Comparative Transcriptome Analysis of Cell-Free Fetal RNA from Amniotic Fluid and RNA from Amniocytes in Uncomplicated Pregnancies

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.

Immunological observations and transcriptomic analysis of trimester‐specific full‐term placentas from three Zika virus‐infected women

“…In such circumstances, abnormalities in the numbers of leucocytes and biomarkers indicative of ongoing inflammation or oxidative stress and presence of any microbial infections should be screened as advised by the clinic. Likewise, RNA from the amniotic fluid or amniocytes can be profiled to determine the transcript abundance of molecules involved in important biological pathways . Adopting these steps will potentially improve the clinical care administered to affected patients, by identifying potential danger signs associated with ZIKV infection.…”

“…Likewise, RNA from the amniotic fluid or amniocytes can be profiled to determine the transcript abundance of molecules involved in important biological pathways. 42 Adopting these steps will potentially improve the clinical care administered to affected patients, by identifying potential danger signs associated with ZIKV infection.…”

Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy

“…For decades, AF sampled through transabdominal amniocentesis has been used to assess the fetal karyotype [7][8][9][10][11], lung maturity [12][13][14][15], and presence of inflammatory conditions, such as intra-amniotic infection and sterile intra-amniotic inflammation . Although the ultimate goal is to develop fetal testing via non-invasive sampling, such as urine or maternal blood, the advantages of AF for biomarker discovery have often been recognized [83][84][85][86][87].…”

Trimester-specific Zika virus infection affects placental responses in women

“…In such circumstances, abnormalities in the numbers of leukocytes [48, 49] as well as biomarkers indicative of ongoing inflammation [50] or oxidative stress [51] and presence of any microbial infections [52] should be screened as advised by the clinic. Likewise, RNA from the amniotic fluid or amniocytes, can be profiled to determine the transcript abundance of molecules involved in important biological pathways [53]. Importantly, fetal development (e.g.…”