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

Ethnic 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 contrasted 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

The Relationship of the Serotonin Transporter (SLC6A4) Extra Long Variant to Gene Expression in an African American Sample

The serotonin transporter (SLC6A4) is a key regulator of serotonergic neurotransmission. Like most genes, SLC6A4 expression is partially regulated by genetic variation. The most heavily studied variant affecting this expression is the polymorphism known as the serotonin transporter linked polymorphic region (5HTTLPR). In those of northern European ancestry, this variation exclusively consists of two alleles; a long (l) variant that consists of 16 repeats and a short (s) variant that consists of 14 repeats of ~22 bp element. In a large number of studies, it has been repeatedly demonstrated that the short variant is associated with 60% of the transcriptional activity as long allele [Lesch et al., 1996]. Unfortunately, the mechanism through which this differential expression is conveyed is unclear but may be mediated via the diverse interactions of a number of transcription factors including CCCTC-binding factor (CTCF) [Ali et al., 2010].This is a manuscript of an article from American Journal of Medical Genetics, 2012, 159B(5); 611-612. DOI: 10.1002/ajmg.b.32054. Posted with permission.</p

The Relationship of Deiodinase 1 Genotype and Thyroid Function to Lifetime History of Major Depression in Three Independent Populations

Major depression (MD) is often associated with disturbances of the hypothalamic/pituitary/thyroid (HPT) axis. Unfortunately, whether this association is secondary to common underlying genetic variation or whether the MD‐associated disturbances in HPT function are chronic or state‐dependent is unknown. To examine these questions, we genotyped 12 single nucleotide polymorphisms identified in previous genome wide association analyses of thyroid function in DNA contributed by 1,555 subjects from three longitudinal ethnically diverse studies that are well‐characterized for lifetime MD and thyroid function. We then examined associations between genetic variants and key outcomes of thyroid stimulating hormone, free thyroxine (FT4) and depression. We confirmed prior findings that two variants in deiodinase 1 (DIO1), including a variant in the 3′UTR of DIO1 (rs11206244), were associated with altered FT4 levels in both White and African American subjects. We also found that rs11206244 genotype was associated with lifetime MD in White female subjects, in particular those from high‐risk cohorts. However, we found no association of current FT4 levels with lifetime MD in either ethnic group. We conclude that genetic variation influencing thyroid function is a risk factor for MD. Given the evidence from prior studies, further investigations of role of HPT variation in etiology and treatment of MD are indicated.This is the peer-reviewed version of the following article: Philibert, Robert A., Steven RH Beach, Tracy D. Gunter, Alexandre A. Todorov, Gene H. Brody, Meeshanthini Vijayendran, Lilly Elliott, Nancy Hollenbeck, Daniel Russell, and Carolyn Cutrona. "The relationship of deiodinase 1 genotype and thyroid function to lifetime history of major depression in three independent populations." American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 156, no. 5 (2011): 593-599, which has been published in final form at DOI: 10.1002%2Fajmg.b.31200. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. Posted with permission.</p