Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA Methylation Profiling in Mummified Human Remains from the Eighteenth-Century

ABSTRACT: Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimen from mummies of the 18th century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we detected characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions were in line with the fact that the specimen was lung tissue of a female 28-year-old donor. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.

ORGANISM(S): Homo sapiens

PROVIDER: GSE169595 | GEO | 2021/08/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Intra-gene DNA methylation variability is a technically and clinically independent prognostic marker in women’s cancers

Project description:Differences in DNA methylation (DNAm) levels are amongst the earliest changes in human carcinogenesis, and are a hallmark of cancer, offering the potential for novel strategies to predict cancer biology and outcome. Hence, DNAm markings might provide a valuable lead for the development of DNA-based cancer biomarkers in tissue and bodily fluids. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 221 samples, including 171 serous, 18 endometrioid, 14 clear cell, 9 mucinous and 9 other histological cancer subtypes. Bisulphite converted DNA from the 221 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

2015-08-13 | E-GEOD-72021 | biostudies-arrayexpress

Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation

Project description:Background: The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, characterizations of inter-individual DNAm variability and DNAm concordance across tissues have been largely performed in adult tissues and therefore are limited in their relevance to DNAm profiles from pediatric samples. Given that DNAm patterns in early life undergo rapid changes and have been linked to a wide range of health outcomes and environmental exposures, direct investigations of tissue-specific DNAm variation in pediatric samples may help inform the design and interpretation of DNAm analyses from early life cohorts. In this study, we present a systematic comparison of genome-wide DNAm patterns between matched pediatric buccal epithelial cells (BECs) and peripheral blood mononuclear cells (PBMCs), two of the most widely used peripheral tissues in human epigenetic studies. Specifically, we assessed DNAm variability, cross-tissue DNAm concordance and genetic determinants of DNAm across two independent early life cohorts encompassing different ages. Results: BECs had greater inter-individual DNAm variability compared to PBMCs and highly variable CpGs were more likely to be positively correlated between the matched tissues compared to less variable CpGs. These sites were enriched for CpGs under genetic influence, suggesting that a substantial proportion of DNAm co-variation between tissues can be attributed to genetic variation. Finally, we demonstrated the relevance of our findings to human epigenetic studies by categorizing CpGs from published DNAm association studies of pediatric BECs and peripheral blood. Conclusions: Taken together, our results highlight a number of important considerations and practical implications in the design and interpretation of EWAS analyses performed in pediatric peripheral tissues.

2018-12-27 | GSE124366 | GEO

Intra-gene DNA methylation variability is a clinically independent prognostic marker in women’s cancers

2015-08-13 | GSE72021 | GEO

A core of differentially methylated CpG loci in gMDSCs isolated from neonatal and adult sources

Project description:Using the Illumina EPIC array to measure DNAm of gMDSCs and neutrophils from diverse neonatal and adult blood sources, we found 189 differentially methylated CpGs between gMDSCs and neutrophils with a core of ten differentially methylated CpGs that were consistent across both sources of cells. Genes associated with these loci that are involved in immune responses include VCL, FATS, YAP1, KREMEN2, UBTF, MCC-1, and EFCC1. In two cancer patient groups that reflected those used to develop the methylation markers (head and neck squamous cell carcinoma (HNSCC) and glioma), all of the CpG loci were differentially methylated, reaching statistical significance in glioma cases and controls, while one was significantly different in the smaller HNSCC group. Our findings indicate that gMDSCs have a core of distinct DNAm alterations, informing future research on gMDSC differentiation and function.

2023-05-01 | GSE231417 | GEO

Genome-wide DNA methylation differences in nucleus accumbens of smokers vs. nonsmokers

Project description:Cigarette smoking remains the leading cause of preventable death worldwide. Cigarette smoking behaviors (e.g., initiation, nicotine dependence, cessation) are heritable, and many genetic risk loci have been identified. However, the neurobiological mechanisms underlying the genetic risk loci along the trajectory of smoking are largely unknown. DNA methylation (DNAm) differences between smokers and nonsmokers can provide insight into mechanisms that predispose to smoking behaviors and consequences of the smoking exposure itself. Differential DNAm by smoking has been found at many CpG sites in blood, but because of the tissue specificity of gene regulation, differential DNAm that can only be detected in brain may have been missed. Here, we provide Illumina HumanMethylationEPIC array data generated in nucleus accumbens, an addiction-relevant brain tissue, from 221 deceased individuals: 53 current cigarette smokers, 168 nonsmokers. From these data, we have conducted an epigenome-wide association study (EWAS) and identified several CpG associations with smoking. A subset of the identified CpGs map to genes that were previously indicated as blood-based smoking DNAm biomarkers, but the other CpGs map to genes that were previously undetected in blood and may reflect brain-specific processes related to smoking.

2020-05-01 | GSE147040 | GEO

Project description:Ancient Mitogenomes of 18th Century African remains

| PRJNA658314 | ENA

DNA methylation as a mediator of the association between prenatal adversity and risk factors for metabolic disease in adulthood

Project description:Although it is assumed that epigenetic mechanisms, such as changes in DNA methylation (DNAm), underlie the relationship between adverse intrauterine conditions and adult metabolic health, evidence from human studies remains scarce. Therefore, we evaluated whether DNAm in whole blood mediated the association between prenatal famine exposure and metabolic health in 422 individuals exposed to famine in utero and 463 (sibling) controls. We implemented a two-step analysis, namely, a genome-wide exploration across 342,596 cytosine-phosphate-guanine dinucleotides (CpGs) for potential mediators of the association between prenatal famine exposure and adult body mass index (BMI), serum triglycerides (TG), or glucose concentrations, which was followed by formal mediation analysis. DNAm mediated the association of prenatal famine exposure with adult BMI and TG but not with glucose. DNAm at PIM3 (cg09349128), a gene involved in energy metabolism, mediated 13.4% [95% confidence interval (CI), 5 to 28%] of the association between famine exposure and BMI. DNAm at six CpGs, including TXNIP (cg19693031), influencing β cell function, and ABCG1 (cg07397296), affecting lipid metabolism, together mediated 80% (95% CI, 38.5 to 100%) of the association between famine exposure and TG. Analyses restricted to those exposed to famine during early gestation identified additional CpGs mediating the relationship with TG near PFKFB3 (glycolysis) and METTL8 (adipogenesis). DNAm at the CpGs involved was associated with gene expression in an external data set and correlated with DNAm levels in fat depots in additional postmortem data. Our data are consistent with the hypothesis that epigenetic mechanisms mediate the influence of transient adverse environmental factors in early life on long-term metabolic health. The specific mechanism awaits elucidation.

2018-01-31 | GSE78743 | GEO

Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation [EVOIMMUNOPOP project]

Project description:DNA methylation (DNAm) is a key epigenetic mark that modulates regulatory elements and gene expression, playing a crucial role in mammalian development and physiological function. Despite extensive characterization of DNAm profiles across species, little is known about its evolutionary conservation. Here, we conducted a comparative epigenome-wide analysis of great apes to identify and characterize sequence- and methylation-conserved CpGs (MCCs). Using 202 DNAm arrays, alongside 6 matched genotype and 13 matched transcriptomic datasets, we identified 11,500 MCCs for which methylation was evolutionarily related to sequences of CpGs and methylation quantitative trait loci. MCCs were the most stable across healthy human tissues and exhibited weaker genetic associations than other CpGs. Moreover, MCCs showed minimal associations with demographic, environmental factors, and noncancer diseases, yet demonstrated stronger associations with certain cancers than other CpGs, particularly gastrointestinal cancers. Functional enrichment analysis revealed that genes associated with MCC methylation in cancer were enriched for cancer driver genes and canonical cancer pathways, highlighting a significant regulatory role for MCCs in tumorigenesis. Collectively, our findings reveal the extent of DNAm conservation in great ape evolution, its association with genetic conservation, and its relevance to human diseases. These integrative analyses offer evolutionary insights into epigenetic variation and its functional implications in human populations.

2024-11-11 | GSE281199 | GEO

Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation [CareGiver cohort]

2024-11-11 | GSE281200 | GEO

Epigenetic drift during long-term culture of cells in vitro [4C]

Project description:Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. These changes might be directly regulated or caused by gradual deregulation of the epigenetic state, which is often referred to as “epigenetic drift”. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated in the course of culture expansion of mesenchymal stem cells (MSCs) and other cell types. During reprogramming into induced pluripotent stem cells (iPSCs) particularly the culture-associated hypomethylation is reversed simultaneously with age-associated and pluripotency-associated DNAm changes. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that upon passaging the DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpolulations of MSCs at later passages. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no preferential interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results indicate that DNAm changes during culture-expansion resembles epigenetic drift.

2021-05-26 | GSE165603 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data