Researchers use single-cell RNA-Seq to dissect the cellular heterogeneity of the human placenta

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, researchers from the Chinese University of Hong Kong 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. Their  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, they resolved the longitudinal cellular dynamics of hematopoietic and placental cells in pregnancy progression. Furthermore, the researchers were able to noninvasively uncover the cellular dysfunction of extravillous trophoblasts in early preeclamptic placentas. This 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.

Dissection of the cellular heterogeneity and annotation of
cellular identity in the human placenta

(A) Biaxial scatter plot showing the distribution of cells of predicted fetal/maternal origin in the original t-SNE clustering distribution as in Fig. 1B. Data from PN2 libraries have not been plotted, as no genotyping information was available for fetomaternal origin prediction. (B) The four major cellular groups in the human placenta: decidual (P1; green), stromal (P2–P4; olive), hematopoietic (P5–P9; red), and trophoblastic (P10–P12; turquoise). (C) Expression pattern of stromal (COL1A1, COL3A1, THY1, and VIM) and myeloid (CSF1R, CD14, AIF1, and CD53) markers in P5–P7 subgroups. (D) t-SNE analysis showed clustering of P5 cells (gray) with artificial P4/P7 duplets (light green) generated in silico, suggesting that P5 cells are likely multiplets. (E) Biaxial scatter plots showing the expression pattern of genes encoding for HLAs among different subgroups of placental cells. (F) Cellular subgroup composition heterogeneity in different single-cell transcriptomic datasets. PN3P/PN3C and PN4P/PN4C represent paired biopsies taken proximal to the umbilical cord insertion sites (PN3C/PN4C) and distal at the periphery of the placental disk (PN3P/PN4P). (G) Table summarizing the annotated nature of each cellular subgroup.