Abstract
ObjectivesWe aimed to compare tissue-specific expression profiles and biological pathways of RNA from amniocytes and amniotic fluid supernatant (AFS) from second-trimester pregnancies by using transcriptome analysis. Additionally, we wanted to explore whether cell-free RNA from AFS exhibits a unique gene expression signature that more adequately reflects the fetal developmental process than amniocyte RNA.MethodsAmniotic fluid samples were prospectively collected in the second trimester of pregnancy from euploid fetuses. Total RNA was extracted from amniocytes and AFS and hybridized to Affymetrix GeneChip Human Arrays. Significantly differentially expressed transcripts between amniocytes and AFS were obtained by using Welch’s t-test. Unsupervised hierarchical clustering was used to visualize overall expression characteristics and differences in transcripts between AFS and amniocytes. The biological functions of selected genes were analyzed using various online Gene Ontology databases.ResultsA total of 3,072 and 15,633 transcripts were detected in the second-trimester AFS and amniocytes, respectively. Hierarchical clustering revealed differential transcript expression between AFS and amniocytes. We found 353 genes that were specifically enriched in the AFS only, and tissue expression analysis showed enrichment of brain-specific genes in the AFS. Biological pathway analysis revealed that AFS-specific transcripts were mainly involved in embryonic development, cardiovascular development, and cellular morphology pathways.ConclusionThis study demonstrated differential tissue-specific gene expression profiles and biological pathways between AFS and amniocytes. The results suggested that AFS is the preferred RNA source to investigate potential biomarkers of fetal neurodevelopment.
Highlights
Amniotic fluid is a dynamic solution that performs multiple functions for the developing fetus at different ages
We found 353 genes that were enriched in the Amniotic fluid supernatant (AFS) only, and tissue expression analysis showed enrichment of brain-specific genes in the PLOS ONE | DOI:10.1371/journal.pone
This study demonstrated differential tissue-specific gene expression profiles and biological pathways between AFS and amniocytes
Summary
Amniotic fluid is a dynamic solution that performs multiple functions for the developing fetus at different ages. The amniotic fluid composition is similar to that of fetal plasma with rapid bi-directional diffusion via non-keratinized fetal skin between the fetus and the amniotic fluid [1]. Amniotic fluid supernatant (AFS) is the fraction of amniotic fluid after centrifugation. AFS contains suspended fetal transcripts including cell-free RNA and RNA released from amniocytes. Amniotic fluid mRNA can be associated with membrane-derived vesicles, which greatly enhance the mRNA stability and are released from healthy cells in exosomes or virtosomes. RNA of AFS consists of cell-free fetal RNA from fetal circulation and RNA particles from amniocytes. It is assumed that cell-free fetal RNA particles in amniotic fluid include cell-free RNA in fetal circulation, and that they play an important role in fetal development in health and disease
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