Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity

Abstract

BackgroundAmniotic fluid (AF) is a proximal fluid to the fetus containing higher amounts of cell-free fetal RNA/DNA than maternal serum, thereby making it a promising source for identifying novel biomarkers that predict fetal development and organ maturation. Our aim was to compare AF transcriptomic profiles at different time points in pregnancy to demonstrate unique genetic signatures that would serve as potential biomarkers indicative of fetal maturation.MethodsWe isolated AF RNA from 16 women at different time points in pregnancy: 4 from 18 to 24 weeks, 6 from 34 to 36 weeks, and 6 from 39 to 40 weeks. RNA-sequencing was performed on cell-free RNA. Gene expression and splicing analyses were performed in conjunction with cell-type and pathway predictions.ResultsSample-level analysis at different time points in pregnancy demonstrated a strong correlation with cell types found in the intrauterine environment and fetal respiratory, digestive and external barrier tissues of the fetus, using high-confidence cellular molecular markers. While some RNAs and splice variants were present throughout pregnancy, many transcripts were uniquely expressed at different time points in pregnancy and associated with distinct neonatal co-morbidities (respiratory distress and gavage feeding), indicating fetal immaturity.ConclusionThe AF transcriptome exhibits unique cell/organ-selective expression patterns at different time points in pregnancy that can potentially identify fetal organ maturity and predict neonatal morbidity. Developing novel biomarkers indicative of the maturation of multiple organ systems can improve upon our current methods of fetal maturity testing which focus solely on the lung, and will better inform obstetrical decisions regarding delivery timing.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0138-5) contains supplementary material, which is available to authorized users.

Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

“…The aim of the present study was to analyse the microbial (prokaryotic and eukaryotic) and parasitic diversity in the AF of these two cases (patients 1 and 2). Additionally, we compared these two cases with metatranscriptomic sequences from 16 pregnant women collected at various times in their pregnancies (four Prenatal samples [18–24 weeks], six late Preterm samples [34–36] weeks, and six Term samples [39–40 weeks]) [8]. …”

“…The Illumina sequences obtained from these two cases [9] and the 16 metatranscriptomes used as controls [8] were pre-processed using Prinseq software to remove reads smaller than 35 bp and sequences with quality scores lower than Phred 20. The PEAR program (Paired-End read mergeR) [10] was used to merge and extend the paired-end Illumina reads using the default parameters, with max-overlap = 400 bp.…”

“…The BLASTn results were processed using MEGAN 6 software, and the taxonomic assignment of the sequences was obtained using the Last Common Ancestor method with default parameters [12]. Sequences generated by Kamath-Rayne and colleagues were used as the three controls (I.E., Prenatal, Preterm and Term) [8]. Control sequences were processed following the same protocol used for the previous sequences (Patients 1 and 2).…”

“…This finding suggests that ZIKV is a major cause of new microcephaly cases in Brazil [2]. Inside the uterus, the foetus is surrounded by the Amniotic Fluid (AF), a proximal fluid that contains foetal and maternal cells as well as microorganisms [3–8]. The most common bacterial species found in the AF of women who undergo preterm labour with intact membranes are Ureaplasma urealyticum , Fusobacterium sp., and Mycoplasma hominis [5].…”

Extracellular RNA in aging

“…Circulating RNAs have been identified in a variety of other human fluids (Figure ). Extracellular mRNAs have been identified in serum, CSF, amniotic fluid, seminal fluid, and saliva . Fragments of GAPDH and VEGF mRNA have been identified in urine and fragments of ACTB and DDX4 mRNA are in seminal fluid .…”