DNA methylation and waist-to-hip ratio: an epigenome-wide association study in Chinese monozygotic twins

Causation and familial confounding as explanations for the associations of polygenic risk scores with breast cancer: Evidence from innovative ICE FALCON and ICE CRISTAL analyses

A polygenic risk score (PRS) combines the associations of multiple genetic variants that could be due to direct causal effects, indirect genetic effects, or other sources of familial confounding. We have developed new approaches to assess evidence for and against causation by using family data for pairs of relatives (Inference about Causation from Examination of FAmiliaL CONfounding [ICE FALCON]) or measures of family history (Inference about Causation from Examining Changes in Regression coefficients and Innovative STatistical AnaLyses [ICE CRISTAL]). Inference is made from the changes in regression coefficients of relatives' PRSs or PRS and family history before and after adjusting for each other. We applied these approaches to two breast cancer PRSs and multiple studies and found that (a) for breast cancer diagnosed at a young age, for example, <50 years, there was no evidence that the PRSs were causal, while (b) for breast cancer diagnosed at later ages, there was consistent evidence for causation explaining increasing amounts of the PRS-disease association. The genetic variants in the PRS might be in linkage disequilibrium with truly causal variants and not causal themselves. These PRSs cause minimal heritability of breast cancer at younger ages. There is also evidence for nongenetic factors shared by first-degree relatives that explain breast cancer familial aggregation. Familial associations are not necessarily due to genes, and genetic associations are not necessarily causal.

Genome-wide methylation association study in monozygotic twins discordant for curve severity of adolescent idiopathic scoliosis

BACKGROUND CONTEXT

Emerging evidence suggests that abnormal DNA methylation patterns may play a role in the progression of adolescent idiopathic scoliosis (AIS). However, the mechanisms underlying the influence of DNA methylation on curve severity remain largely unknown.

PURPOSE

To characterize the DNA methylation profiles associated with the curve severity of AIS.

STUDY DESIGN

Retrospective study with prospectively collected clinical data and blood samples.

METHODS

A total of 7 AIS monozygotic twin pairs discordant for curve severity were included. Genome-wide methylation profile from blood samples were quantified by Illumina Infinium MethylationEPIC BeadChip (850K chip). Cell type composition of the samples was estimated by RefbaseEWAS method. Differentially methylated CpG sites were identified through comparison between patients with low and high Cobb angle. We also performed a gene-based collapsing analysis using mCSEA by aggregating the CpG sites based on promoter region. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed using clusterProfiler package.

RESULTS

Genome-wide DNA methylation analysis identified multiple differentially methylated positions across the genome. Gene-based collapsing analysis identified 212 differentially methylated genes (FDR adjusted p<0.05), most of which (186/212) were hypermethylated in the group with high Cobb angle. Some of the identified genes were well-documented in AIS literature, such as TBX1, PAX3 and LBX1. Functional enrichment analysis revealed that the differentially methylated genes (DMGs) were involved in pattern specification process, skeletal development, muscle function, neurotransmission and several signaling pathways (cAMP, Wnt and prolactin).

CONCLUSIONS

The study represents the largest systematic epigenomic analyses of monozygotic twins discordant for curve severity and supports the important role of altered DNA methylation in AIS.

CLINICAL SIGNIFICANCE

The identified CpG sites provide insight into novel biomarkers predicting curve progression of AIS. Furthermore, the differentially methylated genes and enriched pathways may serve as interventional therapy target for AIS patients.

Transcriptional Control of Subcutaneous Adipose Tissue by the Transcription Factor CTCF Modulates Heterogeneity in Fat Distribution in Women

Determining the mechanism driving body fat distribution will provide insights into obesity-related health risks. We used functional genomics tools to profile the epigenomic landscape to help infer the differential transcriptional potential of apple- and pear-shaped women's subcutaneous adipose-derived stem cells (ADSCs). We found that CCCTC-binding factor (CTCF) expression and its chromatin binding were increased in ADSCs from pear donors compared to those from apple donors. Interestingly, the pear enriched CTCF binding sites were located predominantly at the active transcription start sites (TSSs) of genes with active histone marks and YY1 motifs and were also associated with pear enriched RNAPII binding. In contrast, apple enriched CTCF binding sites were mainly found at intergenic regions and when identified at TSS, they were enriched with the bivalent chromatin signatures. Altogether, we provide evidence that CTCF plays an important role in differential regulation of subcutaneous ADSCs gene expression and may influence the development of apple vs. pear body shape.

Genetics and Epigenetics in Obesity: What Do We Know so Far?

PURPOSE OF REVIEW

Enormous progress has been made in understanding the genetic architecture of obesity and the correlation of epigenetic marks with obesity and related traits. This review highlights current research and its challenges in genetics and epigenetics of obesity.

RECENT FINDINGS

Recent progress in genetics of polygenic traits, particularly represented by genome-wide association studies, led to the discovery of hundreds of genetic variants associated with obesity, which allows constructing polygenic risk scores (PGS). In addition, epigenome-wide association studies helped identifying novel targets and methylation sites being important in the pathophysiology of obesity and which are essential for the generation of methylation risk scores (MRS). Despite their great potential for predicting the individual risk for obesity, the use of PGS and MRS remains challenging. Future research will likely discover more loci being involved in obesity, which will contribute to better understanding of the complex etiology of human obesity. The ultimate goal from a clinical perspective will be generating highly robust and accurate prediction scores allowing clinicians to predict obesity as well as individual responses to body weight loss-specific life-style interventions.

Blood-based genome-wide DNA methylation correlations across body-fat- and adiposity-related biochemical traits

The recent increase in obesity levels across many countries is likely to be driven by nongenetic factors. The epigenetic modification DNA methylation (DNAm) may help to explore this, as it is sensitive to both genetic and environmental exposures. While the relationship between DNAm and body-fat traits has been extensively studied, there is limited literature on the shared associations of DNAm variation across such traits. Akin to genetic correlation estimates, here, we introduce an approach to evaluate the similarities in DNAm associations between traits: DNAm correlations. As DNAm can be both a cause and consequence of complex traits, DNAm correlations have the potential to provide insights into trait relationships above that currently obtained from genetic and phenotypic correlations. Utilizing 7,519 unrelated individuals from Generation Scotland with DNAm from the EPIC array, we calculated DNAm correlations between body-fat- and adiposity-related traits by using the bivariate OREML framework in the OSCA software. For each trait, we also estimated the shared contribution of DNAm between sexes. We identified strong, positive DNAm correlations between each of the body-fat traits (BMI, body-fat percentage, and waist-to-hip ratio, ranging from 0.96 to 1.00), finding larger associations than those identified by genetic and phenotypic correlations. We identified a significant deviation from 1 in the DNAm correlations for BMI between males and females, with sex-specific DNAm changes associated with BMI identified at eight DNAm probes. Employing genome-wide DNAm correlations to evaluate the similarities in the associations of DNAm with complex traits has provided insight into obesity-related traits beyond that provided by genetic correlations.

Role of DNA methylation in diabetes and obesity

Due to the fact that the upward trend of several metabolic disorders such as diabetes and obesity, in individuals especially monozygotic twins, who are under the same effects from the environment, are not similar, the role of epigenetic elements like DNA methylation needs taking into account. In this chapter, emerging scientific evidence supporting the strong relationship between changes in DNA methylation and those diseases' development was summarized. Changing in the expression level of diabetes/obesity-related genes through being silenced by methylation can be the underlying mechanism of this phenomenon. Genes with abnormal methylation status are potential biomarkers for early prediction and diagnosis. Moreover, methylation-based molecular targets should be investigated as a new treatment for both T2D and obesity.