Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology

Abstract

Placental abnormalities are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ∼5% of all pregnancies. An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities, but there have been no systematic attempts to assess their molecular similarities or differences. We collected protein and mRNA expression data through shot‐gun proteomics and microarray expression analysis of the highly vascular exchange region, microdissected from the human and mouse near‐term placenta. Over 7000 ortholog genes were detected with 70% co‐expressed in both species. Close to 90% agreement was found between our human proteomic results and 1649 genes assayed by immunohistochemistry for expression in the human placenta in the Human Protein Atlas. Interestingly, over 80% of genes known to cause placental phenotypes in mouse are co‐expressed in human. Several of these phenotype‐associated proteins form a tight protein–protein interaction network involving 15 known and 34 novel candidate proteins also likely important in placental structure and/or function. The entire data are available as a web‐accessible database to guide the informed development of mouse models to study human disease. ### Synopsis The modeling of human disease in mouse has had success, but there have also been many failures. A priori , it is unclear if mutation of the orthologous gene in mouse will recapitulate the human phenotype. Although, many large‐scale datasets for microarray and proteomics exist for both mouse and human, they are rarely integrated and compared. To better predict if mutation in a mouse gene will give the equivalent phenotype as the human ortholog, a detailed molecular understanding of the orthologous/homologous tissues from human and mouse are needed. By using a dataset of ortholog gene and protein expression, comparisons can be made as to the conservation of protein interaction networks and regarding the co‐expression of phenotype‐associated proteins. One organ that can be obtained from non‐pathological human samples is the placenta. This organ is also the source of the primary defect in two of the most prevalent diseases of pregnancy, intrauterine growth restriction (IUGR) and preeclampsia (PE). Although the placentas of no two mammalian species are the same, the placentas of humans and mice have strong similarities. In both species, maternal blood from the uterine arteries enters the placenta from large diameter, spiral arteries located in the maternal decidua. The maternal blood then percolates through a dense mesh of channels created and lined by fetal trophoblast cells in which an equally dense network of fetal capillaries is localized. This region is the site of feto‐maternal exchange and is called the villous tree in humans and the labyrinth in mice. In both species, the umbilical vessels connect the fetal capillaries of the placental exchange region with the fetal body circulation. IUGR and PE, which combined affect ∼5% of all pregnancies are both associated with serious morbidity and mortality, and the only known treatment is premature delivery, which places the baby at high risk of prematurity‐related complications. Although, PE and IUGR have been intensely studied for decades, the molecular pathways, etiology and pathogenesis of these diseases remain poorly understood. Our aim was to empirically determine the molecular similarity of these two vascular exchange regions based on subcellular proteomics and transcriptional profiling, to assess the compatibility of mouse placenta to model human placenta biology. Our proteomic analysis was validated by comparison to both matched mRNA samples analyzed by microarray and to 4872 proteins assayed by immunohistochemistry (IHC) on human placenta samples in the Human Protein Atlas ([www.proteinatlas.org][1]). In both cases high correlation was found between the protein to microarray (⩾95%) and protein to IHC ⩾90%. Of key interest was the degree of molecular similarity between the mouse and human vascular exchange regions of the placenta. Data for observed proteins and their corresponding microarray probe sets were paired for human and mouse placenta samples. These protein/probe pairs were then linked between the two species using orthology data form ENSEMBL. This dataset of orthologous proteins/probes was then clustered to identify genes with common expression. This could be further classified into three categories. In all cases microarray data showed expression in both species, and protein data were observed in both species (cluster I), one species (cluster II) or in neither species (cluster III) ([Figure 2A][2]). Organellar localization associated with significant enrichment for appropriate Gene Ontology annotation terms was observed for cluster I proteins ([Figure 2B][2]). Interestingly, organellar localization showed striking agreement for co‐expressed ortholog proteins in cluster I ([Figure 2A and C][2]) as predicted by Pearson correlation, which argues for functional conservation for most ortholog proteins. Overall our analysis revealed ∼70% conserved expression of one‐to‐one ortholog genes between mouse and human placental exchange regions. We made similar comparison of microarray data deposited at the GEO repository, for other matched tissues. We found similar levels of conservation for matched tissues and lower levels against all other tissues. We next compared the level of conservation of genes that when mutant in the mouse give placenta phenotypes. We found an even higher conservation of expression of these phenotypic genes between...