Epigenetics in the public sphere: interdisciplinary perspectives

DNA methylation-environment interactions in the human genome

Previously, we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018). Here, we apply mSTARR-seq to query nearly the entire human genome, including almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. We show that fragments containing these sites are enriched for regulatory capacity, and that methylation-dependent regulatory activity is in turn sensitive to the cellular environment. In particular, regulatory responses to interferon alpha (IFNA) stimulation are strongly attenuated by methyl marks, indicating widespread DNA methylation-environment interactions. In agreement, methylation-dependent responses to IFNA identified via mSTARR-seq predict methylation-dependent transcriptional responses to challenge with influenza virus in human macrophages. Our observations support the idea that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures-one of the tenets of biological embedding. However, we also find that, on average, sites previously associated with early life adversity are not more likely to functionally influence gene regulation than expected by chance.

Researcher perspectives on ethics considerations in epigenetics: an international survey

Over the past decade, bioethicists, legal scholars and social scientists have started to investigate the potential implications of epigenetic research and technologies on medicine and society. There is growing literature discussing the most promising opportunities, as well as arising ethical, legal and social issues (ELSI). This paper explores the views of epigenetic researchers about some of these discussions. From January to March 2020, we conducted an online survey of 189 epigenetic researchers working in 31 countries. We questioned them about the scope of their field, opportunities in different areas of specialization, and ELSI in the conduct of research and knowledge translation. We also assessed their level of concern regarding four emerging non-medical applications of epigenetic testing—i.e., in life insurance, forensics, immigration and direct-to-consumer testing. Although there was strong agreement on DNA methylation, histone modifications, 3D structure of chromatin and nucleosomes being integral elements of the field, there was considerable disagreement on transcription factors, RNA interference, RNA splicing and prions. The most prevalent ELSI experienced or witnessed by respondents were in obtaining timely access to epigenetic data in existing databases, and in the communication of epigenetic findings by the media. They expressed high levels of concern regarding non-medical applications of epigenetics, echoing cautionary appraisals in the social sciences and humanities literature.

Toxicoepigenetics for Risk Assessment: Bridging the Gap Between Basic and Regulatory Science

Toxicoepigenetics examines the health effects of environmental exposure associated with, or mediated by, changes in the epigenome. Despite high expectations, toxicoepigenomic data and methods have yet to become significantly utilized in chemical risk assessment. This article draws on a social science framework to highlight hitherto overlooked structural barriers to the incorporation of toxicoepigenetics in risk assessment and to propose ways forward. The present barriers stem not only from the lack of maturity of the field but also from differences in constraints and standards between the data produced by toxicoepigenetics and the regulatory science data that risk assessment processes require. Criteria and strategies that frame the validation of knowledge used for regulatory purposes limit the application of basic research in toxicoepigenetics toward risk assessment. First, the need in regulatory toxicology for standardized methods that form a consensus between regulatory agencies, basic research, and the industry conflicts with the wealth of heterogeneous data in toxicoepigenetics. Second, molecular epigenetic data do not readily translate into typical toxicological endpoints. Third, toxicoepigenetics investigates new forms of toxicity, in particular low-dose and long-term effects, that do not align well with the traditional framework of regulatory toxicology. We propose that increasing the usefulness of epigenetic data for risk assessment will require deliberate efforts on the part of the toxicoepigenetics community in 4 areas: fostering the understanding of epigenetics among risk assessors, developing knowledge infrastructure to demonstrate applicability, facilitating the normalization and exchange of data, and opening the field to other stakeholders.

[Epigenetics and oncology: Two faces of the personalization of medicine]

In this article, we outline the two dominant concepts of personalized medicine put forward by epigenetics in the field of oncology. First, knowledge on the molecular processes involved in tumor progression contributes to molecularize medicine, extending genomic medicine. Then, the identification of epigenetic mechanisms underlying the environmental causes of cancers brings scientific legitimacy to products and services whose advertising promotes the ability of each person to protect herself from cancer by adapting her lifestyle. Lastly, we argue that research in environmental epigenetics could open a new route for personalized medicine in oncology, where epigenetics contributes to an individualized assessment of patients' life paths.

Epigenetics and DOHaD: how translation to predictive testing will require a better public understanding

Epigenetics is likely to play a role in the mediation of the effects of genes and environment in risk for many non-communicable diseases (NCDs). The Developmental Origins of Health and Disease (DOHaD) theory presents unique opportunities regarding the possibility of early life interventions to alter the epigenetic makeup of an individual, thereby modifying their risk for a variety of NCDs. While it is important to determine how we can lower the risk of these NCDs, it is equally important to understand how the public's knowledge and opinion of DOHaD and epigenetic concepts may influence their willingness to undertake such interventions for themselves and their children. In this review, we provide an overview of epigenetics, DOHaD, NCDs, and the links between them. We explore the issues surrounding using epigenetics to identify those at increased risk of NCDs, including the concept of predictive testing of children. We also outline what is currently understood about the public's understanding and opinion of epigenetics, DOHaD, and their relation to NCDs. In doing so, we demonstrate that it is essential that future research explores the public's awareness and understanding of epigenetics and epigenetic concepts. This will provide much-needed information which will prepare health professionals for the introduction of epigenetic testing into future healthcare.

Public knowledge and opinion of epigenetics and epigenetic concepts

The field of epigenetics is currently one of the most rapidly expanding in biology and has resulted in increasing public interest in its applications to human health. Epigenetics provides a promising avenue for both targeted individual intervention and public health messaging. However, to develop effective strategies for engagement, it is important to understand the public's understanding of the relevant concepts. While there has been some research exploring the public's understanding of genetic and environmental susceptibility to disease, limited research exists on public opinion and understanding of epigenetics and epigenetic concepts. Using an online questionnaire, this study investigated the Australian public's understanding, views, and opinions of epigenetics and related concepts, including the concepts of the developmental origins of health and disease (DOHaD) and the first 1000 days. Over 600 questionnaires were completed, with 391 included in the analysis. The survey included questions on knowledge of epigenetics and perceptions of epigenetic concepts for self and for children. Data were analyzed using predominately descriptive statistics, with free-text responses scored based on concordance with predetermined definitions. While participants' recognition of epigenetic terms and phrases was high, their understanding was limited. The DOHaD theory was more accurately understood than the first 1000 days or epigenetics itself. Female participants without children were more likely to recognize the term epigenetics, while age also had an impact. This research provides a solid foundation for further detailed investigation of these themes, all of which will be important data to help inform future public health messages regarding epigenetic concepts.

Genetic discrimination views in online discussion forums: Perspectives from Canadian forumites

Recent advancements in genetic technologies have made genetic information increasingly sought out in a wide range of non-therapeutic contexts, which has increased the risk that such information be used to discriminate against individuals. Frequently, it is genetic counselors who have to respond to questions about genetic discrimination (GD) from worried patients. Here, we examine the general Canadian public's knowledge, attitudes, and concerns about GD through a comprehensive analysis and categorization of posts from selected Canadian online discussion forums. Overall, we collected 1,638 posts, from which we coded 694 posts originating from newspaper comment sections and Reddit posts that were categorized to yield 6 main themes that consistently concerned Canadian users on the topics of GD: (a) discussions centered around how insurance business practices can be affected by genetic information; (b) issues in employment; (c) 'fear' of genetic testing and eugenics; (d) preventive approaches such as law and human rights instruments; (e) the predictive value and privacy that should be conferred to genetic information; and (f) other ethical issues. Overall, discussions addressed risk stratification models applied to genetic information and personal insurance underwriting. We find that many forum users (aka forumites) fear GD in insurance and employment, consider genetic information private, and strongly support different legal approaches to prevent GD. However, we find dissension among forumites that may represent different advocacy groups such as insurers and employers. From these important concerns and social conceptions, we discuss issues that should be taken into consideration for the development of future policies and information campaigns addressing GD in Canada and other countries.

The social construction of the social epigenome and the larger biological context

Epigenetics researchers in developmental, cell, and molecular biology greatly diverge in their understanding and definitions of epigenetics. In contrast, social epigeneticists, e.g., sociologists, scholars of STS, and behavioural scientists, share a focus and definition of epigenetics that is environmentally caused and trans-generationally inherited. This article demonstrates that this emphasis on the environment and on so-called Lamarckian inheritance, in addition to other factors, reflects an interdisciplinary power struggle with genetics, in which epigenetics appears to grant the social sciences a higher epistemic status. Social scientists' understanding of epigenetics, thus, appears in part to be socially constructed, i.e., the result of extra-scientific factors, such as social processes and the self-interest of the discipline. This article argues that social epigeneticists make far-reaching claims by selecting elements from research labelled epigenetics in biology while ignoring widely confirmed scientific facts in genetics and cell biology, such as the dependence of epigenetic marks on DNA sequence-specific events, or the lack of evidence for the lasting influence of the environment on epigenetic marks or the epigenome. Moreover, they treat as a given crucial questions that are far from resolved, such as what role, if any, DNA methylation plays in the complex biochemical system of regulating gene activity. The article also points out incorrect perceptions and media hypes among biological epigeneticists and calls attention to an apparent bias among scientific journals that prefer papers that promote transgenerational epigenetic inheritance over articles that critique it. The article concludes that while research labelled epigenetics contributes significantly to our knowledge about chromatin and the genome, it does not, as is often claimed, rehabilitate Lamarck or overthrow the fundamental biological principles of gene regulation, which are based on specific regulatory sequences of the genome.

An Understudied Dimension: Why Age Needs to Be Considered When Studying Epigenetic-Environment Interactions

We live in a complex chemical environment where there are an estimated 350 000 chemical compounds or mixtures commercially produced. A strong body of literature shows that there are time points during early development when an organism’s epigenome is particularly sensitive to chemicals in its environment. What is less understood is how gene-environment and epigenetic-environment interactions change with age. This question is bidirectional: (1) how do chemicals in the environment affect the aging process and (2) how does aging affect an organism’s response to its chemical environment? The study of gene-environment interactions with age is especially important because, in many parts of the world, older individuals are a large and rapidly growing proportion of the population and because aging is a process universal to most of the animal kingdom. Epigenetics has emerged as a crucial framework for studying aging as epigenetic pathways, often triggered by environmental stimuli, have been shown to be essential regulators of the aging process. In this perspective article, we delineate the connection between aging, epigenetics, and environmental exposures. We discuss why it is essential to consider age when researching how an organism interacts with its environment. We describe recent advances in understanding how the chemical environment affects aging and the gap in research on how age affects an organism’s response to the environment. Finally, we highlight how model organisms and network approaches can help fill this crucial gap. Taken together, systemic changes that occur in the epigenome with age indicate that adult organisms cannot be treated as a homogeneous population and that there are discrete mechanisms modulating the aging epigenome that we do not yet understand.

Communicating science: epigenetics in the spotlight

Given the public interest in epigenetic science, this study aimed to better understand media representations of epigenetics in national newspaper coverage in various regions in North America, Europe, and Asia. Content analysis was used to study media messages about epigenetics, their policy focus, and the balance of the reporting. We identified several recurring themes in the news reports, including policy messages relating to individual and societal responsibilities. We also found shortcomings in the media's portrayal of epigenetic science, and sought to identify potential causes by considering the underlying scientific evidence that the media reported on. A case study analysis showed that the results of epigenetic studies were often overstated in academic research publications due to common experimental limitations. We suggest that defining standardized criteria with which to evaluate epigenetic studies could help to overcome some of the challenges inherent in translating complex epigenetic research findings for non-technical audiences, and present a Press Kit template that researchers can adapt and use to aid in the development of accurate and balanced press releases.