Improved results of LINE-1 methylation analysis in formalin-fixed, paraffin-embedded tissues with the application of a heating step during the DNA extraction process

Wen, Xianyu; Jeong, Seorin; Kim, Young-Hoon; Bae, Jeong Mo; Cho, Nam Yun; Kim, Jung Ho; Kang, Gyeong Hoon

doi:10.1186/s13148-016-0308-0

Cited by 44 publications

(53 citation statements)

References 28 publications

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“…Chronological GA was based on ultrasound scans, and we applied novel bioinformatics methods to account for any sample contamination by maternal blood 17 and for the effects of cell type heterogeneity 18 and genetic population structure, 19 which are factors strongly influencing epigenetic profiles. 28 Furthermore, we validated our findings by using the bootstrap method and applied a hierarchically structured analysis strategy when we examined child psychiatric problems to decrease the likelihood of false-positive findings.…”

Section: Discussionmentioning

confidence: 99%

“…16 Samples with maternal blood contamination were excluded (n = 9) according to a method described elsewhere. 17 The final dataset contained 428,619 CpG sites.…”

Section: Methodsmentioning

confidence: 99%

“…Based on our previous findings in this cohort, 11 we thereafter made adjustments for maternal age at delivery (≥40 years/<40 years), insulin-treated gestational diabetes mellitus in a previous pregnancy (yes/no), Sjögren syndrome (yes/no), neonate’s 1-minute Apgar score (≤6/>6), and sex (girl/ boy). In the analyses of child psychiatric problems, we made further adjustments for child’s age at follow-up (years) and maternal Beck Depression Inventory–II scores (BDI-II <14/BDI-II ≥14) 22 reported at the child follow-up.…”

Section: Methodsmentioning

confidence: 99%

“…We have extended these analyses by showing that lower epigenetic GA was associated with maternal insulin-treated gestational diabetes mellitus in a previous pregnancy and in Sjögren syndrome, and higher epigenetic GA with a maternal age of more than 40 years at delivery, neonate’s lower 1-minute Apgar score, and female sex. 11 …”

mentioning

confidence: 99%

“…Furthermore, we tested whether child’s epigenetic GA at birth predicted early childhood psychiatric problems, and whether child’s epigenetic GA mediated the associations of maternal antenatal depression with child psychiatric problems. Finally, we tested whether the associations were moderated by child’s sex, as sex biases exist in longevity and aging trajectories, 12 epigenetic age based on the Horvath and the Hannum epigenetic age predictors, 6,9 epigenetic GA at birth, 11 and prevalence and etiology of psychiatric problems. 1,3–5,13 .…”

mentioning

confidence: 99%

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The Epigenetic Clock at Birth: Associations With Maternal Antenatal Depression and Child Psychiatric Problems

Suarez

Lahti

Czamara

et al. 2018

Journal of the American Academy of Child & Adolescent Psych

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Objective: Maternal antenatal depression may compromise the fetal developmental milieu and contribute to individual differences in aging and disease trajectories in later life. We evaluated the association between maternal antenatal depression and a novel biomarker of aging at birth, namely epigenetic gestational age (GA) based on fetal cord blood methylation data. We also examined whether this biomarker prospectively predicts and mediates maternal effects on early childhood psychiatric problems. Method: A total of 694 mothers from the Prediction and Prevention of Preeclampsia and Intrauterine Growth Restriction (PREDO) Study provided information on history of depression diagnosed before pregnancy; 581 completed the Center for Epidemiological Studies Depression Scale throughout pregnancy, and 407 completed the Child Behavior Checklist at child’s age 3.7 years (SD = 0.75 year). DNA methylation (DNAm) GA of fetal cord blood DNA was based on the methylation profile of 148 selected cytosine linked to guanine by phosphate (CpG) sites. Epigenetic GA was calculated as the arithmetic difference between DNAm GA and chronological GA and adjusted for chronological GA. Results: Maternal history of depression diagnosed before pregnancy (mean difference = –0.25 SD units, 95% CI = –0.46 to 0.03) and greater antenatal depressive symptoms (–0.08 SD unit per 1-SD unit increase, 95% CI = –0.16 to –0.004) were associated with child’s lower epigenetic GA. Child’s lower epigenetic GA, in turn, prospectively predicted total and internalizing problems and partially mediated the effects of maternal antenatal depression on internalizing problems in boys. Conclusion: Maternal antenatal depression is associated with lower epigenetic GA in offspring. This lower epigenetic GA seems to be associated with a developmental disadvantage for boys, who, in early childhood, show greater psychiatric problems.

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Section: Discussionmentioning

confidence: 99%

“…16 Samples with maternal blood contamination were excluded (n = 9) according to a method described elsewhere. 17 The final dataset contained 428,619 CpG sites.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The Epigenetic Clock at Birth: Associations With Maternal Antenatal Depression and Child Psychiatric Problems

Suarez

Lahti

Czamara

et al. 2018

Journal of the American Academy of Child & Adolescent Psych

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Consistency of the S5 DNA methylation classifier in formalin‐fixed biopsies versus corresponding exfoliated cells for the detection of pre‐cancerous cervical lesions

et al. 2021

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Methylation biomarkers are promising tools for diagnosis and disease prevention. The S5 classifier is aimed at the prevention of cervical cancer by the early detection of cervical intraepithelial neoplasia (CIN). S5 is based on pyrosequencing a promoter region of EPB41L3 and five late regions of HPV types 16, 18, 31, and 33 following bisulfite conversion of DNA. Good biomarkers should perform well in a variety of sample types such as exfoliated cells, fresh frozen or formalin‐fixed paraffin‐embedded (FFPE) materials. Here, we tested the performance of S5 on 315 FFPE biopsies with paired exfoliated cervical samples using four different conversion kits (Epitect Bisulfite, Epitect Fast Bisulfite, EZ DNA Methylation, and EZ DNA Methylation‐Lightning). The S5 values from FFPE biopsies for all kits were significantly correlated with those obtained from their paired exfoliated cells. For the EZ DNA Methylation kit, we observed an average increased methylation of 4.4% in FFPE. This was due to incomplete conversion of DNA (73% for FFPE vs. 95% for cells). The other kits had a DNA conversion rate in FFPE similar to the cells (95%–97%). S5 performed well at discriminating

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Clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma: prediction of early recurrence based on genome-wide DNA methylation profiling

Endo

Fujimoto

Ito

et al. 2021

J Cancer Res Clin Oncol

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Purpose The present study was conducted to clarify the clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma (PDAC). Methods Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip, and DNA methylation quantification was verified using pyrosequencing. We analyzed fresh-frozen tissues from an initial cohort (17 samples of normal control pancreatic tissue [C] from 17 patients without PDAC, and 34 samples of non-cancerous pancreatic tissue [N] and 82 samples of cancerous tissue [T] both obtained from 82 PDAC patients) and formalin-fixed paraffin-embedded T samples from 34 patients in a validation cohort. Results The DNA methylation profiles of N samples tended to differ from those of C samples, and 91,907 probes showed significant differences in DNA methylation levels between C and T samples. Epigenetic clustering of T samples was significantly correlated with a larger tumor diameter and early recurrence (ER), defined as relapse within 6 months after surgery. Three marker CpG sites, applicable to formalin-fixed paraffin-embedded surgically resected materials regardless of their tumor cell content, were identified for prediction of ER. The sensitivity and specificity for detection of patients belonging to the ER group using a panel combining these three marker CpG sites, including a CpG site in the CDK14 gene, were 81.8% and 71.7% and 88.9% and 70.4% in the initial and validation cohorts, respectively. Conclusion These findings indicate that DNA methylation alterations may have a clinicopathological impact on PDAC. Application of our criteria will ultimately allow prediction of ER after surgery to improve the outcome of PDAC patients.

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Improved results of LINE-1 methylation analysis in formalin-fixed, paraffin-embedded tissues with the application of a heating step during the DNA extraction process

Cited by 44 publications

References 28 publications

The Epigenetic Clock at Birth: Associations With Maternal Antenatal Depression and Child Psychiatric Problems

The Epigenetic Clock at Birth: Associations With Maternal Antenatal Depression and Child Psychiatric Problems

Consistency of the S5 DNA methylation classifier in formalin‐fixed biopsies versus corresponding exfoliated cells for the detection of pre‐cancerous cervical lesions

Clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma: prediction of early recurrence based on genome-wide DNA methylation profiling

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