Trajectory modeling of first trimester placenta highlight differences between cytotrophoblast progenitors and trophoblast stem cells [scRNA-Seq 2]
Cytotrophoblast (CTB) are bipotent progenitor epithelial cells of the human placenta, which can differentiate into invasive extravillous trophoblast (EVT) and multinucleated syncytiotrophoblast (STB). Trophoblast stem cells (TSC) have also been shown to be bipotential. In this study, we set out to probe the transcriptional diversity of first trimester CTB and compare TSC to various subgroups of CTB.  We performed single-cell RNA sequencing on six normal placentae, four 6-week placentae, two of which were separated into basal and chorionic fractions prior to sequencing, and two 13-week placentae. We also sequenced three TSC lines, derived from 6-8 week placentae, to evaluate similarities and differences between primary CTB and TSC.  CTB clusters displayed notable distinctions based on gestational age, with 6-week placentae showing enrichment for specific CTB subtypes, further influenced by origin from the basal or chorionic plate. Differential expression analysis of CTB from basal versus chorionic plate highlighted pathways associated with proliferation, unfolded protein response, and oxidative phosphorylation. We identified trophoblast states representing initial progenitor CTB, precursor STB, precursor and mature EVT, and multiple CTB subtypes. CTB progenitors were enriched at 6-weeks, with basal plate cells biased toward EVT, and chorionic plate cells toward STB, precursors. Clustering and trajectory inference analysis indicated that TSC were most like EVT precursor cells, with only a small percentage of TSC on the pre-STB differentiation trajectory. This was confirmed by flow cytometric analysis of 6 different TSC lines, which showed uniform expression of proximal column markers ITGA2 and ITGA5. Additionally, we found that only ITGA5+ CTB could be plated in 2D, and these cells formed only EVT upon spontaneous differentiation.  Our findings suggest that distinct CTB states exist in different regions of the placenta as early as six weeks gestation and that current TSC lines most closely resemble ITGA5+ CTB, biased toward the EVT lineage. Overall design: For whole placental samples, chorionic villi were minced and subjected to three sequential enzymatic digestions. After filtration, cells were counted and loaded on the 10x Genomics chip. For basal and chorion samples, under a microscope we collected the tips (basal fraction) and the base (chorionic fraction) of the villi while the middle section was discarded. The two fractions were subjected to the same sequential enzymatic digestion and after filtration cells were separated on a Percoll (Sigma-Aldrich) gradient.