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Epigenetic study of early childhood

Scientific organization
Saint-Petersburg State University
Academic degree
Scientific discipline
Life Sciences & Medicine
Epigenetic study of early childhood
The thesis considers the issue of the influence of early experience on both physical and mental health. The notion of epigenome is discussed in the context of deprivation and the review of previous studies in animals and human of this issue is provided. At the end of the thesis a description of the current research of the problem is given, which is carried out under the governmenntal grant of the RF «Impact of early deprivation on bio-behavioral indicators of child development» at the Laboratory of Translational Sciences of Early Childhood, SPSU.
epigenetics, deprivation, early life expirience

Due to the rapid development of scientific disciplines that arose at the intersection of biology and psychology (psychophysiology, neuropsychology, psychogenetics), the use of biological methods in psychological studies is increasingly actual.

One of the promising interdisciplinary areas in terms of research of deprivation impact on human development is behavioral epigenetics. This new psychogenetic branch studies the role of epigenetic mechanisms in the formation of behavioral phenotype under the influence of environmental factors. Currently a special research interest is focused on the transformations of the epigenome (changes in gene expression regulation mechanisms) associated with early adverse external conditions. These transformations are supposed to result in long-term consequences for the physical and mental development and health of the child.

One of the major epigenetic mechanisms of regulation of gene activity is DNA methylation – a process consisting in attachment of a methyl group (CH3) to cytosine, which eventually leads to suppression of expression of the corresponding gene. The set of methylated regions of the genome constitutes structures specific to different types of cells – DNA methylation patterns (Strathdee and Brown, 2002).

The studies of SD Suomi, HF Harlow, SD Kimball, D. Liu, DK Day, carried out on animals, revealed that the early separation from mother has negative effects on the offspring`s behavior and health (Suomi et al., 1971; Liu et al., 2000). Researchers D. Chiccetti, MR Gunnar, M. Dozier, KO Ladd received data confirming the negative impact of early adverse experience on human development (Cicchetti, 2002; Ladd et al., 2000). Furthermore, the study of mental and physical health of children from social institutions conducted by TG O `Conner, MR Gunnar H. Fox, C. Nelson, Ch Zeanah allowed to draw conclusions about the difficulties in the development of emotional, cognitive, motor and communicative spheres of these children (O’Connor et al., 2000; Zeanah et al., 2003).

Negative childhood experience is associated with the risk of a wide range of diseases and behavioral problems in later adulthood (Felliti et al., 1998; Shonkoff et al., 2009). Epidemiological studies show that a range of diseases, such as cardiovascular disease, diabetes, obesity, depression, substance abuse, premature aging and others have their determinants in the early stages of development (Harkonmaki, 2007; Shonkoff et al., 2009; Felliti et al., 1998; Coelho et al., 2014), and a number of them is associated with early deprivation (Kreppner et al., 2007).

Despite the relative "youth" of behavioral epigenetics in general, and studies of epigenetic response to the conditions of early deprivation, in particular, this area is actively being developed by foreign scientists during the last decade. It is reflected in numerous foreign literature reviews in the area (Hoffmann & Spengler, 2014; Lutz & Turecki, 2013; Szyf, 2013). In Russia this area of research remains largely unexplored.

Evidence provided both by animal and human studies support the hypothesis that maternal care has a huge impact on the phenotype of progeny, and that this effect is probably mediated by changes in gene expression and epigenetic regulation of its systems. Consequently, the understanding of the mechanisms involved in the occurrence of the phenomena discussed above, requires the study of "epigenetic response" on a factor of deprivation and its role in shaping the phenotype, in the context of the features of the child's development and long-term effects of deprivation conditions on mental and physical health.

Epigenetics is the science that deals with the study of gene expression changes caused by mechanisms that do not affect the DNA sequence. Epigenetic mechanisms are numerous and complex, with basic one represented by RNA interference, chromatin reconstruction, histone modification and DNA methylation (Turner, 2001). However, we will focus on discussing the DNA methylation. DNA sequence has some specific sites where the methyl group can attach to cytosine using enzymatic reactions. Such sites are usually located within the regulatory regions of gene, near the promoter preceding the initial transcription site. Thus, methylation is a covalent modification of DNA by attachment of a methyl group (CH3) to cytosine contained in the dinucleotide sequence cytosine-guanine (CpG), which leads to suppression of gene activity. At the functional level methylation restricts access of transcription factors and RNA polymerase to the DNA. The link between cytosine and methyl group is very strong, which results in stable, although potentially reversible changes in expression. Patterns of DNA methylation are saved during cell division and are transferred, thus, to the daughter cells, and it is through this mechanism that cell differentiation occurs (Turner, 2001). An important direction is behavioral epigenetics – young psychogenetic area, which aim is to study the patterns of environmental influence on the epigenome and the phenotypic manifestations of such interaction, which include, in particular, the emergence of various diseases, certain forms of behavior and trajectories of mental development.

The molecular basis of long-term effects of maternal deprivation on progeny phenotype was first demonstrated in a series of experiments with rats conducted by Moshe Zif and Michael Meaney. The researchers observed the behavior of  rats exhibiting high and low level of care to their offspring, and then examined the differences in mRNA hippocampal glucocorticoid receptors in the latter (Weaver et al., 2004). At the phenotypic level rats reared by caring mother, showed blunted reaction to a stressful situation from the hypothalamic-pituitary-adrenal axis, and also showed a lower incidence of anxious behavior (Meaney et al., 1996; Liu et al., 1997). It was noted that a high level of caring behavior in mothers changed epigenome of progeny rats at promoters of genes encoding the glucocorticoid receptors of the hippocampus.  The researchers found differences in DNA methylation in pups reared by caring mothers, compared with the offspring of inattentive mothers. The level of glucocorticoid receptors in the hippocampus regulates HPA axis response to stress on the feedback principle: a high level of activity of mRNA glucocorticoid receptor corresponds with poor response to stress (Jacobson and Sapolsky, 1991). 

There are also studies concerning the possibility of transferring the effects of early experience through the generations. For example, T. Franklin on the basis of observations over mice, subjected to prolonged and unexpected separation from the mother during 14 days after birth, succeeded to show that prolonged separation entails manifestation of behavior peculiar to depression at an older age and changes their behavioral reactions towards negative and dangerous environmental factors. Such behavioral changes appeared later in progeny of mice who had experienced maternal separation, in spite of the fact that they grew under normal conditions. Long and unpredictable separation from the mother has also changed the profile of DNA methylation in promoters of several candidate genes of germline in separated males. Similar changes in DNA methylation associated with altered expression of genes have been identified in the brains of their offspring. Described data illustrate the vast deleterious effects of stress on early development and behavioral responses, transmitted across generations through the regulation of DNA methylation. Mouse model presented here reproduces the multiple effects of early stress on behavior and reflects the unique and unprecedented model of inherited behavioral disorders due to early stress. (Franklin et al., 2010).

There are also attempts to study the applicability to human of the thesis, developed on the basis of studies in animal models. Recently there were described studies on genome-wide changes in DNA methylation in peripheral tissues after the experience of interaction with adverse early environment. In the first study, an attempt was made to trace the link between DNA methylation in blood and evidence of early abuse, post-traumatic stress disorder and exposure to stress (Smith et al., 2011). While differential methylation in gene 1 and 5 associated with PTSD and stress, there were found no statistically significant results on the experience of early violence. In another study in the saliva of children who have experienced abuse at early age there were found 2600 CpG sites, which methylation level was different from the level of methylation in children, who have never faced with violence and had no mental illness (Yang et al., 2013). Along with the previous findings, these studies suggest that the violence faced in early childhood, and the related stressor experience have profound genome-wide epigenetic consequences for peripheral tissues.

Of particular interest to us is the study conducted recently by O. Naumova and colleagues, which checks for a connection between the experience of deprivation conditions in early childhood and changes in gene expression (Naumova et al., 2012). The aim of this study was to compare the genome methylation patterns in children-orphans and children from biological families. Comparative analysis of methylation of two groups of children identified about 800 differently methylated gene and showed that the most important intergroup difference was the increased level of methylation of the genomes of children in orphanages, as compared with children living in biological families. Thus, there were many high-methylated genes in children from these institutions, which play an important role in controlling the immune response and cell signaling systems as well as in the development and functioning of the brain.

Our interdisciplinary research project called «Impact of early deprivation on bio-behavioral indicators of child development» represents another attempt to study change of the epigenome in early childhood, in the context of various and dynamic social environments – institutional care (IC), foster care (FC) and typical family environment (typically developing, TD). The research is a cross-sectional study of the complex of behavioral, neurophysiological and epigenetic indicators of children.

Our hypothesis is that institutional care may cause systematic changes in the DNA-methylation profiles of children, that in turn may exert an impact on biological and behavioral levels of the children`s development. These alterations may be neutralized or reversed with changes in care, such as the children’s placement into foster families.

The study involves a sample of children with Down syndrome, which gives an opportunity to examine the character of epigenetic perversions in their genomes. We hypothesize that analysis of data collected will provide new evidence on global alterations in the epigenome related to trisomy, and will allow to identify some features of epigenetic patterns associated with cognitive impairments in DS children.

We suggest that our unique data will provide significant results of epigenome-wide association with behavioral phenotypes on early stages of the development.


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22 Zeanah, C.H., Nelson, C.A., Fox, N.A., Smyke, A.T., Marshall, P., Parker, S.W., & Koga, S. Designing research to study the effects of institutionalization on brain and behavioral development: The Bucharest Early Intervention Project // Development and Psychopathology. 2003. Vol. 15. pp. 885-907.