Single-cell Analysis Reveals Essential lncRNAs Regulating Human Trophoblast Lineage Differentiation

Abstract The human placenta sustains pregnancy through intricate trophoblast lineage dynamics that are critical for fetal development and pregnancy success. While studies on protein coding genes (PCGs) have advanced our understanding of placental biology, the regulatory roles of noncoding RNAs, particularly long noncoding RNAs (lncRNAs), in trophoblast lineage specification and function remain poorly understood. Here, we profile single-cell lncRNA dynamics across human placental development, revealing distinct cell type- and gestational stage-specific expression profiles. Integrated analysis revealed that lncRNAs modulate histone modification levels at the regulatory regions of target genes via cis-action, thereby regulating the expression of key genes essential for trophoblast differentiation. Functional studies by using in vivo and in vitro models fully identify ECEL1P2–ALPP, SEMA3B-AS1–SEMA3B, and MYCNUT/MYCNOS–MYCN as pivotal regulatory axes driving cytotrophoblast self-renewal, syncytiotrophoblast fusion, and epithelial–mesenchymal transition, respectively, which are essential for trophoblast identity and function. Notably, dysregulation of lncRNA–PCG pairs in pathological pregnancies underscores the clinical relevance of these noncoding networks. Together, our findings uncover an unappreciated layer of lineage-specific noncoding regulation, providing mechanistic insight and potential biomarkers for placental development and associated disorders.