Transcriptomic Analysis of Cell-free Fetal RNA in the Amniotic Fluid of Vervet Monkeys (Chlorocebus sabaeus)

Abstract

NHP are important translational models for understanding the genomic underpinnings of growth, development, fetal programming, and predisposition to disease, with potential for the development of early health biomarkers. Understanding how prenatal gene expression is linked to pre- and postnatal health and development requires methods for assessing the fetal transcriptome. Here we used RNAseq methodology to analyze the expression of cell-free fetal RNA in the amniotic fluid supernatant (AFS) of vervet monkeys. Despite the naturally high level of degradation of free-floating RNA, we detected more than 10,000 gene transcripts in vervet AFS. The most highly expressed genes were H19, IGF2, and TPT1, which are involved in embryonic growth and glycemic health. We noted global similarities in expression profiles between vervets and humans, with genes involved in embryonic growth and glycemic health among the genes most highly expressed in AFS. Our study demonstrates both the feasibility and usefulness of prenatal transcriptomic profiles, by using amniocentesis procedures to obtain AFS and cell-free fetal RNA from pregnant vervets.

The amniotic fluid proteome changes with gestational age in normal pregnancy: a cross-sectional study

“…Amniotic fluid contains increased amounts of fetal cells, hair, and vernix as the pregnancy advances 97 . Herein, all amniotic fluid samples were centrifuged at 1300 × g for 10 min at 4 °C, and the clear AF supernatant free of any particulate matter was stored at −80 °C, which was used for proteomics analysis 98 – 100 . Furthermore, samples contaminated by meconium or blood were not included in this study.…”

Epigenetic clock and methylation studies in vervet monkeys

“…Vervets from diverse African populations and the bottlenecked founder populations in the Caribbean have been phylogenetically characterized and, together with the genetically characterized extended pedigree of Caribbean-origin vervets in the Vervet Research Colony (VRC) at Wake Forest School of Medicine, are used for genetic, gene-phenotype, developmental, and infectious disease studies [40,[46][47][48][49][50][51][52][53]. To advance use of the vervet as a model for developmental and aging studies and facilitate DNAm-based assessments of the age effects of various environmental exposures, including preclinical testing of anti-aging therapies, here we created a multi-tissue epigenetic age estimator for the vervet, which is based on the blood, liver, and brain prefrontal cortex.…”

Epigenetic clock and methylation studies in vervet monkeys

“…Vervets from diverse African populations and the bottlenecked founder populations in the Caribbean have been phylogenetically characterized, and together with the genetically characterized extended pedigree Caribbean-origin vervets in the Vervet Research Colony (VRC) at Wake Forest School of Medicine, are used for genetic, gene-phenotype, developmental, and infectious disease studies (Jasinska et al 2012;Warren et al 2015;Huang et al 2015;Svardal et al 2017;Turner et al 2018;Jasinska et al 2017;Jasinska, Rostamian, et al 2020;Ramensky et al 2019;Schmitt et al 2020). To advance use of the vervet as a model for developmental and aging studies, and facilitate DNAm-based assessments of the age effects of various environmental exposures, including preclinical testing of anti-aging therapies, here we created a multi-tissue epigenetic age estimator for the vervet, which is based on the blood, liver, and brain prefrontal cortex.…”