Publication: High-throughput miRNA-sequencing of the human placenta: expression throughout gestation

High-throughput miRNA-sequencing of the human placenta: expression throughout gestation
Epigenomics, 2021 July; 13(13):995-1012. doi: 10.2217/epi-2021-0055. Epub 2021 May 25.

• Next generation sequencing of small RNAs in human placenta, with emphasis on microRNAs (miRNAs)
• N=113 late first trimester placenta samples from leftover tissue after chorionic villus sampling ("CVS", a prenatal diagnostic test)
• This is the earliest timepoint that we can directly study human placenta in continuing (non-termination) pregnancies.
• Chorionic villi are stringy tissue that grow on the outside of the placenta to maximize surface area with maternal tissue. They share the same genetics as the fetus.
• N=47 third trimester placenta samples collected after delivery
• miRNA profiles of:
• All expressed miRNAs, normalized counts over 10
• We considered lower expression thresholds, but expression was inconsistent across all patients
• Similarly expressed miRNAs, P>=0.05, fold-change<=2, normalized counts>10
• These miRNAs are fairly consistently expressed between first and third trimester
• They are not significantly different between first and third trimester
• Their expression may be altered by other variables (e.g. patient health, environmental factors, any developmental differences that affect pregnancy outcomes) - for future research!
• Differentially expressed miRNAs (still significant after adjusting for multiple comparisons), FDR<0.05, fold-change>2, normalized counts>10
• Note that all FDR<0.05 miRNAs are also P<0.05. The Benjamini-Hochberg false discovery rate P value adjustment is a stricter criteria than P<0.05.
• These miRNAs change expression as the pregnancy progresses
• Chromosome 14 and 19 microRNA cluster (C14MC, C19MC) members
• These clusters are known to be expressed in placenta, per prior microarray studies
• We identified many C14MC and C19MC expressed in first and third trimester, some similarly expressed and some significantly different between trimesters
• C14MC produced some miRNAs very upregulated in first trimester
• C19MC members were generally more highly expressed in both first and third trimester
• Some of these miRNAs also enter maternal circulation, per prior research
• Chromosome 13 has two small miRNA clusters significantly upregulated in first trimester placenta, with lower expression in third trimester. 
• Two C13MC regions in human placenta identified for the first time

Authors:

Tania L Gonzalez,  Laura E Eisman, Nikhil V Joshi, Amy E Flowers, Di Wu, Yizhou Wang, Chintda Santiskulvong, Jie Tang, Rae A Buttle, Erica Sauro, Ekaterina L Clark, Rosemarie DiPentino, Caroline A Jefferies, Jessica L Chan, Yayu Lin,  Yazhen Zhu,  Yalda Afshar,  Hsian-Rong Tseng, Kent Taylor, John Williams III,  Margareta D Pisarska

Links:

• Preprint full text at bioRxiv (February 2021)
• https://doi.org/10.1101/2021.02.04.429392
• Peer-reviewed and published at Epigenomics (May 2021)
• https://doi.org/10.2217/epi-2021-0055
• Added additional supplemental information on within-chromosome hot spots including two clusters at chromosome 13 that show increased expression in first trimester, compared to third trimester placenta.
• Added additional principal components analysis supplemental figures to show that samples clustering was explained by trimester, not fetal sex or race or ethnicity or paternal ages or maternal BMI.
• Additional clarifications to methods and results, per our reviewer feedback.
• Otherwise very similar to the pre-print version. Same dataset, analysis, and conclusions.
• PubMed ID: 34030457
• PubMed Central ID (PMCID): PMC8244582
• Raw data and counts: NCBI GEO accession GSE184860 (160 samples) = Bulk small RNA-seq
• Counts include miRNAs and piRNAs, but only miRNAs were used in the differential expression analysis.
• ResearchGate - full text available for free
• Also see our follow up manuscript focusing on miRNA sex differences in this cohort, Flowers et al. 2021, using the same data.