biostudies-literatureKeenen MMNational Institute of Allergy and Infectious DiseasesHoward Hughes Medical InstituteNIAID NIH HHSNCI NIH HHSNational Science FoundationRP101170https://www.ebi.ac.uk/biostudies/studies/S-EPMC12113261biostudies-literatureUnknown13The syncytiotrophoblast (STB) is a multinucleated cell layer that forms the outer surface of human chorionic villi. Its unusual structure, with billions of nuclei in a single cell, makes it difficult to resolve using conventional single-cell methods. To better understand STB differentiation, we performed single-nucleus and single-cell RNA sequencing on placental tissue and trophoblast organoids (TOs). Single-nucleus RNA-seq was essential for capturing STB populations, revealing three nuclear subtypes: a juvenile subtype co-expressing CTB and STB markers, one enriched in oxygen sensing genes, and another in transport and GTPase signaling. Organoids grown in suspension culture (STBout) showed higher expression of STB markers, hormones, and a greater proportion of the transport-associated nuceLifeComparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing.PMC12113261AI145828K00 CA245719R01 AI145828NSF 743900HHMI Faculty Scholar awardWorota RECoyne CBFarmer VJYang LGladfelter ASLiang HKeenen MMSingh RfalseComparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing.The syncytiotrophoblast (STB) is a multinucleated cell layer that forms the outer surface of human chorionic villi. Its unusual structure, with billions of nuclei in a single cell, makes it difficult to resolve using conventional single-cell methods. To better understand STB differentiation, we performed single-nucleus and single-cell RNA sequencing on placental tissue and trophoblast organoids (TOs). Single-nucleus RNA-seq was essential for capturing STB populations, revealing three nuclear subtypes: a juvenile subtype co-expressing CTB and STB markers, one enriched in oxygen sensing genes, and another in transport and GTPase signaling. Organoids grown in suspension culture (STBout) showed higher expression of STB markers, hormones, and a greater proportion of the transport-associated nuc2025-01-01T00:00:00Z2025 May2026-06-02T22:41:24.097Z2026-04-21T03:13:31.565ZS-EPMC121132614042418110.7554/eLife.101170