Global gene expression analysis of cell-free RNA in amniotic fluid from women destined to develop preeclampsia

Abstract

Preeclampsia (PE) is a disorder specific to pregnancy characterized by new-onset hypertension and proteinuria after 20 weeks of gestation. There is no definite treatment for PE except delivery of the placenta. The purpose of this study was to elucidate the biological pathways involved in the development of PE and to discover a novel biomarker for PE by performing global gene expression analysis of amniotic fluid cell-free RNA.The participants were recruited from the Department of Obstetrics and Gynecology of CHA Gangnam Medical Center (Seoul, Korea) between March 2014 and February 2015. Eight samples were collected from 8 subjects at second trimester who were later diagnosed with PE. From the amniotic fluid samples, cell-free RNA extraction was performed and gene expression was analyzed using the GeneChip PrimeView Array. Transcriptome data previously analyzed by our group from 9 euploid mid-trimester amniotic fluid samples were used as the control for comparative analysis. Functional analysis of the probe sets was performed using the online Database for Annotation, Visualization, and Integrated Discovery (DAVID) toolkit 6.7.We identified 1841 differentially expressed genes (DEGs) between the PE group and the control. Of these, 1557 genes were upregulated in the PE group, while 284 genes were upregulated in the control. The functional annotation of DEGs identified specific enriched functions such as “transport,” “signal transduction,” and “stress response.” Functional annotation clustering with enriched genes in the PE group revealed that translation-related genes, cell–cell adhesion genes, and immune-related genes were enriched. KEGG pathway analysis showed that several biological pathways, including the ribosome pathway and various immune pathways, were dysregulated. Several genes, including RPS29, IGF-2, and UBC, were significantly upregulated in PE, up to tenfold.This study provides the first genome-wide expression analysis of amniotic fluid cell-free RNA in PE. The results showed that gene expression involving the ribosome pathway and immunologic pathways are dysregulated in PE. Our results will aid in understanding the underlying pathogenesis of PE.

The Amniotic Fluid Cell-Free Transcriptome Provides Novel Information about Fetal Development and Placental Cellular Dynamics

“…In 2019, Jung et al [ 72 ] investigated global gene expression and the AF-cell-free-transcriptome associated with the development of PE during the second trimester to identify biological pathways involved in the pathogenesis of PE. They showed that genes associated with the ribosome pathway and immune-related pathway were enriched in the AF- cell-free-transcriptome of PE.…”

The amniotic fluid cell-free transcriptome in spontaneous preterm labor

“…The cell-free supernatant that remains upon removing the AF's cellular components reflects fetal well-being and pregnancy status 46 , 47 , 49 – 56 . Indeed, studies have described changes in the AF cell-free transcriptome in fetal genetic disorders, such as trisomy 18 50 , trisomy 21 49 , and Turner syndrome 52 , as well as in fetal growth restriction 54 and preeclampsia 55 . Others have investigated the association between the AF cell-free transcriptome and maternal factors such as race, obesity, and smoking status 51 , 56 , as well as neonatal morbidity 53 ; yet, the AF cell-free transcriptome in spontaneous preterm labor was not assessed in prior investigations.…”

Annotation of Gene Alteration in Amniotic Fluid Cell Free RNA Transcriptome via Weighted Gene Co-expression Network Analysis

“…The sources of AF cfRNA are not only limited to cells in amniotic uid [4]. The AF cfRNA could be in uenced by fetal sex [2], gestation age [2,[5][6][7], genetic disorders [1,[8][9][10][11], developmental disorders [12][13][14][15], maternal obesity [16], and preeclampsia [17]. Therefore analysis of the transcriptome for the AF cfRNA may provide feasible markers for organ development and fetal malformation [18].…”

“…Enrichment analyses of different expressed genes in abnormal fetus AF cfRNA include Gene Ontology analysis [13,23], Kyoto Encyclopedia of Genes and Genomes pathway analysis [17], and QIAGEN's Ingenuity Pathway Analysis (IPA) [23]. Gene Ontology analysis was the most frequent method used.…”