Effects of Genotype and Child Abuse on DNA Methylation and Gene Expression at the Serotonin Transporter

Altered regulation of the serotonin transporter (SLC6A4) is hypothesized to be a key event in many forms of neuropsychiatric illness, yet our understanding of the molecular mechanisms through which changes in gene function could lead to illness remains incomplete. In prior studies, we and others have demonstrated that methylation of CpG residues in the promoter associated CpG island alters SLC6A4 gene expression, that the extent of that DNA methylation in child abuse is genotype dependent, and that adverse childhood experiences such as child sex abuse are related to methylation. However, we have not examined whether these effects are splice variant specific, whether the association of methylation to gene expression varies as a function of genotype, and whether methylation in other SLC6A4 gene regions are more likely candidates for GxE effects. In the current investigation we measured methylation in lymphoblast DNA from 158 female subjects in the Iowa Adoption Studies at 16 CpG residues spread across the SLC6A4 locus, and analyzed their relationship to gene expression for two SLC6A4 splice variants. Methylation of two CpG residues in the shore of the CpG island (cg22584138 and cg05951817), a location immediately upstream from exon 1A, predicted gene expression for the splice variant containing Exon 1A + 1B. Methylation at two residues in the CpG island itself (cg 25769822 and cg05016953) was associated with total SLC6A4 expression. Examination of these four CpG residues indicated that methylation of cg22584138 was influenced by both genotype and sex abuse, whereas methylation of cg05016953 was influenced only by sex abuse history. Factors influencing methylation at other CpG dinucleotide pairs were not identified. We conclude that methylation effects on transcription may vary as a function of underlying gene motif and splice variant, and that the shore of CpG islands, upstream of TSS, may be of particular interest in examining environmental effects on methylation

A Longitudinal Study of Racial Discrimination and Risk for Death Ideation in African American Youth

Though multiple studies have found that African Americans commonly experience racial discrimination, available studies have yet to examine how perceived racism might be related to suicide vulnerability in African American youth. The purpose of this study was to examine a framework for how perceived racial discrimination contributes to symptoms of depression and anxiety as well as subsequent suicide ideation and morbid ideation. Data were obtained from 722 African American youth at mean age 10.56 years (SD=0.64); a second wave of data was obtained two years later. Results revealed both a direct effect and mediated effects of perceived racism on later suicide and morbid ideation. For boys and girls the effect of perceived racism was mediated by symptoms of depression. However, the association was mediated by anxiety for girls, but not for boys in the current sample. Implications for future research and intervention are discussed

African American Children’s Depressive Symptoms: The Prospective Effects of Neighborhood Disorder, Stressful Life Events, and Parenting

The prospective effects of observed neighborhood disorder, stressful life events, and parents’ engagement in inductive reasoning on adolescents’ depressive symptoms were examined using data collected from 777 African American families. Multilevel analyses revealed that stressful life events experienced at age 11 predicted depressive symptoms at age 13. Furthermore, a significant interaction between neighborhood disorder and parents’ engagement in inductive reasoning was found, indicating that parental use of inductive reasoning was a protective factor for depressive symptoms particularly for youths living in highly disordered neighborhoods. The importance of examining correlates of depressive symptoms from a contextual framework, focusing on individuals, families, and neighborhood contexts, is emphasized

Methylation array data can simultaneously identify individuals and convey protected health information: an unrecognized ethical concern

BACKGROUND: Genome-wide methylation arrays are increasingly used tools in studies of complex medical disorders. Because of their expense and potential utility to the scientific community, current federal policy dictates that data from these arrays, like those from genome-wide genotyping arrays, be deposited in publicly available databases. Unlike the genotyping information, access to the expression data is not restricted. An underlying supposition in the current nonrestricted access to methylation data is the belief that protected health and personal identifying information cannot be simultaneously extracted from these arrays. RESULTS: In this communication, we analyze methylation data from the Illumina HumanMethylation450 array and show that genotype at 1,069 highly informative loci, and both alcohol and smoking consumption information, can be derived from the array data. CONCLUSIONS: We conclude that both potentially personally identifying information and substance-use histories can be simultaneously derived from methylation array data. Because access to genetic information about a database subject or one of their relatives is critical to the de-identification process, this risk of de-identification is limited at the current time. We propose that access to genome-wide methylation data be restricted to institutionally approved investigators who accede to data use agreements prohibiting re-identification

Determinants and Long‐Term Effects of Attendance Levels in a Marital Enrichment Program for African American Couples

Although most efficacious marital enrichment programs are multisession, few studies have explored whether outcomes differ according to session attendance, particularly among minority groups with lower than average participation in prevention programs. This study therefore investigates attendance levels and long‐term improvements in couple functioning among 164 couples participating in the Promoting Strong African American Families program. Structural equation models indicated session attendance predicted 2‐year changes for men\u27s reports of communication, commitment, and spousal support (marginally) but not for women\u27s. Individual and couple characteristics that predicted attendance levels were also identified. Results highlight distinct gender differences in the effects of sustained attendance as well as characteristics that provide early identifiers for African American couples at increased risk of low program attendance

The Impact of Recent Alcohol Use on Genome Wide DNA Methylation Signatures

Chronic alcohol intake is associated with a wide variety of adverse health outcomes including depression, diabetes, and heart disease. Unfortunately, the molecular mechanisms through which these effects are conveyed are not clearly understood. To examine the potential role of epigenetic factors in this process, we examined the relationship of recent alcohol intake to genome wide methylation patterns using the Illumina 450 Methylation Bead Chip and lymphoblast DNA derived from 165 female subjects participating in the Iowa Adoption Studies. We found that the pattern of alcohol use over the 6-months immediately prior to phlebotomy was associated with, severity-dependent changes in the degree of genome wide methylation that preferentially hypermethylate the central portion of CpG islands with methylation at cg05600126, a probe in ABR, and the 5′ untranslated region of BLCAP attaining genome wide significance in two point and sliding window analyses of probe methylation data, respectively. We conclude that recent alcohol use is associated with widespread changes in DNA methylation in women and that further study to confirm these findings and determine their relationship to somatic function are in order

Rural-urban differences in substance use among African-American adolescents

Purpose: To examine substance use differences among African‐American adolescents living in rural and more urban areas in Iowa and Georgia and factors thought to be related to those differences. Specifically, negative affect and perceived availability were examined as mediators of the relation between community size and alcohol, tobacco, and drug use. Methods: In‐home interviews with the adolescents (Time 1: N = 897, Mean age = 10.5) assessed their use, perceived substance availability, and negative affect across 3 waves. Their parents’ use was also assessed. Census data were used to determine community size (rural ≤ 2,500; urban ≥ 2,500). Findings: Perceived substance availability and use were both higher among the more urban adolescents. As expected, negative affect was a primary antecedent to use at each wave. Structural Equation Modeling indicated that the relation between population and use was mediated by perceived availability of the substances. Additional multigroup analyses indicated that the relations between negative affect and use were significantly stronger among the urban adolescents at all waves. Conclusions: Results suggest that stress or negative affect is an important antecedent to use among African‐American adolescents, especially when it occurs at an early age, but living in rural areas may be a buffer for both problems, in part, because exposure to this type of risk is lower in these environments

Ethnicity and smoking-associated DNA methylation changes at HIV co-receptor GPR15

Smoking is associated with poorer health outcomes for both African and European Americans. In order to better understand whether ethnic-specific genetic variation may underlie some of these differences, we compared the smoking-associated genome-wide methylation signatures of African Americans with those of European Americans, and followed up this analysis with a focused examination of the most ethnically divergent locus, cg19859270, at the GPR15 gene. We examined the association of methylation at this locus to the rs2230344 SNP and GPR15 gene and protein expression. Consistent with prior analyses, AHRR residue cg05575921 was the most differentially methylated residue in both African Americans and European Americans. However, the second most differentially methylated locus in African Americans, cg19859270, was only modestly differentially methylated in European Americans. Interrogation of the methylation status of this CpG residue found in GPR15, a chemokine receptor involved in HIV pathogenesis, showed a significant interaction of ethnicity with smoking as well as a marginal effect of genotype at rs2230344, a neighboring non-synonymous SNP, but only among African Americans. Gene and protein expression analyses showed that demethylation at cg19859270 was associated with an increase in both mRNA and protein levels. Since GPR15 is involved in the early stages of viral replication for some HIV-1 and HIV-2 isolates, and the prevalence of HIV is increased in African Americans and smokers, these data support a possible role for GPR15 in the ethnically dependent differential prevalence of HIV

Methylomic Aging as a Window onto the Influence of Lifestyle: Tobacco and Alcohol Use Alter the Rate of Biological Aging

Objectives—To examine the effect of the relationship between alcohol and cigarette consumption on biological aging using deoxyribonucleic acid (DNA) methylation-based indices. Design—We examined the association between DNA methylation indices of smoking and alcohol to those for biological aging in two independent cohorts using the epigenetic “clock” provided by Hannum and colleagues. Setting—Longitudinal studies of aging and the effect of psychosocial stress. Participants—Publicly available genome-wide methylation data from participants in two ethnically informative cohorts (n=656 white, n=180 black). Measurements—Deviation of biological age from chronological age as a result of smoking and alcohol consumption. Results—Greater cigarette consumption was associated with accelerated biological aging, with strong effects evident at even low levels of exposure. In contrast, alcohol consumption was associated with a mixed effect on biological aging and pronounced nonlinear effects. At low and heavy levels of alcohol consumption, there was accelerated biological aging, whereas at intermediate levels of consumption there was a relative decelerating effect. The decelerating effects of alcohol were particularly notable at loci for which methylation increased with age. Conclusion—These data support prior epidemiological studies indicating that moderate alcohol use is associated with healthy aging, but we urge caution in interpreting these results. Conversely, smoking has strong negative effects at all levels of consumption. These results also support the use of methylomic indices as a tool for assessing the impact of lifestyle on aging