glyphosate at lower concentrations than AMPA upregulated the expression of the tested genes. Both compounds studied altered expression of genes, which are characteristic for the regulation of transcriptionally inactive chromatin. However, the unknown activity of many other proteins involved in chromatin structure regulation prevents to carry out an unambiguous evaluation of the effect of tested xenobiotics on the studied process. Undoubtedly, we have observed that glyphosate and AMPA affect epigenetic processes that regulate chromatin architecture.

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Hudon Thibeault, Andrée-Anne, and Catherine Laprise. "Cell-Specific DNA Methylation Signatures in Asthma." Genes 10, no. 11 (November 15, 2019): 932. http://dx.doi.org/10.3390/genes10110932.

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Asthma is a complex trait, often associated with atopy. The genetic contribution has been evidenced by familial occurrence. Genome-wide association studies allowed for associating numerous genes with asthma, as well as identifying new loci that have a minor contribution to its phenotype. Considering the role of environmental exposure on asthma development, an increasing amount of literature has been published on epigenetic modifications associated with this pathology and especially on DNA methylation, in an attempt to better understand its missing heritability. These studies have been conducted in different tissues, but mainly in blood or its peripheral mononuclear cells. However, there is growing evidence that epigenetic changes that occur in one cell type cannot be directly translated into another one. In this review, we compare alterations in DNA methylation from different cells of the immune system and of the respiratory tract. The cell types in which data are obtained influences the global status of alteration of DNA methylation in asthmatic individuals compared to control (an increased or a decreased DNA methylation). Given that several genes were cell-type-specific, there is a great need for comparative studies on DNA methylation from different cells, but from the same individuals in order to better understand the role of epigenetics in asthma pathophysiology.

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Tamm, Ingo, Nicole Sattler, Mandy Wagner, Michael Lübbert, Philipp leCoutre, Bernd Dörken, and Karin Schmelz. "Decitabine: Where Is the Target?." Blood 106, no. 11 (November 16, 2005): 495. http://dx.doi.org/10.1182/blood.v106.11.495.495.

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Abstract The methylation inhibitor 5-Aza-2′-deoxycytidine (decitabine) has therapeutic efficacy in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Using microarray analysis, we investigated global changes in gene expression after decitabine treatment in AML. In the AML cell line OCI-AML2, decitabine induced the expression of 81 out of 22 000 genes; 96 genes were downregulated (X2-fold change in expression). RT-PCR analysis of 10 randomly selected genes confirmed the changes of expression in AML cells. Similar results were obtained with primary AML and MDS cells after treatment with decitabine ex vivo and in vivo, respectively. In contrast, significantly fewer changes in gene expression and cytotoxicity were detected in normal peripheral blood mononuclear and bone marrow cells or transformed epithelial cells treated with decitabine. Interestingly, only 50.6% of the induced genes contain putative CpG islands in the 5′ region. To further investigate the significance of promoter methylation in the induced genes, we analyzed the actual methylation status of randomly selected decitabine-inducible genes. We detected hypermethylation exclusively in the 5′ region of the myeloperoxidase (MPO) gene. DNA methylation inversely correlated with MPO expression in newly diagnosed untreated AML patients (P<0.004). In contrast, all other analyzed decitabine-inducible genes revealed no CpG methylation in the promoter region, suggesting a methylation-independent effect of decitabine.

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Deng, Keyong, Xiaotong Ning, Xiaoxiao Ren, Bin Yang, Jianxin Li, Jie Cao, Jichun Chen, Xiangfeng Lu, Shufeng Chen, and Laiyuan Wang. "Transcriptome-wide N6-methyladenosine methylation landscape of coronary artery disease." Epigenomics 13, no. 10 (May 2021): 793–808. http://dx.doi.org/10.2217/epi-2020-0372.

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Aim: To reveal transcriptome-wide N6-methyladenosine (m6A) methylome of coronary artery disease (CAD). Materials & methods: The m6A levels of RNA from peripheral blood mononuclear cells measured by colorimetry were significantly decreased in CAD cases. Transcriptome-wide m6A methylome profiled by methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified differentially methylated m6A sites within both mRNAs and lncRNAs between CAD and control group. Results: Bioinformatic analysis indicated that differentially methylated genes were involved in the pathogenesis of atherosclerosis. MeRIP-quantitative real-time PCR assay confirmed the reliability of MeRIP-seq data. Finally, the rat carotid artery balloon injury model was performed to confirm the role of m6A demethylase FTO in neointima formation. Conclusion: Our study provided a resource of differentially methylated m6A profile for uncovering m6A biological functions in the pathogenesis of CAD.

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Yang, Xiaoming, Alex C. Rutkovsky, Juhua Zhou, Yin Zhong, Julian Reese, Timothy Schnell, Helmut Albrecht, William B. Owens, Prakash S. Nagarkatti, and Mitzi Nagarkatti. "Characterization of Altered Gene Expression and Histone Methylation in Peripheral Blood Mononuclear Cells Regulating Inflammation in COVID-19 Patients." Journal of Immunology 208, no. 8 (April 4, 2022): 1968–77. http://dx.doi.org/10.4049/jimmunol.2101099.

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Sun, Libo, Kang Li, Guihai Liu, Yuan Xu, Aiying Zhang, Dongdong Lin, Haitao Zhang, et al. "Distinctive pattern of AHNAK methylation level in peripheral blood mononuclear cells and the association with HBV-related liver diseases." Cancer Medicine 7, no. 10 (September 27, 2018): 5178–86. http://dx.doi.org/10.1002/cam4.1778.

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Bossolasco, Patrizia, Francesco Onida, Giorgia Saporiti, Carla Bozzi, Clara Ricci, Agostino Cortelezzi, and Giorgio Lambertenghi Deliliers. "High Frequency of Tumor Suppressor Genes Promoter Hypermethylation in Peripheral Blood of Patients with Myelodysplastic Syndromes." Blood 112, no. 11 (November 16, 2008): 4468. http://dx.doi.org/10.1182/blood.v112.11.4468.4468.

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Abstract Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic stem cell disorders characterized by ineffective hematopoiesis and peripheral blood cytopenias, with very little established about their pathogenesis. DNA methylation is a common modification thought to be relevant to carcinogenesis. The epigenetic silencing, through methylation of CpG islands within the promoter regions, is one of the mechanisms by which numerous genes are inactivated in MDS and acute myeloid leukemias (AML). In particular, the promoter of CDKN2B (encoding p15INK4b), has been shown to be hypermethylated in poor-risk subtypes of MDS and often predicts transformation to AML. In this study, we examined the promoter methylation status of 7 genes in peripheral blood (PB) cells collected from 19 patients affected by untreated MDS. We investigated genes involved in cell cycle regulation (p14ARF, p15INK4b, p16INK4a), apoptosis (SPARC, DAPK1), differentiation (RARb) and response to growth factors (RASSF1A) previously reported as being abnormally hypermethylated in acute leukemia and in a variety of solid malignancies. DNA was extracted from PB low-density mononuclear cells and promoters methylation status was analyzed by means of methylation-specific PCR assay (MSP). MSP distinguishes unmethylated from methylated alleles in a given gene based on sequence changes produced after bisulfite treatment of DNA, which converts unmethylated (but not methylated) cytosines to uracil, and subsequent PCR using primers designed for either methylated or unmethylated DNA. Sodium bisulfite modification was performed using the Methylamp DNA Modification Kit (Epigentek) following manufacturer‘s instructions. Our series included 4 RA, 3 RARS, 3 RCMD, 2 RCMD/RS, 5 RAEB-1, 1 RAEB-2 and 1 CMML-1; according to the IPSS, 17 patients (89%) were classified as either low- or intermediate-1 risk. Median age was 72 years (range 49–86). Cytogenetics were normal in 12 patients (63%), while in 3 patients showed the 5q- abnormality. Median CBC counts were: WBC 3.1 × 109/L (0.9–12.5), Hb 10 g/dl (6.4–15), PLT 106 × 109/L (9–406). The cell cycle regulator p15INK4b was found to be the most frequently hypermethylated gene (14/19 pts, 74%) in our MDS series, followed by the p14ARF (13/19 pts, 68%). The latter was hypermethylated in 100% of our 5q- cases. Ninety-five percent (18/19 pts) of the MDS samples were found to be hypermethylated in at least one of the seven genes, with the only exception being the patient with CMML (unmethylated in all the tested genes). Hypermethylation of the cell cycle regulator p16INK4a was detected in 47% of samples. In 3 patients (16%) we found hypermethylation in all genes but RASSF1A, which indeed was found unmethylated in all but one of the samples analyzed (5%). The tumor suppressor gene SPARC was hypermethylated in 58% of patients (including 2 out of the 3 cases of 5q-), whereas 42% and 47% of samples, respectively, showed hypermethylation of the RARb and DAPK1 genes promoter. Although in a limited number of samples, we detected a differential rate of hypermethylation of the tested genes in peripheral blood of MDS patients. Altogether, our results seem to confirm high frequency of hypermethylation genes involved in regulation of cell cycle and apoptosis in MDS. We conclude that mononuclear cells from peripheral blood represents an easily accessible sample for detection and monitoring of genes promoter hypermethylation in myelodysplastic syndromes.

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Ng, Christopher J., Alice Liu, Katrina J. Ashworth, Kenneth L. Jones, and Jorge Di Paola. "Epigenetic Profiles of Primary Endothelial Cells from Patients with Low VWF Levels." Blood 132, Supplement 1 (November 29, 2018): 983. http://dx.doi.org/10.1182/blood-2018-99-116719.

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Abstract Background Von Willebrand disease (VWD) type 1 is characterized by low von Willebrand factor (VWF) levels and mucocutaneous bleeding (MCB). Approximately 50% of patients with VWD type 1 exhibit mutations in VWF. However, a large number of patients with VWF levels between 30-50 IU/dL do not show mutations in VWF indicating that other mechanisms are involved. Blood outgrowth endothelial cells (BOECs) are a source of donor-specific endothelial cells and have demonstrated impairments in VWF release and packaging in patients with VWD. BOECs have not been evaluated in individuals with low VWF levels. Hypothesis/Objective We hypothesize that BOECs from individuals with low VWF levels will reveal unique VWF and genome wide epigenetic signatures that may explain the altered plasma VWF levels seen in these patients. Methods BOEC Derivation: Patients with low VWF levels and MCB (30-50 IU/dL) were enrolled in an IRB-approved study. The mononuclear layer from whole blood was isolated and plated onto collagen coated plates. After extended incubation, the presence of BOECs was confirmed by visual morphology and flow cytometry. VWF Transcriptional Analysis: 9 cells lines including: a) 2 BOEC cell lines from control individuals and a HUVEC cell line and c) BOECs from individuals with low VWF, were assayed via single cell RNA sequencing. Bioinformatic analysis included generalized transcriptional expression and single cell expression of VWF. RNA-sequencing expression data was filtered according to the following standardized algorithm. Cells that were defined as monocytes (TYROBP expression > 2 copies) were excluded. Following monocyte exclusions, cells were determined to be of endothelial origin if they demonstrated the presence of PECAM1, CDH5, ROBO4, ESAM, TIE1, or NOTCH4 transcripts, as previously reported by Butler et al. (Cell Reports, 2016). Epigenetic Profiling:Genomic DNA was extracted from BOECs and from peripheral leukocytes (paired to the BOEC draw sample) and analyzed for DNA methylation via an Illumina 850K methylation array. Results BOEC Derivation:A total of eight BOEC lines were generated, 6 from individuals with MCB and VWF levels between 30-50 IU/dL (5:1 female: male ratio, age range 11-54 years) and 2 from healthy controls (2 female, age range 22-39 years) with normal VWF levels and no symptoms of MCB. VWF Expression is decreased in Low VWF Samples: Overall transcript expression of VWF was significantly decreased in low VWF BOEC samples (5.341 transcripts/cell) vs. control endothelial cells (9.076 transcripts/cell), P <0.0001. Generalized Methylation Profiling:Via adjusted P-values, there were 129 methylation sites across multiple genes that were differentially methylated in Low VWF BOECs vs. control endothelial cells. A cluster plot demonstrates that the two control BOEC samples were generally clustered as compared to the other samples (Figure 1A). VWF Specific Methylation: The Illumina 850K array covers 70 prospective methylation sites in VWF, ranging from upstream of the transcriptional start site through the length of the gene. A previous report demonstrated that differences in 8 methylation sites in the VWF promoter correlated with VWF expression (Yuan et al. Nature Communications 2016). 7 of these sites are covered in our assay. Across all of those 7 sites, there was significant increased methylation of the CpG islands in the Low VWF BOECs when compared to the control endothelial cells (Figure 1B). Stability of VWF Methylation:To ensure that the isolation and culture of BOECS does not significantly affect the methylation status of VWF, we conducted a Pearson correlation analysis and demonstrated that peripheral leukocyte (at time of blood draw) and BOEC methylation is highly correlated at VWF specific methylation sites (R2 0.6, P = 0.0004) (Figure 1C). Conclusions Single cell RNA sequencing and genome wide methylation assays of BOECs from individuals with low VWF reveal significant differences in generalized methylation status when compared to BOECs from individuals with normal VWF levels and HUVECs. There is transcriptional downregulation of VWF in low VWF BOECs that is associated with hypermethylation of 7 specific VWF CpG sites in the VWF promoter. Additional sites are being evaluated. Finally, we validated the methylation status of BOECs by demonstrating high correlation with the methylation status of leukocytes from the same individuals. Figure 1 Figure 1. Disclosures Ng: Shire: Consultancy; CSL Behring: Consultancy.

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Journal articles on the topic 'Peripheral blood mononuclear cells methylation'

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