Sex differences in the late first trimester human placenta transcriptome

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.

Keywords: Chorionic villus sampling; First trimester placenta; Pregnancy; RNA-sequencing; Sex differences.

Fig. 1

Normative late first trimester placenta transcriptome. a Box and whisker plot showing log₂FPKM distribution of expressed genes. All: average log₂FPKM of 14,250 expressed genes over all 39 samples. F, M: all genes over the FPKM cutoff in either female or male samples, respectively. The whiskers range is the interquartile range ± 50%, with outliers shown as blue circles. Median is red line. b Chromosome distribution of 14,250 genes expressed in chorionic villi, all biotypes (gray bars). Expressed genes are shows as a percentage of total genes in each chromosome (green diamonds). c Biotype categories of all expressed genes and each FPKM quartile are shown. The proportion of each biotype is shown as a percentage and labeled if ≥ 3%

Fig. 2

Significantly differentially expressed genes in placenta. a Chromosome and biotype distribution of the 58 DEGs, 35 upregulated in females (F) and 23 upregulated in males (M). “Auto” = autosomal chromosomes. b Ideogram of chromosome X showing the 25 significantly differentially expressed X-linked genes between first trimester male and female placentas (FDR < 0.05). Left: 3 genes upregulated in males. Right: 22 genes upregulated in females. The consensus calls for X inactivation status were adapted from Balaton et al. [42]

Fig. 3

Functions of significantly differentially expressed genes in placenta. Venn diagrams of function categories for DEGs with known gene ontologies [, , , , , , –, –126]. Autosome genes are underlined. Sense/antisense pairs of DEGs are linked with dashed lines, with antisense genes outside the circles. *Homologous X/Y genes. **Genes with an X-linked homolog which is not differentially expressed. Functions predicted from sequence only are denoted with “(?)” next to the gene name. Genes without known or predicted function were omitted: ANOS2P, ARMCX6, FRG1JP, IQCJ-SCHIP1-AS1, LINC00278, LINC00643, PSMA6P1, RP13-36G14.4, RPL23AP11, TTTY14, TTTY15, and TXLNGY. a Genes upregulated in females. b Genes upregulated in males