Cell-specific Characterization of the Placental Methylome

Yuan, Victor; Hui, Diane; Yin, Yifan; Peñaherrera, Maria S.; Beristain, Alexander G.; Robinson, Wendy P.

doi:10.21203/rs.3.rs-38223/v2

“…Using tools from the PlaNET R package (48,49), we also estimated additional variables in the discovery cohort from the DNAme data itself: the proportion of six major placental cell types, and placental epigenetic age. Cell type proportions were not significantly associated with either SSRI treatment or mean maternal Hamilton Depression score across gestation (t-test for cell type proportions ~ SSRI exposed (yes/no), all p values > 0.05; Pearson correlation for mean maternal Hamilton Depression score and each cell type proportion, all p values > 0.05), see Supplementary Figure 3.…”

Section: Covariate Selectionmentioning

confidence: 99%

Profiling placental DNA methylation associated with maternal SSRI treatment during pregnancy

Inkster

¹

,

Konwar

²

,

Peñaherrera

³

et al. 2022

Preprint

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Background Selective serotonin reuptake inhibitors (SSRIs), used to treat prenatal maternal depression, have been associated with neurobehavioral disturbances in exposed neonates, though the underlying molecular mechanisms remain poorly understood. In utero exposure to SSRIs may have an effect on DNA methylation (DNAme) in the human placenta, which is an epigenetic mark that is established during development and is associated with gene expression. Methods Chorionic villus samples from 64 human placentas were profiled with the Illumina MethylationEPIC BeadChip and clinical assessments of maternal mood were collected at multiple time points during pregnancy. Case distribution was 20 SSRI-exposed cases and 44 SSRI non-exposed cases. Maternal depression using a mean maternal Hamilton Depression score >8 to indicate symptomatic depressed mood (maternally-depressed) 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). To provide a replication cohort, Illumina 450K DNAme profiles were obtained from 34 additional cases from an independent cohort (n=17 SSRI-exposed, n=17 SSRI non-exposed). Results No CpGs were differentially methylated at FDR < 0.05 comparing SSRI-exposed to non-exposed placentas, while adjusting for mean maternal Hamilton Depression score, nor comparing SSRI- exposed maternally-depressed to SSRI-non-exposed maternally-depressed cases. At a relaxed threshold of FDR < 0.25, five CpGs were differentially methylated (|Δβ| > 0.03) by SSRI exposure status. Four of these CpGs were covered by the 450K array and were examined in the replication cohort, but none replicated. Amongst SSRI non-exposed cases, 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. Conclusions We did not observe large-scale alterations of DNAme in placentas exposed to maternal SSRI treatment 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.

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“…We also note that library preparation reagents for wht-RNAseq libraries and tar-RNAseq libraries were from different manufacturers. Although we did not try to estimate ASE in relation to the cellular composition of the fetal compartment of the placenta, a recent single cell study showed that placental samples collected using a protocol similar to ours were mostly comprised of trophoblast and syncytiotrophoblast cells of the fetus ( Yuan et al 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas

Wu

¹

,

Lovett

²

,

Shedden

³

et al. 2021

G3 Genes|Genomes|Genetics

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Genomic imprinting is an epigenetic mechanism that results in allele specific expression (ASE) based on parent of origin. It is known to play a role in the prenatal and postnatal allocation of maternal resources in mammals. ASE detected by whole transcriptome RNA-seq (wht-RNAseq) has been widely used to analyze imprinted genes using reciprocal crosses in mice to generate large numbers of informative SNPs. Studies in humans are more challenging due to the paucity of SNPs and the poor preservation of RNA in term placentas and other tissues. Targeted RNA-seq (tar-RNAseq) can potentially mitigate these challenges by focusing sequencing resources on the regions of interest in the transcriptome. Here we compared tar-RNAseq and wht-RNAseq in a study of ASE in known imprinted genes in placental tissue collected from a healthy human cohort in Mali, West Africa. As expected, tar-RNAseq substantially improved the coverage of SNPs. Compared to wht-RNAseq, tar-RNAseq produced on average four times more SNPs in twice as many genes per sample and read depth at the SNPs increased 4-fold. In previous research on humans, discordant ASE values for SNPs of the same gene have limited the ability to accurately quantify ASE. We show that tar-RNAseq reduces this limitation as it unexpectedly increased the concordance of ASE between SNPs of the same gene, even in cases of degraded RNA. Studies aimed at discovering associations between individual variation in ASE and phenotypes in mammals and flowering plants will benefit from the improved power and accuracy of tar-RNAseq.

show abstract

“…We also note that library preparation reagents for wht-RNAseq libraries and tar-RNAseq libraries were from different manufacturers. Although we did not try to estimate ASE in relation to the cellular composition of the fetal compartment of the placenta, a recent single cell study showed that placental samples collected using a protocol similar to ours were mostly comprised of trophoblast and syncytiotrophoblast cells of the fetus 57 .…”

Section: Discussionmentioning

confidence: 99%

Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas

Wu

¹

,

Lovett

²

,

Shedden

³

et al. 2021

Preprint

View full text Add to dashboard Cite

Genomic imprinting is an epigenetic mechanism that results in allele specific expression (ASE) based on parent of origin. It is known to play a role in the prenatal and postnatal allocation of maternal resources in mammals. ASE detected by whole transcriptome RNA-seq (wht-RNAseq) has been widely used to analyze imprinted genes using reciprocal crosses in mice to generate large numbers of informative SNPs. Studies in humans are more challenging due to the paucity of SNPs and the poor preservation of RNA in term placentas and other tissues. Targeted RNA-seq (tar-RNAseq) can potentially mitigate these challenges by focusing sequencing resources on the regions of interest in the transcriptome. Here we compared tar-RNAseq and wht-RNAseq in a study of ASE in known imprinted genes in placental tissue collected from a healthy human cohort in Mali, West Africa. As expected, tar-RNAseq substantially improved the coverage of SNPs. Compared to wht-RNAseq, tar-RNAseq produced on average four times more SNPs in twice as many genes per sample and read depth at the SNPs increased 4-fold. In previous research on humans, discordant ASE values for SNPs of the same gene have limited the ability to accurately quantify ASE. We show that tar-RNAseq reduces this limitation as it unexpectedly increased the concordance of ASE between SNPs of the same gene, even in cases of degraded RNA. Studies aimed at discovering associations between individual variation in ASE and phenotypes in mammals and flowering plants will benefit from the improved power and accuracy of tar-RNAseq.

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Cell-specific Characterization of the Placental Methylome

Cited by 15 publications

References 31 publications

Profiling placental DNA methylation associated with maternal SSRI treatment during pregnancy

Profiling placental DNA methylation associated with maternal SSRI treatment during pregnancy

Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas

Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas

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