Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Abstract

The human placenta is a dynamic and heterogeneous organ critical in the establishment of the fetomaternal interface and the maintenance of gestational well-being. It is also the major source of cell-free fetal nucleic acids in the maternal circulation. Placental dysfunction contributes to significant complications, such as preeclampsia, a potentially lethal hypertensive disorder during pregnancy. Previous studies have identified significant changes in the expression profiles of preeclamptic placentas using whole-tissue analysis. Moreover, studies have shown increased levels of targeted RNA transcripts, overall and placental contributions in maternal cell-free nucleic acids during pregnancy progression and gestational complications, but it remains infeasible to noninvasively delineate placental cellular dynamics and dysfunction at the cellular level using maternal cell-free nucleic acid analysis. In this study, we addressed this issue by first dissecting the cellular heterogeneity of the human placenta and defined individual cell-type-specific gene signatures by analyzing more than 24,000 nonmarker selected cells from full-term and early preeclamptic placentas using large-scale microfluidic single-cell transcriptomic technology. Our dataset identified diverse cellular subtypes in the human placenta and enabled reconstruction of the trophoblast differentiation trajectory. Through integrative analysis with maternal plasma cell-free RNA, we resolved the longitudinal cellular dynamics of hematopoietic and placental cells in pregnancy progression. Furthermore, we were able to noninvasively uncover the cellular dysfunction of extravillous trophoblasts in early preeclamptic placentas. Our work showed the potential of integrating transcriptomic information derived from single cells into the interpretation of cell-free plasma RNA, enabling the noninvasive elucidation of cellular dynamics in complex pathological conditions. single-cell transcriptomics | cell-free RNA | noninvasive prenatal testing | placenta | preeclampsia

The inflammasome of circulatory collapse: single cell analysis of survival on extracorporeal life support

“…This technology holds the promise to uncover new information about the pathophysiology of complex disease states in high detail. Initial efforts in this direction with human material have focused on cancer (4,(19)(20)(21), although examples in other diseases are emerging (22,23) including one example of identification of a PBMC repertoire associated tuberculosis progression (2) and a second related to survival in acute infectious disease based on analysis of ~100 cells from 2 patients (3).…”

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

“…We also assessed whether ACE2, TMPRSS2, and CTSL are expressed in the human placenta during pregnancy, using data from three published scRNA-seq studies: two from the first trimester (64,000 cells and 14,000 cells) and one from full-term placenta (20,518 cells) [76][77][78] . ACE2 was expressed (1.4%) in maternal decidual/stromal cells, maternal pericytes, and fetal extravillous trophoblasts, cytotrophoblasts, and syncytiotrophoblast in both first-trimester and term placenta ( Fig.…”

Epitranscriptomic profiling in human placenta: N6‐methyladenosine modification at the 5′‐untranslated region is related to fetal growth and preeclampsia

“…Poly(A) enrichment of RNA from total RNA of a placenta and HEK293T cells was performed in two rounds using Dynabeads Oligo(dT) 25 (Thermo Fisher Scientific). The quality of each total RNA and poly(A) RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).…”

“…21 Placental DNA generally tends to be less methylated than that in other organs, 22 with retrotransposon-derived genes playing a role in placental development and maintenance. 25 Therefore, placental gene expression regulation is unique, and the gene expression profile of a postpartum placenta may reveal essential information regarding the long-term functions of the placenta throughout pregnancy. 25 Therefore, placental gene expression regulation is unique, and the gene expression profile of a postpartum placenta may reveal essential information regarding the long-term functions of the placenta throughout pregnancy.…”