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Molecular signatures of labor and nonlabor myometrium with parsimonious classification from 2 calcium transporter genes
William E. Ackerman IV, … , Guomao Zhao, Irina A. Buhimschi
William E. Ackerman IV, … , Guomao Zhao, Irina A. Buhimschi
Published May 4, 2021
Citation Information: JCI Insight. 2021;6(11):e148425. https://doi.org/10.1172/jci.insight.148425.
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Research Article Reproductive biology

Molecular signatures of labor and nonlabor myometrium with parsimonious classification from 2 calcium transporter genes

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Abstract

Clinical phenotyping of term and preterm labor is imprecise, and disagreement persists on categorization relative to underlying pathobiology, which remains poorly understood. We performed RNA sequencing (RNA-seq) of 31 specimens of human uterine myometrium from 10 term and 21 preterm cesarean deliveries with rich clinical context information. A molecular signature of 4814 transcripts stratified myometrial samples into quiescent (Q) and nonquiescent (NQ) phenotypes, independent of gestational age and incision site. Similar stratifications were achieved using expressed genes in Ca2+ signaling and TGF-β pathways. For maximal parsimony, we evaluated the expression of just 2 Ca2+ transporter genes, ATP2B4 (encoding PMCA4) and ATP2A2 (coding for SERCA2), and we found that their ratio reliably distinguished NQ and Q specimens in the current study, and also in 2 publicly available RNA-seq data sets (GSE50599 and GSE80172), with an overall AUC of 0.94. Cross-validation of the ATP2B4/ATP2A2 ratio by quantitative PCR in an expanded cohort (by 11 additional specimens) achieved complete separation (AUC of 1.00) of NQ versus Q specimens. While providing additional insight into the associations between clinical features of term and preterm labor and myometrial gene expression, our study also offers a practical algorithm for unbiased classification of myometrial biopsies by their overall contractile program.

Authors

William E. Ackerman IV, Catalin S. Buhimschi, Ali Snedden, Taryn L. Summerfield, Guomao Zhao, Irina A. Buhimschi

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Figure 2

Differentially expressed RNA transcripts in myometrial specimens in term and preterm labor.

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Differentially expressed RNA transcripts in myometrial specimens in term...
(A) Plot of log2 ratio to average baseline (TNL) expression for the 4814 transcripts differentially abundant (FDR < 0.1, minimum fold-change ± 1.5, DESeq2 algorithm) between term myometrial specimens in the absence (TNL, n = 5) or presence (TL, n = 5) of labor. Transcripts with increased abundance are depicted in red, while those with decreased levels are shown in blue. (B) Correlation matrix with unsupervised hierarchical cluster analysis showing a higher degree of similarity among samples within each cohort (blue circles, TNL; red squares, TL) than between cohorts when considering the differentially abundant transcripts. (C) Scree plot of principal components following application of PCA to the differentially expressed genes in term myometrial specimens. The first principal component, PC1, accounted for most (57%) of the explained variance in the data. (D) Scatterplot of PC1 and PC2 with accompanying box-and-whisker plots (below) showing the distribution of TL (red squares), TNL (blue circles), and preterm birth (PTB, gray symbols) in PC space based on the expression signature of 4184 transcripts. Spontaneous initiation of PTB is denoted by light gray boxes, while dark gray circles indicate the absence of spontaneous labor initiation as determined clinically. (E) Scatterplot as in D but recolored to indicate in greater detail the clinical disposition of the pregnancies from which the PTB myometrial specimens were derived: intact membranes with Triple I (green squares); intact membranes without Triple I (Group 5, PTB-PI, yellow circles); preterm premature rupture of membranes (PPROM) with Triple I (pink squares); and PPROM without Triple I (purple squares). Two clusters comprising mostly nonquiescent (NQ) and quiescent (Q) myometrial specimens were evident (dashed circles). PTB cases with complex mixed phenotypes (MY25 and MY28), as well as a NQ specimen (MY31) that distributed between the term specimen clusters, are indicated.

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