Deciphering hallmark combination distinct for peri-implantation stem cell models
Development of new 2D and 3D models of human development such as trophoblast stem cells, gastruloids or blastoids widened possibilities to study early timepoints of development and brightened up ever so slightly the black box of human development. While opening new horizons, the cell sources of those models need proper benchmarking to clarify which hallmark is associated with which lineage and developmental stage. Here, we propose a thorough characterization of pluripotent and trophoblastic stem cell models by transcriptomic, proteomic, epigenetic and metabolic approaches. Extended pluripotent stem cells are similar to primed pluripotent stem cells for most criteria, except metabolic activity, which might explain their ability to convert directly into trophoblast stem cells. We show that trophoblast stem cells are hypo-methylated and that they have a high metabolic activity. Our results clarify the fact that hallmarks of pluripotency are not predictive of each other and have to be used in combination. Multiplying hallmarks alleviate stage matching bias.