Targeted bisulfite sequencing: A novel tool for the assessment of DNA methylation with high sensitivity and increased coverage

Moser, Dirk; Muller, Stella Torres; Hummel, Elisabeth; Limberg, Alicia; Dieckmann, Linda; Frach, Leonard; Pakusch, Johanna; Flasbeck, Vera; Brüne, Martin; Beygo, Jasmin; Klein-Hitpaß, Ludger; Kumsta, Robert

doi:10.1016/j.psyneuen.2020.104784

Cited by 19 publications

(20 citation statements)

References 49 publications

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“…[23,52,59,60]. We believe that studies reporting methylation patterns beneath a certain methodological detection threshold need to be interpreted with caution and warrant replication [17,43,[61][62][63]. Another shortcoming of the present study relates to the sample, which was exclusively female.…”

Section: Plos Onementioning

confidence: 73%

“…With regard to NR3C1, we found lower methylation in individuals with BPD compared with healthy subjects. However, the overall degree of methylation was small, such that a group difference of 0.08% needs to be critically discussed in terms of its biological relevance, especially in light of methodological limitations due a detection threshold of 0.46% [43]. However, post-hoc power analysis showed that the statistical power of 0.757 was fairly large.…”

Section: Plos Onementioning

confidence: 99%

“…The analyses of DNA methylation were conducted by using next-generation sequencing (NGS). The method and quality control procedures are reported in detail in Moser et al [43]. In short, 500 ng genomic DNA were bisulfite converted by using the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine-USA).…”

Section: Epigenetic Analysesmentioning

confidence: 99%

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Association between childhood maltreatment, psychopathology and DNA methylation of genes involved in stress regulation: Evidence from a study in Borderline Personality Disorder

Flasbeck

Brüne

2021

PLoS ONE

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Previous research suggests that childhood maltreatment is associated with epigenetic modification of genes involved in hypothalamic-pituitary-adrenal (HPA) functioning, which could cause dysregulation of the stress response system. If pervasive, this may be associated with the development of stress-related disorder in adults, including affective disorders, anxiety disorders, post-traumatic stress disorder (PTSD) or borderline-personality disorder (BPD). The majority of studies have focused on DNA methylation of the glucocorticoid receptor gene (NR3C1) and the FKBP5 encoding gene, which regulates the sensitivity of the glucocorticoid receptor (GR). How methylation of NR3C1 and FKBP5 interferes with childhood adversity and psychopathology as well as empathy is an under-researched issue. Here, we sought to investigate the association of childhood maltreatment in a sample of 89 individuals (44 healthy participants and 45 patients diagnosed with BPD) with the methylation of the 1F promoter region of NR3C1 and the intron 7 of FKBP5 as well as with different measures of psychopathology and empathy. Methylation of FKBP5 (bin 2) correlated with anxiety (SCL-90-R) and the global psychopathological symptom load index (GSI), as well as with lower empathic perspective-taking abilities. Psychopathology and empathy impairments correlated with the level of childhood maltreatment. No difference in FKBP5 methylation was observed between the clinical and the non-clinical group. Methylation of NR3C1 was lower in BPD patients compared to controls, yet with small differences. The results are discussed regarding their biological relevance, including possible evolutionary explanations. In short, the regulation of the GR sensitivity by methylation of FKBP5 correlated with psychopathology and empathy scores, while no correlation emerged with the severity of childhood adversity.

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Section: Plos Onementioning

confidence: 73%

Section: Plos Onementioning

confidence: 99%

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Association between childhood maltreatment, psychopathology and DNA methylation of genes involved in stress regulation: Evidence from a study in Borderline Personality Disorder

Flasbeck

Brüne

2021

PLoS ONE

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“…We report four major findings. First, by using highly sensitive bisulfite sequencing (22), we point out 166 CpG sites with desirable statistical properties for research of interindividual differences (see assay sensitivity in Supplementary Table 1 for details). CpG sites with insufficient variance and low mean DNA methylation values (1%) can be disregarded in future studies.…”

Section: Discussionmentioning

confidence: 99%

The DNA methylation landscape of the human oxytocin receptor gene (OXTR): Recommendations for future research

Muller

Sicorello

Moser

et al. 2022

Preprint

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The oxytocin receptor gene (OXTR) is of interest when investigating the effects of early adversity on DNA methylation. However, there is heterogeneity regarding the selection of the most promising CpG sites to target for analyses. The goal of this study was to determine functionally relevant clusters of CpG sites within the OXTR CpG island in 113 mother-infant dyads, with 58 of the mothers having experienced childhood maltreatment (CM). OXTR DNA methylation and gene expression was analyzed in peripheral/umbilical blood mononuclear cells. Different complexity reduction approaches were used to reduce the 188 CpG sites into clusters of co-methylated sites. Furthermore, associations between OXTR DNA methylation (cluster- and site-specific level) and OXTR gene expression and CM were investigated. Results showed that, first, CpG sections differed strongly regarding their statistical utility for research of individual differences in DNA methylation. Second, cluster analyses and Partial Least Squares (PLS) suggested two clusters consisting of intron1/exon2 and the protein-coding region of exon 3, respectively, as most strongly associated with outcome measures. Third, cross-validated PLS regression explained 7% of variance in CM, with low cross-validated variance explained for the prediction of gene expression. Fourth, very high mother-child correspondence was observed in correlation patterns within the identified clusters, but only modest correspondence outside these clusters. This study characterized the DNA methylation landscape of the OXTR CpG island by highlighting clusters of CpG sites that show desirable statistical properties and predictive value. We provide a Companion Web Application to guide future studies in their choice of CpG sites.

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“…For DBS in both cohorts, DNA was bisulfite-modified with the EZ DNA Methylation Gold Kit (Zymo Research, Orange, CA, USA) and processed as described elsewhere [34,35] using primers as indicated in Supplementary Table 3, Additional File 1.…”

Section: Targeted Bisulfite Sequencingmentioning

confidence: 99%

No evidence for intervention-associated DNA methylation changes in monocytes of patients with posttraumatic stress disorder or anorexia nervosa

Hummel

Elgizouli

Beygo

et al. 2020

Preprint

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BackgroundDNA methylation patterns can be responsive to environmental influences. This observation has sparked interest in the potential for psychological interventions to influence epigenetic processes. Recent studies have observed correlations between DNA methylation changes and therapy outcome. However, most did not control for changes in cell composition from pre- to post-therapy. Here, we addressed this limitation and analyzed DNA methylation patterns by targeted deep bisulfite sequencing (DBS) of commonly assessed candidate genes in isolated monocytes from 60 female patients with post-traumatic stress disorder (PTSD) before and after in-patient treatment. Furthermore, in two patients with PTSD and three patients with anorexia nervosa (AN), whole-genome bisulfite sequencing (WGBS) was performed before and after intervention with the aim of identifying novel genomic regions with notable pre-to-post intervention DNA methylation changes.ResultsWGBS yielded only a limited set of candidate regions with suggestive evidence of differential methylation pre- to post-therapy. These differential methylation patterns did not prove replicable when investigated in the entire cohort. Furthermore, equivalence testing and Bayesian analyses provided evidence against physiologically meaningful intervention associated DNA methylation changes in monocytes of PTSD patients in commonly investigated target genes (NR3C1, FKBP5, SLC6A4, OXTR).ConclusionsWe conclude that there is no evidence for major, recurrent intervention-associated DNA methylation changes in the investigated genes in monocytes of patients with either PTSD or anorexia nervosa.

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Targeted bisulfite sequencing: A novel tool for the assessment of DNA methylation with high sensitivity and increased coverage

Cited by 19 publications

References 49 publications

Association between childhood maltreatment, psychopathology and DNA methylation of genes involved in stress regulation: Evidence from a study in Borderline Personality Disorder

Association between childhood maltreatment, psychopathology and DNA methylation of genes involved in stress regulation: Evidence from a study in Borderline Personality Disorder

The DNA methylation landscape of the human oxytocin receptor gene (OXTR): Recommendations for future research

No evidence for intervention-associated DNA methylation changes in monocytes of patients with posttraumatic stress disorder or anorexia nervosa

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