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Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques
Augusto F. Schmidt, Daniel J. Schnell, Kenneth P. Eaton, Kashish Chetal, Paranthaman S. Kannan, Lisa A. Miller, Claire A. Chougnet, Daniel T. Swarr, Alan H. Jobe, Nathan Salomonis, Beena D. Kamath-Rayne
Augusto F. Schmidt, Daniel J. Schnell, Kenneth P. Eaton, Kashish Chetal, Paranthaman S. Kannan, Lisa A. Miller, Claire A. Chougnet, Daniel T. Swarr, Alan H. Jobe, Nathan Salomonis, Beena D. Kamath-Rayne
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Research Article Reproductive biology

Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques

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Abstract

Accurate estimate of fetal maturity could provide individualized guidance for delivery of complicated pregnancies. However, current methods are invasive, have low accuracy, and are limited to fetal lung maturation. To identify diagnostic gestational biomarkers, we performed transcriptomic profiling of lung and brain, as well as cell-free RNA from amniotic fluid of preterm and term rhesus macaque fetuses. These data identify potentially new and prior-associated gestational age differences in distinct lung and neuronal cell populations when compared with existing single-cell and bulk RNA-Seq data. Comparative analyses found hundreds of genes coincidently induced in lung and amniotic fluid, along with dozens in brain and amniotic fluid. These data enable creation of computational models that accurately predict lung compliance from amniotic fluid and lung transcriptome of preterm fetuses treated with antenatal corticosteroids. Importantly, antenatal steroids induced off-target gene expression changes in the brain, impinging upon synaptic transmission and neuronal and glial maturation, as this could have long-term consequences on brain development. Cell-free RNA in amniotic fluid may provide a substrate of global fetal maturation markers for personalized management of at-risk pregnancies.

Authors

Augusto F. Schmidt, Daniel J. Schnell, Kenneth P. Eaton, Kashish Chetal, Paranthaman S. Kannan, Lisa A. Miller, Claire A. Chougnet, Daniel T. Swarr, Alan H. Jobe, Nathan Salomonis, Beena D. Kamath-Rayne

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Figure 4

In silico tissue maturation analysis predicts optimal corticosteroid regimens from amniotic fluid.

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In silico tissue maturation analysis predicts optimal corticosteroid reg...
(A) Measurement of lung gas volume at 40 cmH2O on the pressure volume curve (PV40) was performed on fetal lungs immediately following euthanasia. Preterm samples had the lowest PV40 and term samples the highest, with substantial variation among antenatal corticosteroid treated animals. Male and female fetuses are separately indicated. (B) Statistical enrichment of gene sets from diverse single-cell data sets (n > 2,000) for lung and amniotic fluid transcripts that are positively correlated with PV40, across the collection of rhesus samples (2 outlier animals removed). Cell type signatures associated with endothelial cells, lung cells, immune, and cell type signatures associated with endothelial cells, lung cells, immune, and other annotated cell types are highlighted, along with significant enrichment results (Z score > 2, Fisher’s exact P < 0.05 [FDR corrected]) in either or both lungs and amniotic fluid. (C) Data plotted as in B, comparing statistically enriched single-cell signatures from brain and amniotic fluid samples. (D) RNA maturity scoring algorithm design. Differentially expressed genes for term versus preterm control animals are calculated (see Methods) and selected for PCA of term and preterm samples to capture the loadings for PC1 to compute scores for all samples using the PCATools predict function. (E) In silico maturity scores from each fetus lung, brain, or amniotic fluid sample are displayed according to treatment group using either the scoring schema from that same tissue (left 3 plots) or for amniotic fluid scored based on the lung scoring schema for lung PC1 loading genes. Data on A and E are presented as individual values, with box representing the median and the 25th and 75th percentile and whiskers extending to ± 1.5 IQR. n = 47 animals for lung, 35 animals for amniotic fluid, and 46 animals for hippocampus.

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