Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks

Abstract

A prerequisite for successful embryo implantation is adequate preparation of receptive endometrium and the establishment and maintenance of a viable embryo. The success of implantation further relies upon a two-way dialogue between the embryo and uterus. However, molecular bases of these preimplantation and implantation processes in humans are not well known. We performed genome expression analyses of human embryos (n = 128) and human endometria (n = 8). We integrated these data with protein-protein interactions in order to identify molecular networks within the endometrium and the embryo, and potential embryo-endometrium interactions at the time of implantation. For that, we applied a novel network profiling algorithm HyperModules, which combines topological module identification and functional enrichment analysis. We found a major wave of transcriptional down-regulation in preimplantation embryos. In receptive-stage endometrium, several genes and signaling pathways were identified, including JAK-STAT signaling and inflammatory pathways. The main curated embryo-endometrium interaction network highlighted the importance of cell adhesion molecules in the implantation process. We also identified cytokine-cytokine receptor interactions involved in implantation, where osteopontin (SPP1), leukemia inhibitory factor (LIF) and leptin (LEP) pathways were intertwining. Further, we identified a number of novel players in human embryo-endometrium interactions, such as apolipoprotein D (APOD), endothelin 1 (END1), fibroblast growth factor 7 (FGF7), gastrin (GAST), kringle containing trnasmembrane protein 1 (KREMEN1), neuropilin 1 (NRP1), serpin peptidase inhibitor clade A member 3 (SERPINA3), versican (VCAN), and others. Our findings provide a fundamental resource for better understanding of the genetic network that leads to successful embryo implantation. We demonstrate the first systems biology approach into the complex molecular network of the implantation process in humans.

Fig. 1.

Transcriptional profiling of the embryo-endometrium interface. A, Number of Affymetrix probe sets (left) and corresponding HUGO Gene Nomenclature Committee gene symbols (right) detected in microarray analysis. em, Embryo; en, endometrium; em-en, coregulated in embryo and endometrium; red, up-regulation; green, down-regulation. B, Functional scores of known genes in embryonic and endometrial gene lists from GO and pathway enrichment analysis.

Fig. 2.

Embryonic and endometrial interaction networks constructed from induced genes with protein-protein interactions. A, Protein counts (right) and interaction counts (left) in constructed networks. blue, Embryonic network (em); red, endometrial network (en); purple, embryo-endometrium network (em-en); orange, high-confidence em-en network. B, Distribution of protein interactions in constructed networks (protein degree, log-scale). Black line represents the global degree distribution of all protein-protein interactions in the HPRD. C, Global coexpression of interacting pairs in constructed networks. The y-axis represents significance score (log₁₀ of P value) of coexpression across hundreds of experiments, as assessed by the MEM tool. Rightmost boxplot (white) shows coexpression for randomly selected pairs of nondifferentially expressed genes. Values of P show that constructed networks tend to have higher coexpression scores than random pairs (one-sided Kolmogorov-Smirnov test). D, Tissue-specific expression of proteins in full embryo-endometrium network (left) and high-confidence embryo-endometrium network (right). Purple bars represent proteins with induced expression in both tissues.

Fig. 3.

Functional enrichment analysis of embryonic and endometrial interaction networks: embryonic (A), endometrial (B), and embryo-endometrium (C). Bar color denotes different types of evidence from GO and pathway databases. The x-axis denotes functional enrichment score, computed as log₁₀ sum of related P values from all topological modules, as identified by the HyperModules algorithm. The 10 most significant functional categories are shown for each source of evidence.

Fig. 4.

One hundred and five topological protein modules identified from the embryo-endometrium interaction network. Node color represents tissue-specific differential gene expression. blue, Expressed in embryo; red, expressed in endometrium; gray, expressed in both tissues. Node size represents number of interaction partners in the module.

Fig. 5.

High-confidence embryo-endometrium interaction network from protein-protein interaction data and literature curation. Node color represents tissue-specific differential gene expression. blue, Expressed in embryo; red, expressed in endometrium; gray, expressed in both tissues.