Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18

Abstract

Trisomy 18 is a common human aneuploidy that is associated with significant perinatal mortality. Unlike the well-characterized "critical region" in trisomy 21 (21q22), there is no corresponding region on chromosome 18 associated with its pathogenesis. The high morbidity and mortality of affected individuals has limited extensive investigations. In order to better understand the molecular mechanisms underlying the congenital anomalies observed in this condition, we investigated the in utero gene expression profile of second trimester fetuses affected with trisomy 18. Total RNA was extracted from cell-free amniotic fluid supernatant from aneuploid fetuses and euploid controls matched for gestational age and hybridized to Affymetrix U133 Plus 2.0 arrays. Individual differentially expressed transcripts were obtained by two-tailed t tests. Over-represented functional pathways among these genes were identified with DAVID and Ingenuity(®) Pathways Analysis. Results show that three hundred and fifty-two probe sets representing 251 annotated genes were statistically significantly differentially expressed between trisomy 18 and controls. Only 7 genes (2.8% of the annotated total) were located on chromosome 18, including ROCK1, an up-regulated gene involved in valvuloseptal and endocardial cushion formation. Pathway analysis indicated disrupted function in ion transport, MHCII/T cell mediated immunity, DNA repair, G-protein mediated signaling, kinases, and glycosylation. Significant down-regulation of genes involved in adrenal development was identified, which may explain both the abnormal maternal serum estriols and the pre and postnatal growth restriction in trisomy 18. Comparison of this gene set to one previously generated for trisomy 21 fetuses revealed only six overlapping differentially regulated genes. This study contributes novel information regarding functional developmental gene expression differences in fetuses with trisomy 18.

Figure 1

Heatmap showing hierarchical clustering of control (C1–C6; solid red bar) and trisomic (T1–T5; solid blue bar) samples. Clustering is based on data from 345 probe sets: the 352 from the Individual Gene Set, minus the 7 from chromosome 18. If these 7 are not removed, the dendrogram looks quite similar; in particular, it similarly separates the control and trisomic samples. Expression values in each row are z-score normalized.

Figure 2

A Venn diagram depicting the number of differentially regulated genes that overlap between trisomies 18 and 21.

Figure 3

Network associated with adrenal gland development as generated by Ingenuity® Pathways Analysis (IPA). Focus genes found to be down-regulated in trisomy 18 are shaded gray. Genes related to canonical pathways whose functions include corticotropin releasing hormone signaling and EGF, FGF, and IGF-1 signaling are outlined in orange.