Global Gene Expression Analysis of Term Amniotic Fluid Cell-Free Fetal RNA

Abstract

Objective To identify the tissue expression patterns and biological pathways enriched in term amniotic fluid (AF) cell-free fetal RNA by comparing functional genomic analyses of term and second trimester AF supernatants. Methods This was a prospective whole genome microarray study comparing eight AF samples collected from eight women at term who underwent prelabor cesarean delivery and eight second trimester AF samples from routine amniocenteses. A functional annotation tool was used to compare tissue expression patterns in term and second trimester samples. Pathways analysis software identified physiological systems, molecular and cellular functions and upstream regulators that were significantly overrepresented in term AF. Results There were 2,871 significantly differentially regulated genes. In term AF, tissue expression analysis showed enrichment of salivary gland, tracheal, and renal transcripts, as compared with brain and embryonic neural cells in second trimester. Functional analysis of genes upregulated at term revealed pathways that were highly specific for postnatal adaptation, such as immune function, digestion, respiration, carbohydrate metabolism and adipogenesis. Inflammation and prostaglandin synthesis, two key processes involved in normal labor, were also activated in term AF. Conclusions Transcriptomic analysis of AF cell-free fetal RNA detects fetal maturation processes activated in term pregnancy. These findings further develop the concept of AF supernatant as a real-time gene expression “summary fluid” and support its potential for future studies of fetal development.

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