Background: The current process used to prescribe antidepressant medication is markedly inefficient, as more than 50% of treated patients fail to reach remission. Antidepressant treatment success has been associated with genetic variation, but studies are not well replicated and epigenetic mechanisms remain under investigated at this time. DNA methylation, an epigenetic modification, may provide more information regarding antidepressant response and further improve the genomic guidance to physicians in choosing the most effective medication for each patient. In fact, hypomethylation of the serotonin transporter gene has previously been associated with impaired antidepressant response. We investigated the influence of 5-HTT methylation and long/short variant (LPR) genotypes on antidepressant response in our sample.

Methods: A subset of Major Depressive Disorder (MDD) patients (European Caucasian, n=166), which had the most complete clinical data, were selected from our large discovery sample (IMPACT; N=8,000). All patients were previously referred to our study for failure to respond, or intolerance to, their psychiatric medication. Genetic testing was done of cytochrome P450 liver enzymes, 5HTTLPR and 5HT2A variants to guide clinical choice and dosage of psychotropic medications. As such, a significant component of our sample includes treatment refractory, as well as medication intolerant patients. Saliva samples were collected at enrollment and DNA was extracted using a standard, high-salt method. DNA was then bisulfite converted and modification profiles were interrogated using the Infinium HumanMethylation450 Beadchip array. Nine CpG probes located across the 5-HTT promoter region were selected, based on previous studies, to quantify methylation levels. Additionally, patients were genotyped for the functional 5-HTTLPR long/short variant. Change in Beck Depression Inventory II (BDI-II) score was used to measure antidepressant response and remission over eight weeks. The relationship between 5-HTTLPR genotype, methylation levels, and antidepressant response was then investigated using linear regression modeling.

Results: Increased methylation in the promoter region of the 5-HTT gene was nominally associated with impaired response to antidepressants in our sample. The effect was driven by methylation site cg05016953, located in exon 1A. Increased methylation level as measured by CpG cg05016953 was associated with less improvement in BDI-II score over eight weeks of antidepressant treatment (F(3,163)=6.14, p_uncorr=0.012). 5-HTTLPR genotype was not associated with 5-HTT DNA methylation or antidepressant treatment response.

Conclusions: An increase in 5-HTT DNA methylation at cg05016953 may be associated with impaired response to antidepressant medications in our sample. The 5-HTT transcriptional control region contains a CpG island, which has been previously shown to functionally influence mRNA levels depending on 5-HTTLPR genotypes [2]. Typically, hypermethylation in promoter regions is associated with decreased 5-HTT gene expression. Theoretically, hypermethylation of the 5-HTT promoter would reduce the number of serotonin transporters, and reduce serotonin re-uptake, which in simple terms should improve response to SSRI treatment. Alternatively, the SSRIs may require a sufficient amount of the 5-HTT protein present in the synapse in order to enact their pharmacologic inhibition of 5-HT reuptake. Further pharmaco-epigenetic studies are required to illuminate the effect of DNA methylation changes on antidepressant response.