Gene expression analysis in pregnant women and their infants identifies unique fetal biomarkers that circulate in maternal blood

Abstract

The discovery of fetal mRNA transcripts in the maternal circulation holds great promise for noninvasive prenatal diagnosis. To identify potential fetal biomarkers, we studied whole blood and plasma gene transcripts that were common to 9 term pregnant women and their newborns but absent or reduced in the mothers postpartum. RNA was isolated from peripheral or umbilical blood and hybridized to gene expression arrays. Gene expression, paired Student's t test, and pathway analyses were performed. In whole blood, 157 gene transcripts met statistical significance. These fetal biomarkers included 27 developmental genes, 5 sensory perception genes, and 22 genes involved in neonatal physiology. Transcripts were predominantly expressed or restricted to the fetus, the embryo, or the neonate. Real-time RT-PCR amplification confirmed the presence of specific gene transcripts; SNP analysis demonstrated the presence of 3 fetal transcripts in maternal antepartum blood. Comparison of whole blood and plasma samples from the same pregnant woman suggested that placental genes are more easily detected in plasma. We conclude that fetal and placental mRNA circulates in the blood of pregnant women. Transcriptional analysis of maternal whole blood identifies a unique set of biologically diverse fetal genes and has a multitude of clinical applications.

Figure 1. A Venn diagram depicting presumed fetal gene transcripts detected in antepartum maternal blood.

Those gene transcripts that were detected in both the antepartum mother and fetus, but were not seen in the postpartum samples were targeted as unique fetal markers.

Figure 2. Boxplots of paired t scores comparing gene expression in plasma and whole blood samples.

The boxes mark the first quartile, median, and third quartile of the t scores for each comparison. Vertical dotted lines represent t scores within 1.5 times the interquartile range. Positive t scores represent transcripts higher in plasma samples; negative t scores represent transcripts higher in whole blood. (A) Distribution of paired t scores for all 22,283 transcripts measured in antepartum, umbilical cord, and postpartum samples. What appear to be bold vertical lines are actually numerous dots. (B) Distribution of paired t scores for 50 previously identified placental transcripts. Dots indicate outliers.