Establishment of the MethyLight Assay for Assessing Aging, Cigarette Smoking, and Alcohol Consumption

Endo, Kazuhira; Li, Jiawei; Nakanishi, Masayoshi; Asada, Takashi; Ikesue, Masahiro; Goto, Yoichi; Fukushima, Yasue; Iwai, Naoharu

doi:10.1155/2015/451981

Cited by 16 publications

(9 citation statements)

References 31 publications

(36 reference statements)

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“…We calculated the average standard deviation, ranging between 0.010 and 0.044 ( Table A2 ). Compared to other methods like SYBR Green-based qPCR [ 30 ], pyrosequencing [ 54 ], and massively parallel sequencing [ 52 ], these values are considered low for methylation assays and are in concordance with other MethyLight studies [ 55 ].…”

Section: Resultssupporting

confidence: 71%

Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting

Vidaki

Kalamara

Carnero‐Montoro

et al. 2018

Genes

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Monozygotic (MZ) twins are typically indistinguishable via forensic DNA profiling. Recently, we demonstrated that epigenetic differentiation of MZ twins is feasible; however, proportions of twin differentially methylated CpG sites (tDMSs) identified in reference-type blood DNA were not replicated in trace-type blood DNA. Here we investigated buccal swabs as typical forensic reference material, and saliva and cigarette butts as commonly encountered forensic trace materials. As an analog to a forensic case, we analyzed one MZ twin pair. Epigenome-wide microarray analysis in reference-type buccal DNA revealed 25 candidate tDMSs with >0.5 twin-to-twin differences. MethyLight quantitative PCR (qPCR) of 22 selected tDMSs in trace-type DNA revealed in saliva DNA that six tDMSs (27.3%) had >0.1 twin-to-twin differences, seven (31.8%) had smaller (<0.1) but robustly detected differences, whereas for nine (40.9%) the differences were in the opposite direction relative to the microarray data; for cigarette butt DNA, results were 50%, 22.7%, and 27.3%, respectively. The discrepancies between reference-type and trace-type DNA outcomes can be explained by cell composition differences, method-to-method variation, and other technical reasons including bisulfite conversion inefficiency. Our study highlights the importance of the DNA source and that careful characterization of biological and technical effects is needed before epigenetic MZ twin differentiation is applicable in forensic casework.

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Section: Resultssupporting

confidence: 71%

Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting

Vidaki

Kalamara

Carnero‐Montoro

et al. 2018

Genes

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“…DNA methylation, one of the most studied and stable epigenetic modifications, is capable of controlling gene expression of common traits and influencing the development of aberrant health outcomes under external exposures [12]. Previous epigenomewide association studies (EWASs) based on whole blood DNA methylation have identified numerous CpG sites that are associated with aging [13], various cancers and other chronic diseases [14,15], as well as with many forms of exogenous exposures and lifestyle-related factors, such as environmental pollutants [16], body mass index (BMI) [17], alcohol consumption [18] and smoking [18,19]. DNA methylation signatures have furthermore been considered as potential indicators of mortality from specific diseases and consequently with all-cause mortality [20].…”

Section: Introductionmentioning

confidence: 99%

Leukocyte telomere length and epigenetic-based mortality risk score: associations with all-cause mortality among older adults

et al. 2018

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Telomere length (TL) has been established as a biomarker of aging and aging-related health outcomes, but showed only a weak or inconsistent association with all-cause mortality in previous epidemiological studies. Recently, an epigenetic 'mortality risk score' (MS) based on whole blood DNA methylation at 10 mortality-related CpG sites has been demonstrated to be strongly related to all-cause mortality at the population level. This study aimed to address the association between TL and this MS, and to assess and compare their associations with all-cause mortality. The MS was derived from the DNA methylation profiles measured by Illumina Human Methylation450K Beadchip and TL was measured by quantitative PCR at baseline among 1517 participants aged 50-75 of the German ESTHER cohort study. In cross-sectional bi- and multivariable analyses, the MS was strongly associated and showed monotonic dose-response relationships with TL (p-values <0.05). However, only the MS but not TL was associated with all-cause mortality during a median follow-up of 12.5 years. After controlling for potential covariates and TL, hazard ratios (95% CI) for all-cause mortality for low, moderate and high levels of the MS defined by 1, 2-5 and >5 CpG sites with aberrant methylation were 2.24 (1.13-4.41), 3.31 (1.76-6.22) and 6.33 (3.22-12.41) compared to a MS of 0, respectively. Our investigation shows that the epigenetic-based MS is strongly associated with TL, a broadly accepted aging biomarker, and at the same time shows much stronger associations with all-cause mortality than the latter.

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“…In the ROC analysis, the AUC for the DNA methylation rate was 0.746 for habitual alcohol consumers. Although the DNA methylation rates of AHRR and HNRNPA1 did not correlate with the frequency of smoking and alcohol consumption (82) , DNA methylation at these sites seems to have the potential to monitor the lifestyle of the blood sample donors. Further analyses with more various types of tissues would be also helpful.…”

Section: Forensic Applications Of Dna Methylationmentioning

confidence: 90%

“…In an effort to establish tools to aid diagnosis and monitor treatment response by environmental exposures, Endo et al . (82) developed an assay to measure DNA methylation at smoking and alcohol consumption-associated CpGs using the MethyLight method that utilizes fluorescence-based real-time PCR technology. They selected cg23576855 in the AHRR gene as smoking and cg02583484 in the HNRNPA1 gene as alcohol consumption biomarkers and tested their specificity in 33 blood samples from healthy donors.…”

Section: Forensic Applications Of Dna Methylationmentioning

confidence: 99%

“…The sensitivity varied from 0.01 to 0.5 ng of bisulfite-converted DNA (0.05 to 10 ng of genomic DNA) depending on the marker (44 , 85 , 87) , indicating the importance of primer design and sequence analyzed in the assay. Alternatives such as MethyLight and Epityper methods employing real time-PCR or MALDI-TOF mass spectrometry could also be used for assay design, but they do not provide 1 bp resolution (61 , 82) .…”

Section: Forensic Applications Of Dna Methylationmentioning

confidence: 99%

See 1 more Smart Citation

Forensic DNA methylation profiling from evidence material for investigative leads

Lee¹,

Lee²,

Shin³

2016

BMB Reports

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DNA methylation is emerging as an attractive marker providing investigative leads to solve crimes in forensic genetics. The identification of body fluids that utilizes tissue-specific DNA methylation can contribute to solving crimes by predicting activity related to the evidence material. The age estimation based on DNA methylation is expected to reduce the number of potential suspects, when the DNA profile from the evidence does not match with any known person, including those stored in the forensic database. Moreover, the variation in DNA implicates environmental exposure, such as cigarette smoking and alcohol consumption, thereby suggesting the possibility to be used as a marker for predicting the lifestyle of potential suspect. In this review, we describe recent advances in our understanding of DNA methylation variations and the utility of DNA methylation as a forensic marker for advanced investigative leads from evidence materials. [BMB Reports 2016; 49(7): 359-369]

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Establishment of the MethyLight Assay for Assessing Aging, Cigarette Smoking, and Alcohol Consumption

Cited by 16 publications

References 31 publications

Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting

Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting

Leukocyte telomere length and epigenetic-based mortality risk score: associations with all-cause mortality among older adults

Forensic DNA methylation profiling from evidence material for investigative leads

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