Metastable Epiallele: Role of Epigenetic Variability for the Development of Metabolic and Endocrine Diseases

Project Information

E-VarEndo

Grant agreement ID: 101043991

DOI

10.3030/101043991

EC signature date 25 October 2022

Start date 1 February 2023

End date 31 January 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 997 969,00

EU contribution

€ 1 997 969,00

Coordinated by

CHARITE - UNIVERSITAETSMEDIZIN BERLIN
Germany

Periodic Reporting for period 1 - E-VarEndo (Metastable Epiallele: Role of Epigenetic Variability for the Development of Metabolic and Endocrine Diseases)

Reporting period: 2023-02-01 to 2025-07-31

Summary of the context and overall objectives of the project

The increasing prevalence of obesity worldwide in industrial and also in low- and middle-income countries has led to a severe burden for affected patients and health care systems. It is estimated that worldwide approximately 40 % of women and 39 % of men are overweight or obese. As obesity is one major risk-factor for the development of cardiovascular diseases or type 2 diabetes mellitus, it is of importance to understand the physiological background of body weight regulation to adapt treatment options and to plan prevention approaches for these individuals, which are at risk to become obese later in life. So far, verified monogenic causes for obesity are rare. Nearly all identified mutations are located in genes embedded in hypothalamic body weight regulation. Phenotyping of affected patients has provided important insights into the regulation of this pathway. To identify additional factors and delineate the genetic contribution for the development of obesity, a number of large genome-wide association studies (GWAS) have been performed in recent years and polygenic risk scores have been established. Collectively, all identified SNPs (single nucleotide polymorphisms) and polygenic risk scores explain less than 25 % of individual body weight variability. These observations are in stark contrast to results of large twin studies, in which a high grade of BMI (body-mass-index) concordance between monozygotic twins has been shown and which has been interpreted pointing towards a high grade of body weight heritability of up to 0.71-0.86. This discrepancy has been termed missing heritability. One approach to address this problem is to acknowledge that, in addition to genetic factors, epigenetic modifications could likewise contribute to body weight regulation.
Differences in DNA methylation are established factors for development of imprinting diseases and various cancer types. In addition, there is accumulating evidence that DNA methylation contributes to the development and predisposition for common diseases like obesity. Specifically, this project focuses on the role of so-called metastable epialleles, DNA regions defined as having stochastically regulated methylation patterns that are set during early embryonic development and that are invariable across all cell types and stable over time. Certain mouse models such as the agouti viable yellow (Avy) mice showed that in these cases DNA methylation variability at particular regions like metastable epialleles is associated with phenotype variation. Triggered by these observations, we are aiming to gain further knowledge about the relationship between epigenetic marks like DNA methylation/ histone modifications and induvial risk of developing metabolic diseases. Thereby we want to optimize treatment and prevention strategies for affected individuals with obesity and related comorbidities.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Epigenetic modifications are playing a critical role for several physiological processes. Especially rodent models were of importance to understand how epigenetic marks could contribute to phenotypic variability and to which extent environmental factors could potentially modulate epigenetic modifications. In humans, key findings have been made by analysing especially DNA methylation in large cohort samples (epigenome-wide associations studies). Thereby, an association between DNA methylation changes and individual risk to develop certain diseases like obesity has been described. However, it remains a critical question, if there is a causal relationship between epigenetic changes and disease risk and if and how epigenetic variability is leading to any functional consequences and affect related gene function. Additionally, it is difficult to study, how environmental factors during e.g. embryonic development are interfering with epigenetic profiling. Currently, animal models are the gold standard to study these research questions. For this reason, it might be of advantage to add a human cell model, which could be added to re-investigate findings made in animal models or human cohorts to gain further knowledge about epigenetic regulation and disease risk.
Therefore, we started to establish a human stem-cell based in vitro system with the aim to recapitulate DNA methylation patterning for certain regions (especially metastable epialleles). Human embryonic stem cells (hESC) were guided initially in a naïve state (representing pre-implantation state). This led to reduced levels of DNA methylation. Thereafter, naïve hESC were differentiated via a formative state into hypothalamic neurons. This is leading to increase levels of DNA methylation. In a first pilot study, we evaluated candidate regions and investigated the cellular response to external stimuli like changes of carbon1 metabolites in cell culture media. In a second step, ongoing work examine this hESC model methylome and transcriptome wide and in regards to different histone marks. These experiments are planned to evaluate, whether this stem cell model could help to understand more about the underlying mechanism of DNA methylation profile establishment and the relevance of DNA methylation variability for gene function.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The relevance of epigenetic marks for gene function and (patho-)physiological processes has been studied in detail by several research groups since decades. Especially animal models contributed to a better understanding how epigenetic variability may lead to phenotypic variation. Some studies suggested that this finding would also be relevant in humans. A large number of epigenome wide association studies identified interesting results and observed associations between DNA methylation differences and diseases such as obesity and diabetes mellitus type 2. However, potential tissue specificity, age- and sex dependent changes and influence from environmental factors impede epigenetic studies and their interpretation especially from human samples. Using human cohort samples (peripheral blood cells), postmortem samples (hypothalamic neurons, blood cells), samples from longitudinal studies (blood collection after birth and later in life) allowed to identify DNA methylation differences at a certain gene (pro-opiomelanocortin, POMC), which were associated with increased BMI (body mass index) in female adults. Further studies with a cohort from The Gambia provided evidence for a relevance of Carbon 1 metabolites (e.g. Betaine) for POMC methylation profile development in utero. Based on these findings in primary samples, POMC methylation has been studies in a stem cell based in vitro system. Here, POMC methylation correlated negatively with gene expression. This experimental set-up exemplified, that the combination of human primary tissue examination and in vitro stem-cell based systems could be an advantage in the future to learn more about the functional consequences of DNA methylation alterations on gene function and thereby potentially individual disease risk.