Profiling placental DNA methylation associated with maternal SSRI treatment during pregnancy

Abstract

Selective serotonin reuptake inhibitors (SSRIs) for treatment of prenatal maternal depression have been associated with neonatal neurobehavioral disturbances, though the molecular mechanisms remain poorly understood. In utero exposure to SSRIs may affect DNA methylation (DNAme) in the human placenta, an epigenetic mark that is established during development and is associated with gene expression. Chorionic villus samples from 64 human placentas were profiled with the Illumina MethylationEPIC BeadChip; clinical assessments of maternal mood and SSRI treatment records were collected at multiple time points during pregnancy. Case distribution was 20 SSRI-exposed cases and 44 SSRI non-exposed cases. Maternal depression was defined using a mean maternal Hamilton Depression score > 8 to indicate symptomatic depressed mood ("maternally-depressed"), and we further classified cases into SSRI-exposed, maternally-depressed (n = 14); SSRI-exposed, not maternally-depressed (n = 6); SSRI non-exposed, maternally-depressed (n = 20); and SSRI non-exposed, not maternally-depressed (n = 24). For replication, Illumina 450K DNAme profiles were obtained from 34 additional cases from an independent cohort (n = 17 SSRI-exposed, n = 17 SSRI non-exposed). No CpGs were differentially methylated at FDR < 0.05 comparing SSRI-exposed to non-exposed placentas, in a model adjusted for mean maternal Hamilton Depression score, or in a model restricted to maternally-depressed cases with and without SSRI exposure. However, at a relaxed threshold of FDR < 0.25, five CpGs were differentially methylated (|Δβ| > 0.03) by SSRI exposure status. Four were covered by the replication cohort measured by the 450K array, but none replicated. No CpGs were differentially methylated (FDR < 0.25) comparing maternally depressed to not depressed cases. In sex-stratified analyses for SSRI-exposed versus non-exposed cases (females n = 31; males n = 33), three additional CpGs in females, but none in males, were differentially methylated at the relaxed FDR < 0.25 cut-off. We did not observe large-scale alterations of DNAme in placentas exposed to maternal SSRI treatment, as compared to placentas with no SSRI exposure. We also found no evidence for altered DNAme in maternal depression-exposed versus depression non-exposed placentas. This novel work in a prospectively-recruited cohort with clinician-ascertained SSRI exposure and mood assessments would benefit from future replication.

Figure 1

Comparisons for analysis of differential DNAme associated with SSRI exposure and maternal depression in the discovery cohort. (A) The SSRI model investigates SSRI exposure in the full cohort (n = 64), comparing SSRI-exposed (n = 20) to SSRI non-exposed (n = 44) cases, adjusting for mean maternal Hamilton Depression score across gestation. (B) The SSRIs in maternal depression model investigates SSRI exposure in all maternally-depressed cases (mean maternal Hamilton Depression score > 8, n = 34), this model compares SSRI-exposed, maternally depressed cases (n = 14) to SSRI non-exposed, maternally depressed cases (n = 20). (C) The maternal depression without SSRIs model investigates the effect of maternal depression in cases not exposed to SSRIs (n = 44), this model compares SSRI non-exposed, maternally depressed cases (n = 20) to SSRI non-exposed and not maternally depressed cases (n = 24).

Figure 2

Volcano plots for differential DNAme in association with SSRI exposure and categorical depression. For all plots HamD refers to the mean maternal Hamilton Depression score across gestation for each individual. False discovery rate (FDR) is shown along the Y axis with more significant (lower FDR) values at the top of the plot. Vertical dashed intercepts demarcate |Δβ| = 0.03, horizontal dashed intercepts indicate, from top to bottom, FDR = 0.05, FDR = 0.15, and FDR = 0.25. (A) Volcano plot for the SSRI model, investigating differential DNAme associated with SSRI exposure adjusted for mean maternal HamD score, (n = 64). Difference in DNAme (Δβ) is plotted along the X axis and was calculated as Δβ = β_SSRI-exposed – β_{SSRI non-exposed}. (B) Volcano plot for the SSRIs in maternal depression model, differential DNAme associated with SSRI exposure in cases with mean maternal HamD score > 8, (n = 34). Difference in DNAme (Δβ) is plotted along the X axis and was calculated as Δβ = β_SSRI-exposed – β_{SSRI non-exposed}. (C) Volcano plot for the maternal depression without SSRIs model, differential DNAme associated HamD score > 8 across gestation, in SSRI non-exposed cases, (n = 44). Difference in DNAme (Δβ) is plotted along the X axis and was calculated as Δβ = β_{Hamilton > 8} – β_{Hamilton ≤ 8}, “Depr” indicates “Depressed”, i.e. HamD > 8.

Figure 3

Boxplots of differentially methylated CpGs by SSRI exposure. For all plots, points are colored by SSRI exposure (blue = SSRI non-exposed, dark yellow = SSRI-exposed), and boxplots indicate mean DNAme β value ± one standard deviation. (A) Boxplot of cg12900404, identified in the SSRI model, model A. (B) Boxplot of cg20877313, identified in the SSRI model, model A. (C) Boxplot of cg12655501, identified in the SSRIs in maternal depression model, model B. (D) Boxplot of cg26993610, identified in the SSRIs in maternal depression model, model B. (E) Boxplot of cg14340829, identified in the SSRIs in maternal depression model, model B.

Figure 4

Assessment of literature candidates for SSRI and depression-associated DNAme in the discovery cohort. (A) Scatterplot showing the association between DNAme and maternal Edinburgh Postnatal Depression Score (EPDS) at cg06670742 which was previously found to be differentially methylated in association with maternal EPDS score in Tesfaye et al. and is differentially methylated by SSRI exposure at FDR < 0.05 in our discovery cohort. DNAme β value at this CpG is plotted along the Y axis, mean maternal EPDS score is plotted along the X axis and each point is a case; Δβ per unit increase in EPDS is Δβ =  + 0.003. (B) Boxplot showing mean DNAme β value ± one standard deviation by SSRI exposure status at cg22159628 in ZNF575, previously found to be differentially methylated in cord blood with antidepressant exposure. Linear modelling p value = 0.67, points are colored by SSRI exposure (blue = SSRI non-exposed, dark yellow = SSRI-exposed), n.s. = not significant. (C) Boxplot showing mean DNAme β value ± one standard deviation by SSRI exposure status at cg00331486 in LOC284930 on chromosome 22, previously found to be differentially methylated in cord blood by SSRI exposure status.