Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface

Abstract

Organismal function is, to a great extent, determined by interactions among their fundamental building blocks, the cells. In this work, we studied the cell-cell interactome of fetal placental trophoblast cells and maternal endometrial stromal cells, using single-cell transcriptomics. The placental interface mediates the interaction between two semiallogenic individuals, the mother and the fetus, and is thus the epitome of cell interactions. To study these, we inferred the cell-cell interactome by assessing the gene expression of receptor-ligand pairs across cell types. We find a highly cell-type-specific expression of G-protein-coupled receptors, implying that ligand-receptor profiles could be a reliable tool for cell type identification. Furthermore, we find that uterine decidual cells represent a cell-cell interaction hub with a large number of potential incoming and outgoing signals. Decidual cells differentiate from their precursors, the endometrial stromal fibroblasts, during uterine preparation for pregnancy. We show that decidualization (even in vitro) enhances the ability to communicate with the fetus, as most of the receptors and ligands up-regulated during decidualization have their counterpart expressed in trophoblast cells. Among the signals transmitted, growth factors and immune signals dominate, and suggest a delicate balance of enhancing and suppressive signals. Finally, this study provides a rich resource of gene expression profiles of term intravillous and extravillous trophoblasts, including the transcriptome of the multinucleated syncytiotrophoblast.

Figure 1.

The gene expression in the single-cell experiment. (A) Expression of the top 300 genes with greater than twofold differential expression between clusters that were previously established by hierarchical clustering. x-axis: The cells with roman II denote the second batch of cells. Note that the cells from both batches are represented in all clusters. (B) Known trophoblast markers are shown separately, with general trophoblast markers in black, extravillous trophoblasts in blue, and cytotrophoblast-specific expression in gray. (C) First three principal components based on 300 marker genes (full PCA in Supplemental Fig. S8). Clusters correspond to the clustering in the heat map in A.

Figure 2.

Putative signaling between expressed receptors and their ligands in pregnant uterus at term. Compartments represent cell types, and their expressed ligands and receptors are noted along the outer margin. Average cluster gene expression was used, with expression threshold 30 TPM. Black arrows denote putative interactions between directly adjacent maternal and placental cells (maternal decidua and placental EVT and SYN), and dotted gray lines denote putative interactions with cytotrophoblasts.

Figure 3.

Decidualization increases the cell-cell signaling potential with the adjacent EVT (purple, A) and syncytiotrophoblast (light blue, B). Average cluster gene expression is shown, with genes expressed >5 TPM included. (C) Average numbers of putative interactions per cell type, separated into in- and out-edges. Asterisks refer to the number of interactions in the context of decidua, rather than undifferentiated endometrial stromal fibroblasts.

Figure 4.

Distribution of G-protein-coupled receptors among cell types. (A) The expression heat map of GPCRs across sampled cells. (B) Characterization of cell clusters by class of G-protein alpha subunit used.

Figure 5.

Proof of concept: Canonical Wnt signaling is induced in decidualization in maternal cells, as well as in fetal cells conditioned with supernatant of maternal decidualized cells. Anti-beta-catenin antibody is shown in green, and DAPI nuclear staining in blue. The translocation of beta-catenin into the nucleus marks activation of the canonical Wnt signaling pathway. (A) Endometrial stromal fibroblasts (HESC) show beta catenin nuclear localization upon decidualization (Nikon, 20×). (B) BeWo show no nuclear localization in normal growth medium; however, the nuclear localization occurs upon addition of the supernatant from decidualized cells (Nikon, 40×).