Abstract 428: DNA Methylation of ASC is Associated with Decreased ASC and IL-1β Expression in Heart Failure

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Brittany Butts ◽  
Javed Butler
Keyword(s):  
Heart Failure ◽  
Dna Methylation ◽  
Inflammatory Cytokines ◽  
Epigenetic Modification ◽  
Cpg Islands ◽  
Inflammasome Activation ◽  
Cpg Sites ◽  
Exon 1 ◽  
Vital Component ◽  
Intron Region

Introduction: Heart failure (HF) is associated with formation and activation of inflammasome, a complex of intracellular interaction proteins that trigger maturation of inflammatory cytokines to initiate inflammatory response. ASC, a vital component of the inflammasome, is controlled through epigenetic modification via methylation of CpG islands surrounding exon 1. Methods: To assess the relationships between DNA methylation of ASC, ASC expression, and inflammatory cytokines IL-1β and IL-18 in HF, stored samples from 155 chronic HF patients (age 56.9±12.0 yr, 64% male, 47% black, and ejection fraction 29.9±14.9) were analyzed. DNA extracted from PMBCs were analyzed by pyrosequencing for percent methylation of seven CpG sites in the intron region preceding exon 1 of the ASC gene. ASC mRNA was quantified via real-time PCR and analyzed as the ratio ASC:GAPDH. Serum ASC, IL-1β, and IL-18 were measured by ELISA. Results: Higher ASC methylation was associated with lower ASC mRNA (r=0-.328, p<0.001) and protein (r=-.464, p<0.001) expression. Lower ASC mRNA expression was associated with lower ASC protein expression (r=0.494, p<0.001). Decreased IL-1β expression was associated with higher ASC methylation (r=-.424, p=0.005) and lower ASC mRNA (r=.619, p<0.001) and ASC protein (r=.433, p<0.001). IL-18 expression was not significantly associated with ASC methylation or expression. Conclusions: Increased ASC methylation was associated with lower IL-1β, likely via decreased ASC gene expression. As ASC is required for inflammasome activation of IL-1β, this study implicates the inflammasome pathway as a driver of inflammation in HF, proving a potential target for novel interventions.

scholarly journals Comparative Analysis of CpG Sites and Islands Distributed in Mitochondrial DNA of Model Organisms

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 665 ◽  
Author(s):  
Krzysztof Kowal ◽  
Angelika Tkaczyk ◽  
Tomasz Ząbek ◽  
Mariusz Pierzchała ◽  
Brygida Ślaska
Keyword(s):  
Mitochondrial Genome ◽  
Epigenetic Modification ◽  
Mitochondrial Gene ◽  
Cpg Islands ◽  
Model Organisms ◽  
12S Rrna ◽  
Cpg Sites ◽  
Starting Point ◽  
D Loop ◽  
Taxonomic Groups

The information about mtDNA methylation is still limited, thus epigenetic modification remains unclear. The lack of comprehensive information on the comparative epigenomics of mtDNA prompts comprehensive investigations of the epigenomic modification of mtDNA in different species. This is the first study in which the theoretical CpG localization in the mtDNA reference sequences from various species (12) was compared. The aim of the study was to determine the localization of CpG sites and islands in mtDNA of model organisms and to compare their distribution. The results are suitable for further investigations of mtDNA methylation. The analysis involved both strands of mtDNA sequences of animal model organisms representing different taxonomic groups of invertebrates and vertebrates. For each sequence, such parameters as the number, length, and localization of CpG islands were determined with the use of EMBOSS (European Molecular Biology Open Software Suite) software. The number of CpG sites for each sequence was indicated using the newcpgseek algorithm. The results showed that methylation of mtDNA in the analysed species involved mitochondrial gene expression. Our analyses showed that the CpG sites were commonly present in genomic regions including the D-loop, CYTB, ND6, ND5, ND4, ND3, ND2, ND1, COX3, COX2, COX1, ATP6, 16s rRNA, and 12s rRNA. The CpG distribution in animals from different species was diversified. Generally, the number of observed CpG sites of the mitochondrial genome was higher in the vertebrates than in the invertebrates. However, there was no relationship between the frequency of the CpG sites in the mitochondrial genome and the complexity of the analysed organisms. Interestingly, the distribution of the CpG sites for tRNA coding genes was usually cumulated in a larger CpG region in vertebrates. This paper may be a starting point for further research, since the collected information indicates possible methylation regions localized in mtDNA among different species including invertebrates and vertebrates.

scholarly journals Genome-wide DNA methylation profiles of porcine ovaries in estrus and proestrus

2018 ◽  
Vol 50 (9) ◽  
pp. 714-723 ◽  
Author(s):  
Xiaolong Zhou ◽  
Songbai Yang ◽  
Feifei Yan ◽  
Ke He ◽  
Ayong Zhao
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Cpg Islands ◽  
Biological Processes ◽  
Hormone Regulation ◽  
Methylated Dna ◽  
Coding Regions ◽  
Genome Wide ◽  
Differentially Methylated Genes ◽  
Flanking Regions

DNA methylation is an important epigenetic modification involved in the estrous cycle and the regulation of reproduction. Here, we investigated the genome-wide profiles of DNA methylation in porcine ovaries in proestrus and estrus using methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in intergenic and intron regions. The methylation levels of coding regions were higher than those of the 5′- and 3′-flanking regions of genes. There were 4,813 differentially methylated regions (DMRs) of CpG islands in the estrus vs. proestrus ovarian genomes. Additionally, 3,651 differentially methylated genes (DMGs) were identified in pigs in estrus and proestrus. The DMGs were significantly enriched in biological processes and pathways related to reproduction and hormone regulation. We identified 90 DMGs associated with regulating reproduction in pigs. Our findings can serve as resources for DNA methylome research focused on porcine ovaries and further our understanding of epigenetically regulated reproduction in mammals.

Genome-Wide DNA Methylation Analysis Shows Enrichment of Differential Methylation in “Open Seas” and Enhancers and Reveals Hypomethylation in DNMT3A Mutated Cytogenetically Normal AML (CN-AML)

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 653-653 ◽  
Author(s):  
Ying Qu ◽  
Andreas Lennartsson ◽  
Verena I. Gaidzik ◽  
Stefan Deneberg ◽  
Sofia Bengtzén ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cpg Island ◽  
Cpg Islands ◽  
Differential Methylation ◽  
Methylation Analysis ◽  
Cpg Sites ◽  
Genome Wide ◽  
Genomic Regions ◽  
Methylation Patterns

Abstract Abstract 653 DNA methylation is involved in multiple biologic processes including normal cell differentiation and tumorigenesis. In AML, methylation patterns have been shown to differ significantly from normal hematopoietic cells. Most studies of DNA methylation in AML have previously focused on CpG islands within the promoter of genes, representing only a very small proportion of the DNA methylome. In this study, we performed genome-wide methylation analysis of 62 AML patients with CN-AML and CD34 positive cells from healthy controls by Illumina HumanMethylation450K Array covering 450.000 CpG sites in CpG islands as well as genomic regions far from CpG islands. Differentially methylated CpG sites (DMS) between CN-AML and normal hematopoietic cells were calculated and the most significant enrichment of DMS was found in regions more than 4kb from CpG Islands, in the so called open sea where hypomethylation was the dominant form of aberrant methylation. In contrast, CpG islands were not enriched for DMS and DMS in CpG islands were dominated by hypermethylation. DMS successively further away from CpG islands in CpG island shores (up to 2kb from CpG Island) and shelves (from 2kb to 4kb from Island) showed increasing degree of hypomethylation in AML cells. Among regions defined by their relation to gene structures, CpG dinucleotide located in theoretic enhancers were found to be the most enriched for DMS (Chi χ2<0.0001) with the majority of DMS showing decreased methylation compared to CD34 normal controls. To address the relation to gene expression, GEP (gene expression profiling) by microarray was carried out on 32 of the CN-AML patients. Totally, 339723 CpG sites covering 18879 genes were addressed on both platforms. CpG methylation in CpG islands showed the most pronounced anti-correlation (spearman ρ =-0.4145) with gene expression level, followed by CpG island shores (mean spearman rho for both sides' shore ρ=-0.2350). As transcription factors (TFs) have shown to be crucial for AML development, we especially studied differential methylation of an unbiased selection of 1638 TFs. The most enriched differential methylation between CN-AML and normal CD34 positive cells were found in TFs known to be involved in hematopoiesis and with Wilms tumor protein-1 (WT1), activator protein 1 (AP-1) and runt-related transcription factor 1 (RUNX1) being the most differentially methylated TFs. The differential methylation in WT 1 and RUNX1 was located in intragenic regions which were confirmed by pyro-sequencing. AML cases were characterized with respect to mutations in FLT3, NPM1, IDH1, IDH2 and DNMT3A. Correlation analysis between genome wide methylation patterns and mutational status showed statistically significant hypomethylation of CpG Island (p<0.0001) and to a lesser extent CpG island shores (p<0.001) and the presence of DNMT3A mutations. This links DNMT3A mutations for the first time to a hypomethylated phenotype. Further analyses correlating methylation patterns to other clinical data such as clinical outcome are ongoing. In conclusion, our study revealed that non-CpG island regions and in particular enhancers are the most aberrantly methylated genomic regions in AML and that WT 1 and RUNX1 are the most differentially methylated TFs. Furthermore, our data suggests a hypomethylated phenotype in DNMT3A mutated AML. Disclosures: No relevant conflicts of interest to declare.

scholarly journals The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development

2020 ◽  
Vol 10 (9) ◽  
pp. 3337-3346
Author(s):  
Yijia Zhou ◽  
Funan He ◽  
Weilin Pu ◽  
Xun Gu ◽  
Jiucun Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mutation Rate ◽  
Germline Mutation ◽  
Developmental Stages ◽  
Rare Variants ◽  
Epigenetic Modification ◽  
Genome Project ◽  
Germline Development ◽  
Cpg Sites ◽  
The Impact

Abstract DNA methylation is a dynamic epigenetic modification found in most eukaryotic genomes. It is known to lead to a high CpG to TpG mutation rate. However, the relationship between the methylation dynamics in germline development and the germline mutation rate remains unexplored. In this study, we used whole genome bisulfite sequencing (WGBS) data of cells at 13 stages of human germline development and rare variants from the 1000 Genome Project as proxies for germline mutations to investigate the correlation between dynamic methylation levels and germline mutation rates at different scales. At the single-site level, we found a significant correlation between methylation and the germline point mutation rate at CpG sites during germline developmental stages. Then we explored the mutability of methylation dynamics in all stages. Our results also showed a broad correlation between the regional methylation level and the rate of C &gt; T mutation at CpG sites in all genomic regions, especially in intronic regions; a similar link was also seen at all chromosomal levels. Our findings indicate that the dynamic DNA methylome during human germline development has a broader mutational impact than is commonly assumed.

scholarly journals DNA methylation patterns of β-globin cluster in β-thalassemia patients

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiuqin Bao ◽  
Yangjin Zuo ◽  
Diyu Chen ◽  
Cunyou Zhao
Keyword(s):  
Dna Methylation ◽  
Cord Blood ◽  
Methylation Level ◽  
Epigenetic Modification ◽  
Fetal Hemoglobin ◽  
Cpg Sites ◽  
Hbf Level ◽  
Globin Promoter ◽  
Methylation Patterns ◽  
Normal Controls

Abstract Background Reactivation of fetal hemoglobin (HbF, α2γ2) holds a therapeutic target for β-thalassemia and sickle cell disease. Although many HbF regulators have been identified, the methylation patterns in β-globin cluster driving the fetal-to-adult hemoglobin switch remains to be determined. Results Here, we evaluated DNA methylation patterns of the β-globin cluster from peripheral bloods of 105 β0/β0 thalassemia patients and 44 normal controls. We also recruited 15 bone marrows and 4 cord blood samples for further evaluation. We identified that the CpG sites in the locus control region (LCR) DNase I hypersensitive site 4 and 3 (HS4-3) regions, and γ- and β-globin promoters displayed hypomethylation in β0/β0-thalassemia patients, especially for the patients with high HbF level, as compared with normal controls. Furthermore, hypomethylations in most of CpG sites of the HS4-3 core regions were also observed in bone marrows (BM) of β0/β0-patients compared with normal controls; and methylation level of γ-globin promoter -50 and + 17 CpG sites showed lower methylation level in patients with high HbF level compared with those with low HbF level and a negative correlation with HbF level among β0-thalassemia patients. Finally, γ-globin promoter + 17 and + 50 CpG sites also displayed significant hypomethylation in cord blood (CB) tissues compared with BM tissues from normal controls. Conclusions Our findings revealed methylation patterns in β-globin cluster associated with β0 thalassemia disease and γ-globin expression, contributed to understand the epigenetic modification in β0 thalassemia patients and provided candidate targets for the therapies of β-hemoglobinopathies.

Digital Restriction Enzyme Analysis of Methylation (DREAM) by Next Generation Sequencing Uncovers Epigenetic Disturbances In Acute Myelogenous Leukemia.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3635-3635
Author(s):  
Frank Neumann ◽  
Jean-Pierre Issa ◽  
Yue Lu ◽  
Marcos R Estecio ◽  
Rong He ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bone Marrow ◽  
Cell Lines ◽  
Cpg Islands ◽  
Leukemia Cell ◽  
Enzyme Analysis ◽  
Restriction Enzyme Analysis ◽  
Cpg Sites ◽  
Leukemia Cell Lines ◽  
Normal Controls

Abstract Abstract 3635 DNA methylation is a key epigenetic mark affecting the configuration of chromatin and the potential for gene expression. Disorganization of DNA methylation contributes to the development of leukemia. There is a need for high resolution, quantitative and cost effective methods to investigate changes of methylome in leukemia. To achieve this goal, we have recently developed a digital restriction enzyme analysis of methylation (DREAM) for quantitative mapping of DNA methylation at approximately 50,000 CpG sites across the whole genome (Jelinek et al., ASH 2009, abstract 567). The method is based on creating distinct DNA signatures at unmethylated or methylated CCCGGG sites by sequential restriction digests of genomic DNA with the SmaI and XmaI endonucleases and on resolving these signatures by massively parallel sequencing. Using the DREAM method, we have analyzed DNA methylation in bone marrow cells from 2 patients with AML, 3 samples of white blood cells from healthy adults and 2 myeloid leukemia cell lines (K562 and HEL). The first patient (Pt#1) was a 72 year-old male with AML transformation of the myelodysplastic syndrome (MDS). He had 32% blasts in the bone marrow and a complex karyotype. He had received lenalidomide treatment only. The second AML patient (Pt#2) was a 28 year-old male suffering from a relapse of an AML FAB M1. The bone marrow showed 87% of blasts and a complex karyotype. The patient was heavily pretreated with daunorubicin, ara-C, etoposide, 6-thioguanine, dexamethasone and l-asparaginase. Neither of the patients received demethylating drugs. Using typically 2 sequencing lanes per sample and paired-end reads of 36 bases on the Illumina Gene Analyzer II platform, we acquired 20–38 (median 33) million sequence tags per sample; of these, 7–17 (median 12) million were mapped to SmaI/XmaI sites unique in the human genome. With a threshold of minimum 20-fold coverage, we obtained quantitative information on the DNA methylation level of 39,603-53,312 (median 44,490) CpG sites associated with 8,939-10,735 (median 9,517) genes. In general, methylation was largely absent within CpG islands (CGI). The CpG sites most protected from methylation were in CGI and within 1 kb from gene transcription start sites (TSS). These regions were represented by 13,474 CpG sites. Focusing our analysis on these CpG sites, methylation >10% was detected only in 268 sites in normal controls (1.9%). The numbers of sites with methylation >10% were significantly higher (P<.0001, chi-square test) in both AML patients: 397 sites in Pt#1 (2.9%) and 2,143 sites in Pt#2 (15.6%), respectively. Leukemia cell lines mirrored the pattern of CGI hypermethylation seen in primary AML cells. Methylation >10% in CGI within 1 kb from TSS was observed at 2,331 sites (17.0%) in K562 and at 2,484 sites (18.1%) in HEL. Differential hypermethylation in AML patients affected 906 genes, including multiple genes previously shown to be methylated in cancer, such as CDKN1B, FOXO3, GATA2, GATA4, GDNF, HOXA9, IGFBP3, SALL1 and WT1. Methylated genes were significantly enriched in canonical pathways affecting embryonic stem cell signaling, Wnt-beta-catenin signaling and pluripotency suggesting an important role in AML stem cells. In contrast to CGI, it is known that CpG sites outside of CpG islands (NCGI) are generally fully methylated in normal cells. We analyzed 11,220 NCGI sites that were >1 kb from gene TSS. Methylation >90% was observed at 5,217 (46%) sites in normal controls, in 5,380 sites (48%) in Pt#1, while only in 1,873 sites (17%) in Pt#2 (P<.0001). Leukemia cell lines also showed this NCGI hypomethylation with only 1,422 (13%) fully methylated sites in K562 and 4,200 sites (37%) in HEL. Thus, significant degrees of hypomethylation in NCGI were observed in Pt#2, and in K562 and HEL cell lines, but not in Pt#1. In conclusion, high resolution quantitative mapping of DNA methylation changes in leukemia is feasible using the DREAM method. Relatively small alterations in DNA methylation observed in the MDS/AML Pt#1 contrasted with extensive hyper and hypomethylation found in Pt#2 with relapsed AML M1. Our results illustrate the complexity and diverse extent of DNA methylation changes in leukemia. Disclosures: No relevant conflicts of interest to declare.

Cancer Drivers Affected by Aberrant DNA Methylation in MDS and AML

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1716-1716 ◽  
Author(s):  
Jaroslav Jelinek ◽  
Shoudan Liang ◽  
Frank Neumann ◽  
Rong He ◽  
Yue Lu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Research Funding ◽  
Cpg Islands ◽  
Enzyme Analysis ◽  
Epigenetic Mark ◽  
Aberrant Methylation ◽  
Healthy Controls ◽  
Cpg Sites ◽  
Normal Controls ◽  
Hypermethylated Genes

Abstract Abstract 1716 Cytosine methylation is an epigenetic mark affecting accessibility of DNA to transcription. Cancer is associated with hypermethylation in CpG islands (dense clusters of CpG sites frequently present around gene transcription starts) and hypomethylation of sparse CpG sites outside CpG islands. Complex changes of DNA methylation in leukemia permanently disturb epigenetic regulation and participate in leukemogenesis. To characterize epigenetic aberrations in myeloid neoplasms, we analyzed DNA methylation in 16 patients with myelodysplastic syndrome (MDS), 7 patients with acute myeloid leukemia (AML) and 5 healthy controls. Using Digital Restriction Enzyme Analysis of Methylation, we quantified DNA methylation at CpG dinucleotides within approximately 40,000 CCCGGG restriction sites across the genome. We analyzed methylation differences between healthy controls and patients with MDS and AML. CpG sites within CpG islands (CGI sites) are typically not methylated in normal tissues. We found 18,738 CGI sites with methylation <5% in normal controls. MDS and AML patients showed heterogeneous hypermethylation >20% in these sites, ranging from 5 to 2720 (median 186) hypermethylated sites in individual patients. The median number of hypermethylated CGI sites was 146 in MDS and 1234 in AML patients. Altogether, we found 5069 CGI sites corresponding to 2183 genes differentially hypermethylated in MDS or AML. GpG sites outside CpG islands (NCGI sites) are generally methylated. We found only 3262 NCGI sites unmethylated (<5% methylation) in normal controls. Hypermethylation pattern of these NCGI sites in individual MDS and AML patients was similar to that of CGI (r=0.85), with 5–388 (median 38) sites hypermethylated over 20%. Altogether, we found 848 NCGI sites corresponding to 629 genes hypermethylated. Hypermethylation affecting both CGI and NCGI sites was found in 273 genes. In order to identify potential drivers in the plethora of methylation changes, we compared the hypermethylated genes with the Sanger Institute “Cancer Consensus” listing 457 genes. The list of 2539 hypermethylated genes contained 74 genes (3%) from the cancer list (51 in CGI, 10 in NCGI and 13 in both CGI and NCGI). Next we analyzed hypomethylation events in MDS and AML. We found 10,509 CpG sites (1210 CGI, 9299 NCGI) with methylation level >80% in normal controls. Methylation levels <30% in MDS and AML patients were observed at 1–439 (median 23) sites. Hypomethylation affected mostly NCGI sites and the numbers of sites hypomethylated in individual patients positively correlated with hypermethylation at CGI sites (r=0.39). The total of 1153 hypomethylated sites corresponded to 777 genes. Twenty-two genes (3%) were present on the cancer list. Six genes (CBFA2T3, FGFR3, FLI1, MLLT1, PHOX2B and PRDM16) showed both hyper and hypomethylation in different parts of the gene when compared to normal controls. Interestingly, translocations involving 5 of these genes have been reported in blood malignancies. The number of ‘cancer’ genes affected by epigenetic events in individual patients was 1–29 (median 8) in MDS and 2–44 (median 20) in AML. In summary, we have detected tens to thousands of CpG sites with aberrant methylation in MDS and AML patients. Our data suggest that approximately 3% of DNA hypermethylation and hypomethylation events are potential drivers in the leukemogenic process in MDS and AML. DNA methylation changes were detected in 90 genes (13%) of the 457 cancer gene list. Our findings thus support the importance of epigenetics in leukemia. Disclosures: Neumann: Sanofi-Aventis: Employment. Issa:GSK: Consultancy; SYNDAX: Consultancy; Merck: Research Funding; Eisai: Research Funding; Celgene: Research Funding; Celgene: Honoraria; Novartis: Honoraria; J&J: Honoraria.

Genome-Wide DNA Methylation Analysis Reveals Biological and Clinical Insights In Relapsed Childhood Acute Lymphoblastic Leukemia: A Report From The COG ALL Target Project

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3736-3736
Author(s):  
Huimin Geng ◽  
Mignon L. Loh ◽  
Richard C. Harvey ◽  
I-Ming Chen ◽  
Meenakshi Devidas ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Lymphoblastic Leukemia ◽  
Cpg Islands ◽  
Gene Promoters ◽  
Methylation Analysis ◽  
Cpg Sites ◽  
Genome Wide ◽  
Organismal Development ◽  
Dna Methylation Analysis

Abstract Although survival of children with B-cell acute lymphoblastic leukemia (B-ALL) has improved substantially over time, 15% to 20% of patients will relapse, and most of those who experience a bone marrow relapse will die. A better understanding of genetic and epigenetic aberrations in relapsed ALL will facilitate new strategies for risk stratification and targeted therapy. In this collaborative study with the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project, we performed high resolution genome-wide DNA methylation profiling using the HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR) array on a total of 178 (110 diagnosis, 68 relapse) leukemia samples from 111 patients with childhood B-ALL enrolled on the Children’s Oncology Group (COG) clinical trials who experienced relapsed, and 12 normal preB samples isolated from the bone marrows of 12 healthy individuals. The HELP array covers 117,521 CpG sites, annotated to ∼22,000 gene promoters. For eight diagnosis/relapse pairs, base-pair resolution DNA methylation using the eRRBS (enhanced Reduced Representation Bisulfite Sequencing) method was also performed on Illumina HiSeq2000. The median relapse time for the 111 patients was 21.8 months (range 2.1 to 56.2). Unsupervised clustering analysis using the HELP data revealed seven clusters: one cluster contained only the 12 normal preB samples; four clusters were enriched with MLLr, ETV6/RUNX1, Trisomy 4+10, and TCF3/PBX1 samples, respectively. The sixth cluster was not enriched for specific cytogenetic cases, but interestingly, all cases in this cluster were NCI High Risk (age>10 years or WBC>=50,000; p<0.0001, Fisher’s Exact test) while the seventh cluster has a mixture of other cases. Supervised analysis of HELP profiles between paired relapse/diagnosis samples (n=67) revealed a markedly aberrant DNA methylation signature (1011 probesets, 888 genes, FDR<0.01 and methylation difference dx >25%, paired t-test), with 70% of the genes hyper- and 30% hypo-methylated in relapse samples. Using a Bayesian predictor and leave-one-out cross validation, this methylation signature could predict a sample as diagnosis or relapse with 95.3% accuracy. When comparing early (<36 months; n=50) versus late relapses (>=36 months; n=18), we detected a profound hypermethylation signature in early relapse (96.6% of the 610 probesets, 544 genes, FDR<0.01, dx >25%). Finally, we identified 1800 probesets (1658 genes) as differentially methylated within all cytogenetic subtypes described above compared to the normal preB samples (Dunnett’s test with normal preB as reference, FDR<0.01, dx>25%). Again the majority (70%) of those genes were hypermethylated in relapse as compared to diagnostic and normal preB. The base-pair resolution and more comprehensive eRRBS methylation analysis for the eight pairs of samples identified 39,679 CpG sites as differentially methylated (dx >25%, FDR<0.01), with 78.2% CpG sites hyper- and 21.2% hypo-methylated in relapse samples. Remarkably, the hypermethylated CpGs are primarily in promoter regions (50%, defined as +/-1kb to TSS), followed by intergenic (26%), then intragenic (14%), and exonic (10%) regions. In contrast, the hypomethylated CpGs are mainly in intragenic (48%), followed by intergenic (31%), exonic (14%) and promoter (7%) regions. The hypermethylated CpGs were mainly in CpG islands (86%) or CpG shores (10%), while hypomethylated CpGs were not (CpG islands: 8%, CpG shores: 27%). We further identified 3040 differentially methylated regions (DMRs) with a median size 426 bp. 78.4% of those DMRs were hyper- (1362 gene promoters) and 21.6% hypo-methylated (98 promoters) in relapse compared to diagnostic samples. Gene set enrichment and Ingenuity pathway analysis showed epigenetically disrupted pathways that are highly involved in cell signaling, and embryonic and organismal development. Taken together, our genome-wide high resolution DNA methylation analysis on a large cohort of relapsed childhood B-ALL from the COG trial identified unique methylation signatures that correlated with relapse and with specific genetic subsets. Those methylation signatures featured prevailing promoter hypermethylation and to a lesser extent, intrageneic hypomethylation. Epigenetically dysregulated gene networks in those relapse samples involved cell signaling, and embryonic and organismal development. Disclosures: No relevant conflicts of interest to declare.

scholarly journals 0027 Adolescent Sleep Timing And Dietary Patterns In Relation To Dna Methylation Of Core Clock Genes

SLEEP ◽  
2019 ◽  
Vol 42 (Supplement_1) ◽  
pp. A11-A11
Author(s):  
Erica C Jansen ◽  
Dana Dolinoy ◽  
Ronald D Chervin ◽  
Karen E Peterson ◽  
Louise M O'Brien ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dietary Patterns ◽  
Dietary Habits ◽  
Clock Genes ◽  
Epigenetic Modification ◽  
Shift Workers ◽  
Wake Time ◽  
Cpg Sites ◽  
Sleep Timing ◽  
Increased Risk

Abstract Introduction Mistimed sleep/wake and eating patterns put adult shift workers at increased risk for chronic disease, and epigenetic modification of core clock genes has been proposed as a mechanism. Although not as extreme as shift workers, adolescents often have delayed sleep timing. Our aim was to assess whether sleep midpoints in adolescents are associated with DNA methylation of circadian genes. A secondary aim was to examine associations between dietary patterns and circadian gene methylation. Methods The study population included 142 Mexican youth (average age 14.0 (SD=2.0) years, 49% male) enrolled in a cohort study. Average sleep midpoint (between bed time and wake time) over 7 days was estimated with actigraphy. Diet was assessed with a semi-quantitative food frequency questionnaire, and three dietary patterns were derived from principal components analysis (a vegetable-based pattern, a meat and starch-based pattern, and a breakfast pattern). DNA methylation was quantified in blood leukocytes with the Infinium MethylatinEPIC BeadChip. We selected 166 loci (CpG sites) within CpG islands of core ‘clock’ genes known to regulate circadian rhythms (CLOCK, BMAL, PER1, PER2, PER3, CRY1, CRYI2, RORA, RORB, REV-VERBA, REV-VERBB). Linear regression was used to analyze associations between sleep midpoint or dietary patterns and logit-transformed percent methylation at the 166 CpG sites. All models were adjusted for sex and age. Results The average midpoint was 3:41 AM (SD=1 hr 15 min); average bed time was 11:29 PM (SD=68 min) and average wake time was 7:53 AM (SD=97 min). Sleep midpoint was positively associated with DNA methylation of CpG sites from the genes REV-VERBA and RORB at the Bonferroni-corrected significance level of p&lt;0.005. The breakfast dietary pattern (rich in eggs, milk, and bread) was inversely associated with DNA methylation at RORA (P=0.003). Conclusion Sleep timing and dietary habits are associated with DNA methylation of core clock genes in adolescents. Epigenetic modification of clock genes could in part underlie relationships between sleep, diet, and metabolic health among adolescents. Support (If Any) Dr. Jansen is supported by the NIH/NHLBI grant 5T32HL110952-05.

scholarly journals Differential DNA Methylation of the IMMP2L Gene in Families with Maternally Inherited 7q31.1 Microdeletions is Associated with Intellectual Disability and Developmental Delay

2021 ◽  
pp. 1-15
Author(s):  
Stanislav A. Vasilyev ◽  
Nikolay A. Skryabin ◽  
Anna A. Kashevarova ◽  
Ekaterina N. Tolmacheva ◽  
Renata R. Savchenko ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Intellectual Disability ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Copy Number Variations ◽  
Incomplete Penetrance ◽  
Cpg Sites ◽  
Transport Chain ◽  
Underlying Mechanisms ◽  
Chromosome 7Q

Most copy number variations (CNVs) in the human genome display incomplete penetrance with unknown underlying mechanisms. One such mechanism may be epigenetic modification, particularly DNA methylation. The <i>IMMP2L</i> gene is located in a critical region for autism susceptibility on chromosome 7q (AUTS1). The level of DNA methylation was assessed by bisulfite sequencing of 87 CpG sites in the <i>IMMP2L</i> gene in 3 families with maternally inherited 7q31.1 microdeletions affecting the <i>IMMP2L</i> gene alone. Bisulfite sequencing revealed comparable levels of DNA methylation in the probands, healthy siblings without microdeletions, and their fathers. In contrast, a reduced DNA methylation index and increased <i>IMMP2L</i> expression were observed in lymphocytes from the healthy mothers compared with the probands. A number of genes were upregulated in the healthy mothers compared to controls and downregulated in probands compared to mothers. These genes were enriched in components of the ribosome and electron transport chain, as well as oxidative phosphorylation and various degenerative conditions. Differential expression in probands and mothers with <i>IMMP2L</i> deletions relative to controls may be due to compensatory processes in healthy mothers with <i>IMMP2L</i> deletions and disturbances of these processes in probands with intellectual disability. The results suggest a possible partial compensation for <i>IMMP2L</i> gene haploinsufficiency in healthy mothers with the 7q31.1 microdeletion by reducing the DNA methylation level. Differential DNA methylation of intragenic CpG sites may affect the phenotypic manifestation of CNVs and explain the incomplete penetrance of chromosomal microdeletions.

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