Publication: Sex differences in the late first trimester human placenta transcriptome

Data: Total RNA-seq of first trimester trimester placenta

Tania L. Gonzalez, Tianyanxin Sun, Alexander F. Koeppel, Bora Lee, Erica T. Wang, Charles R. Farber, Stephen S. Rich, Lauren W. Sundheimer, Rae A. Buttle, Yii-Der Ida Chen, Jerome I. Rotter, Stephen D. Turner, John WilliamsIII, Mark O. Goodarzi and Margareta D. Pisarska. Biology of Sex Differences 2018 Jan 15. Vol 9: issue 4.

Links

• PubMed ID: 29335024
• Biology of Sex Differences journal article [open access!]
• NCBI GEO accession for RNA-seq data: GSE109082
• Spreadsheet for genes above our FPKM threshold is "Additional file 2" (placenta transcriptome at time of chorionic villus sampling)
• Spreadsheet for genes reaching our False Discovery Rate threshold is "Additional file 4" (genes significantly sex different)

Layman's summary

• Background: 
• One of the long-term goals for women's health and fetal health is developing better methods to predict pregnancy outcome. This includes things like predicting risk of gestational diabetes (which can often be treated with diet changes), preterm birth (which can affect the baby's long-term health), and preeclampsia (dangerously high blood pressure in later pregnancy which puts mom and baby at risk).
• Risk for these health issues is affected by fetal sex.
• The placenta is the same sex as the baby because it, like the baby, develops from the fertilized egg. Women pregnant with a baby boy have a placenta with a Y chromosome.
• Early placenta development affects risk for later complications. Preeclampsia, for example, is thought to be due to insufficient placental invasion into maternal tissue in early pregnancy (first trimester).
• Aim:
• To characterize early placenta gene expression and identify differences due to fetal sex.
• Methods:
• It's difficult to study early placenta in continuing pregnancies! Especially human pregnancies. We achieved this by using leftover tissue from "chorionic villus sampling" (CVS), a prenatal diagnostic test that takes a tiny biopsy of the placenta. It is performed in late first trimester to learn about the baby's genetics since the placenta genome is reflective of the fetal genome. The clinician took what they needed for the patient's test and, if the patient agreed to research, they froze any leftover for our research.
• We used RNA-sequencing to look at which genes were turned "on" in late first trimester human placenta. 
• We looked at the genes with the strongest expression and identified some genes which are placenta-specific (not expressed in other human body parts) and some which are first trimester-specific (not in term placenta). 
• Results:
• Some histone-encoding genes are very actively turned on in late first trimester placenta. Histones are proteins which affect the accessibility of DNA, so they are master regulators of gene expression.
• We found 58 genes expressed differently between male and female placentas.
• The strongest differences were on the sex chromosomes, X and Y. A lot of these gene expression differences continue into adulthood.
• As expected, male placentas expressed Y chromosome genes that female placentas didn't have, so these genes came up as statistically significant. There was one Y chromosome gene that was expressed in male placenta, but not statistically significant for sex differences. The reason this happened was because that gene was very variable among the male placenta samples. There is likely something besides fetal sex that strongly affects its expression.
• Female placentas typically had more expression from X chromosome genes. Weirdly, we also found three genes from the X chromosome which were more highly turned on in male placentas. We are not sure why yet. They were not higher in adult males, but one of them (ARMCX6) was also found higher in male term placenta in a different study.
• We also found differences in autosome genes (from non-sex chromosomes). When we compared our results to previously published term placenta and adult human research, the autosome genes were less likely to match other sex difference studies. It seems like sex differences in autosome gene expression change more throughout human development. However, we did find that gene RASSF6 (on chromosome 4) is more highly expressed in both female late first trimester placenta and adult female breast tissue, compared to males.
• All pregnancies in this study resulted in live births. We found that our male group had a significantly higher birth weight compared to our female group. Male babies are typically born larger, so this was expected.
• Conclusion:
• This late first trimester transcriptome is our earliest look into human placenta gene expression. We hope it will provide a useful resource to understand sex differences in placenta development.

Abstract

Background

Development of the placenta during the late first trimester is critical to ensure normal growth and development of the fetus. Developmental differences in this window such as sex-specific variation are implicated in later placental disease states, yet gene expression at this time is poorly understood.

Methods

RNA-sequencing was performed to characterize the transcriptome of 39 first trimester human placentas using chorionic villi following genetic testing (17 females, 22 males). Gene enrichment analysis was performed to find enriched canonical pathways and gene ontologies in the first trimester. DESeq2 was used to find sexually dimorphic gene expression. Patient demographics were analyzed for sex differences in fetal weight at time of chorionic villus sampling and birth.

Results

RNA-sequencing analyses detected 14,250 expressed genes, with chromosome 19 contributing the greatest proportion (973/2852, 34.1% of chromosome 19 genes) and Y chromosome contributing the least (16/568, 2.8%). Several placenta-enriched genes as well as histone-coding genes were identified to be unique to the first trimester and common to both sexes. Further, we identified 58 genes with significantly different expression between males and females: 25 X-linked, 15 Y-linked, and 18 autosomal genes. Genes that escape X inactivation were highly represented (59.1%) among X-linked genes upregulated in females. Many genes differentially expressed by sex consisted of X/Y gene pairs, suggesting that dosage compensation plays a role in sex differences. These X/Y pairs had roles in parallel, ancient canonical pathways important for eukaryotic cell growth and survival: chromatin modification, transcription, splicing, and translation.

Conclusions

This study is the first characterization of the late first trimester placenta transcriptome, highlighting similarities and differences among the sexes in ongoing human pregnancies resulting in live births. Sexual dimorphism may contribute to pregnancy outcomes, including fetal growth and birth weight, which was seen in our cohort, with males significantly heavier than females at birth. This transcriptome provides a basis for development of early diagnostic tests of placental function that can indicate overall pregnancy heath, fetal-maternal health, and long-term adult health.