Gene expression patterns in human placenta

Abstract

The placenta is the principal metabolic, respiratory, excretory, and endocrine organ for the first 9 months of fetal life. Its role in fetal and maternal physiology is remarkably diverse. Because of the central role that the placenta has in fetal and maternal physiology and development, the possibility that variation in placental gene expression patterns might be linked to important abnormalities in maternal or fetal health, or even variations in later life, warrants investigation. As an initial step, we used DNA microarrays to analyze gene expression patterns in 72 samples of amnion, chorion, umbilical cord, and sections of villus parenchyma from 19 human placentas from successful full-term pregnancies. The umbilical cord, chorion, amnion, and villus parenchyma samples were readily distinguished by differences in their global gene-expression patterns, many of which seemed to be related to physiology and histology. Differentially expressed genes have roles that include placental trophoblast secretion, signal transduction, metabolism, immune regulation, cell adhesion, and structure. We found interindividual differences in expression patterns in villus parenchyma and systematic differences between the maternal, fetal, and intermediate layers. A group of genes that was expressed in both the maternal and fetal villus parenchyma sections of placenta included genes that may be associated with preeclampsia. We identified sets of genes whose expression in placenta was significantly correlated with the sex of the fetus. This study provides a rich and diverse picture of the molecular variation in the placenta from healthy pregnancies.

Fig. 1.

Schematic representation of a human term placenta (44). Six parts of placenta from which mRNA was isolated [namely, amnion, chorion, umbilical cord, and three sections of villus parenchyma (fetal, middle, and maternal)] are shown in bold. The amnion and chorion were isolated by peeling them apart from the reflected membranes. The chorionic plate and the basal plate are also shown.

Fig. 2.

Gene expression in villus parenchyma of placenta relative to other normal human tissues. We compared eight placental villus samples and 114 human tissue samples, representing 35 tissue types by using sam (15). We chose 152 genes with a false-discovery rate of <0.06, based on differential expression between placental villus sections and other tissues, and the expression data for these genes are shown with the 35 tissues (columns; organized anatomically) and genes (rows; organized by hierarchical clustering). Expression levels are represented by a color tag, with red representing the highest levels and green representing the lowest levels of expression.

Fig. 3.

Placental gene expression. (A) Unsupervised hierarchical clustering sorts placental samples based on their anatomical location. The 72 samples from 19 patients with successful pregnancies are designated according to the patient number (Pn), part of the placenta, and fetal gender. Because of anatomic similarity in gene expression, the samples cluster to form shorter branches of amnion, chorion, umbilical cord, and villus parenchyma sections. Gene expression among sections of villus parenchyma forms one branch and varies significantly from the other branch that includes amnion, chorion, and umbilical cord samples. Among villus sections, the clustering relies on similarity in anatomical location and individual differences in gene expression. (B) Placental transcriptome. We selected ≈1,500 genes that were the most variably expressed among the samples by using a criterion of 3-fold change in level of expression in a minimum of two arrays. Each expression measurement represents the normalized ratio of fluorescence from the hybridized experimental material to a common internal reference. The prominent clusters of genes are shown on the right.

Fig. 4.

Gene expression in different parts of placenta. Genes have been selectively shown from each of the prominent gene clusters in Fig. 3B to represent the range of diversity in placental gene expression. The clusters showing genes correlated with anatomy or immune function are amnion (A), umbilical cord (B), chorion (D), branch 2 (amnion, chorion, and umbilical cord) gene cluster (E), and branch 1 (villus parenchyma) (F). Also, a cluster of immune-function-related genes (C) expressed in most chorion samples (but, intriguingly, also in villus sections and amnion from P32) are shown. The visualization format is the same as in Fig. 3.

Fig. 5.

Interindividual differences in placental villus parenchyma gene-expression patterns. We calculated an intrinsic score for ≈10,000 genes from this primary data set of villus sections. The intrinsic score was the ratio of the mean squared pairwise difference in the transcript level of that gene between villus sections of different placentas to the mean squared pairwise difference in the transcript levels of the gene between villus sections of the same placenta. We chose 303 genes that had an intrinsic score >1.5 SD from the mean to define genes that are intrinsic to villus parenchyma of each individual placenta. By using these genes, all except one sample clustered together with other villus samples of the same placenta. Genes located on the X and Y chromosome whose expression is associated with placentas of female or male fetuses (colored branches) are shown in red and blue, respectively. The visualization format is the same as in Fig. 3.

Fig. 6.

Genes uniquely expressed in different layers of villus sections. sam algorithm was used to select 230 genes whose expression varied significantly among fetal, middle, and maternal sections. These genes, which were selected with a delta of 0.2 to get a maximum false-discovery rate (q-value) of 0.6, were then used to hierarchically cluster the samples to visualize the expression profile within the villus parenchyma. The three gene clusters were assigned names (shown on the left) based on the sections that show a relatively greater expression of the genes (right). Genes whose names are shown in red are potentially associated with a hypertensive pregnancy disorder, PE, and are expressed mostly in maternal and/or fetal sections. The visualization format is the same as Fig. 3.