Transcriptomic Analysis of Placental Tissue Helps Understand the Pathogenic Mechanisms of SARS-CoV-2 During Pregnancy at the Cellular Level

In a recent study posted on bioRxiv*, researchers investigated the pathogenic mechanisms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during pregnancy using digital spatial profiling of placental tissue.

Study: Complete transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature. Image credit: PH888/Shutterstock


Several studies have reported the development of a preeclampsia-like syndrome in pregnant women exposed to SARS-CoV-2. Vasculopathy and inflammation are increased in the placental tissues of patients with coronavirus disease 2019 (COVID-19). Placental dysfunction is the main cause of preeclampsia. Preeclampsia is subdivided into early onset (< 34 weken zwangerschap) en late aanvang (> 34 weeks) according to the time when symptoms are detected.

Early-onset preeclampsia is associated with poor placentation leading to malperfusion and placental dysfunction, although its causes remain unclear. Maternal pathological factors leading to placental dysfunction, such as endothelial dysfunction and systemic hypertension, are believed to contribute to late-onset preeclampsia.

About the study

In the current study, researchers used full transcriptomic digital spatial profiling of placentas to understand the mechanisms of SARS-CoV-2 pathogenesis during pregnancy. The study involved unvaccinated pregnant individuals showing COVID-19 symptoms in their third trimester. Archived placental tissues collected from 2016 to 2018 served as controls.

SARS-CoV-2 and control groups were matched for gestational age, maternal age and comorbidities. Placental size, weight, macroscopic changes, fetal sex and weight, and mode of delivery were recorded. A trained pathologist analyzed placenta samples and tissue microarrays (TMAs) of the samples were made.

The study focused on seven samples from the SARS-CoV-2 group due to the death of three fetuses. Similarly, one sample of the controls was excluded due to low quality. TMA slides were stained using fluorescent markers to characterize cell types and histological features. TMAs were hybridized using a whole transcriptome atlas (WTA)-barcoded probe set of approximately 18,000 genes.

Raw data were normalized to 134 negative probes in the WTA probe set. Differential gene expression analysis was performed separately for villous nucleated stromal cells and trophoblasts containing regions of interest between SARS-CoV-2 and control groups. Pathway enrichment analyzes were performed and gene set enrichment was clustered and visualized.


Placental cores were obtained from seven participants who tested COVID-19 positive in the past 15 days before delivery and nine controls. No significant differences were observed in placental weight, fetal weight, maternal age, or gestational age between SARS-CoV-2 positive subjects and controls. Three neonates from the SARS-CoV-2 group and four from the control group were born prematurely.

Four SARS-CoV-2 positive subjects and five controls had comorbidities, including gestational diabetes, bipolar disorder, hyperthyroidism, and hypothyroidism. Placenta from three SARS-CoV-2 positive individuals showed infarcts. Placenta from two controls showed hypoplasia leading to preterm delivery.

There was no evidence of SARS-CoV-2 viral load in the placental nuclei of COVID-19 subjects. The SARS-CoV-2 group had a significantly higher number of cluster of differentiation (CD68)-positive immune cells in the terminal villi than controls. Principal component analysis (PCA) revealed the separation of trophoblasts and villous stromal cells between the two groups.

There were more differentially expressed genes (DEGs) in response to SARS-CoV-2 at the anchoring villi than at the terminal villi for stromal cells and trophoblasts in the villi. Furthermore, DEGs at the anchoring and terminal villi strongly overlapped. However, there was minimal overlap in DEGs between villous nuclear stromal cells and trophoblasts.

Pathway enrichment analysis revealed significant activation of several preeclampsia and oxidative stress associated pathways. Villous core stroma cells showed positive enrichment of immune-related pathways. Trophoblasts showed positive enrichment of estrogen response, peroxisome pathway and E2F targets.

In all, 1641 and 1339 genes were significantly up- and down-regulated in trophoblasts at the terminal and anchoring villi, respectively, in response to SARS-CoV-2. In particular, pregnancy-associated plasma protein A (PAPPA), PAPPA2 and placental alkaline phosphatase (ALPP) were upregulated. Downregulated genes include complement component C1Q, osteopontin, caveolin 1, coagulation factor XII and various collagens.

Pathways related to blood pressure and vascular tension were upregulated, and those related to collagen deposition, coagulation, vasoconstriction, graft rejection and complement pathways were downregulated. In stromal cells of the villous nucleus at anchorage and terminal villi, 1026 genes were upregulated and 2697 were downregulated in response to SARS-CoV-2; Pathways related to oxidative stress, methylglyoxal levels and nitrosative stress were enriched in it.


Taken together, the researchers illustrated the unique response of stromal cells of the villous nucleus and trophoblasts of the terminal and anchoring villi of the placenta to SARS-CoV-2. Examining transcriptional changes in these cells revealed the enrichment of preeclampsia-related pathways. This suggests that the placenta in pregnant subjects with SARS-CoV-2 adopts a transcriptional profile similar to that observed in pregnant women with preeclampsia.

*Important announcement

bioRxiv publishes preliminary scientific reports that have not been peer reviewed and therefore should not be considered conclusive, guiding clinical practice/health-related behavior, or established information.

Transcriptomic Analysis of Placental Tissue Helps Understand the Pathogenic Mechanisms of SARS-CoV-2 During Pregnancy at the Cellular Level

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