title: Comparative Transcriptome Analysis of Cell-Free Fetal RNA from Amniotic Fluid and RNA from Amniocytes in Uncomplicated Pregnancies.
abstract: OBJECTIVE
  We 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.
  
  
  METHODS
  Amniotic 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Department of Obstetrics and Gynecology, CHA Graduate School of Medicine, CHA University, Seoul, Republic of Korea; Department of Obstetrics and Gynecology, Zion Women's hospital, Suwon, Republic of Korea.
authors.forename: J H
authors.initials: JH
authors.lastname: Kang
authors.affiliation: Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea.
authors.forename: H J
authors.initials: HJ
authors.lastname: Park
authors.affiliation: Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea.
authors.forename: Y W
authors.initials: YW
authors.lastname: Jung
authors.affiliation: Genetic Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea.
authors.forename: S H
authors.initials: SH
authors.lastname: Shim
authors.affiliation: Genetic Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea.
authors.forename: S R
authors.initials: SR
authors.lastname: Sung
authors.affiliation: Genetic Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea.
authors.forename: J E
authors.initials: JE
authors.lastname: Park
authors.affiliation: Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea.
authors.forename: D H
authors.initials: DH
authors.lastname: Cha
authors.affiliation: Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea.
authors.forename: E H
authors.initials: EH
authors.lastname: Ahn
mesh_terms: D000328:Adult; D000649:Amniocentesis; D000653:Amniotic Fluid / Q000737:chemistry / Q000378:metabolism*; D002478:Cells, Cultured; D005260:Female; D005333:Fetus / Q000166:cytology / Q000378:metabolism*; D020869:Gene Expression Profiling; D006801:Humans; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D055495:Neurogenesis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011247:Pregnancy; D011262:Pregnancy Trimester, Second; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D012313:RNA