Upregulation of the lncRNA XACT sustains pluripotency, blocks lineage specification, and drives germ cell tumor-like transcriptional programs in human pluripotent stem cells

Abstract

Long noncoding RNAs (lncRNAs) represent a vast class of regulatory transcripts and are spatiotemporally controlled, yet only a few have been functionally implicated in human development. Here, we identify the X-linked lncRNA XACT, abundantly but transiently expressed during early human embryogenesis, as a critical regulator of pluripotency, lineage specification, and cancer-like states. In human pluripotent stem cells (hPSCs), XACT overexpression--but not depletion--sustains self-renewal without exogenous factors and prevents lineage commitment. Mechanistically, XACT upregulation drives hyper-elevation of the core pluripotency factors OCT4 and NANOG at the protein level by repressing their 3' untranslated regions (UTRs). XACT overexpression confers context-dependent states: in standard hPSC medium it promotes a naive-like program, whereas in the absence of exogenous factors it drives transcriptomic states resembling testicular germ cell tumors, linking misregulation of a developmentally restricted lncRNA to tumorigenic potential. In hPSC-based models of post-implantation development, XACT expression normally declines, whereas its sustained expression disrupts embryonic progression, while depletion has little effect. Finally, transcriptomic analysis of post-implantation human embryos showed that XACT levels correlate positively with pluripotency-associated gene networks. Together, these findings establish XACT as a potent, human-specific modulator of pluripotency and early embryogenesis, and suggest that its aberrant upregulation may underlie both developmental failure and germ cell tumorigenesis.