Identification of differential gene expression profiles in placentas from preeclamptic pregnancies versus normal pregnancies by DNA microarrays

Abstract

The purpose of this study was to perform a comprehensive analysis of gene expression profiles in placentas from preeclamptic pregnancies versus normal placentas. Placental tissues were obtained immediately after delivery from women with normal pregnancies (n=6) and patients with preeclampsia (n=6). The gene expression profile was assessed by oligonucleotide-based DNA microarrays and validated by quantitative real-time RT-PCR. Functional relationships and canonical pathways/networks of differentially-expressed genes were evaluated by GeneSpring™ GX 11.0 software, and ingenuity pathways analysis (IPA). A total of 939 genes were identified that differed significantly in expression: 483 genes were upregulated and 456 genes were downregulated in preeclamptic placentas compared with normal placentas (fold change ≥ 2 and p<0.05 by unpaired t-test corrected with Bonferroni multiple testing). The IPA revealed that the primary molecular functions of these genes are involved in cellular function and maintenance, cellular development, cell signaling, and lipid metabolism. Pathway analysis provided evidence that a number of biological pathways, including Notch, Wnt, NF-κB, and transforming growth factor-β (TGF-β) signaling pathways, were aberrantly regulated in preeclampsia. In conclusion, our microarray analysis represents a comprehensive list of placental gene expression profiles and various dysregulated signaling pathways that are altered in preeclampsia. These observations may provide the basis for developing novel predictive, diagnostic, and prognostic biomarkers of preeclampsia to improve reproductive outcomes and reduce the risk for subsequent cardiovascular disease.

FIG. 1.

Principal component analysis (PCA) was applied to 12 placental samples that were characterized by the gene expression of all probes on the HumanHT-12 V4 BeadChip arrays, including the control group (blue) and the preeclampsia group (red).

FIG. 2.

Volcano plot of probe sets differing between preeclamptic placentas and normal placentas. Fold change (x axis) is plotted against statistical significance (y axis) for each probe set. Genes upregulated with a fold change ≥2 and p<0.05 are depicted in red, and those downregulated with a fold change ≥2 and p<0.05 are shown in green. Grey represents genes in the arrays that were not found to differ significantly between preeclamptic placentas and normal placentas.

FIG. 3.

Cluster analysis of the probes that were increased and decreased significantly in preeclamptic placentas compared with normal placentas (p<0.05, fold change ≥2). A dendrogram of the cluster correlation is shown on the right. Pseudocolors indicate differential expression (red indicates transcript levels greater than the median; black indicates transcript levels equal to the median; green indicates transcript levels below the median; distance metric, Pearson centered; linkage rule, average).

FIG. 4.

The most significantly enriched network that was identified with ingenuity path analysis (score=39).

FIG. 5.

The top five canonical pathways that were identified with ingenuity path analysis in preeclamptic placentas.

FIG. 6.

Comparison of microarray and quantitative real-time RT-PCR expression measurements for the selected genes. Graph shows log of fold changes for array data and log of fold changes for quantitative real-time RT-PCR data.