Naive Pluripotent Stem Cells as a Model for Studying Human Developmental Epigenomics: Opportunities and Limitations

Next year will mark the 20th anniversary since the discovery of human embryonic stem cells (hESCs) and the demonstration that these remarkable cells can differentiate into all lineages of the body [1]. Impressive progress since then has delivered hESC-derived therapies to the clinic, established hESCs as a cellular platform for drug screening, toxicology assays and disease modeling, and advanced our understanding of human developmental biology. Although derived from epiblast cells of the preimplantation human embryo, the biological properties of hESCs more closely reflect the early postimplantation embryo that is formed several days later in development [2–5]. This distinction in timing is important because it helps to evaluate the characteristics of hESCs by comparing with their equivalent cells in vivo. Classifying the current hESC lines as similar to postimplantation cells also opens up an obvious need to capture hESCs in an alternative state that recapitulates the preimplantation embryo. Several reports of preimplantation-like human stem cells, broadly termed ‘naive’ hESCs, have raised the hope that deriving such a cell type is achievable [6–11]. These recent additions to the stem cell hierarchy are particularly exciting for developmental epigeneticists. Access to an in vitro model that reproduces the epigenetic state of preimplantation epiblast cells would enable new opportunities to study the underlying mechanisms of many key epigenetic processes, such as the regulation of X-chromosome inactivation in humans. As with all novel cell types, there are on-going discussions about how to evaluate this new cell state. The task is complicated further because different cell culture conditions are used to derive and sustain naive hESCs, resulting in a spectrum of cell states and associated difficulties when comparing between studies. Developmental strategies differ between species, and so expectations and extrapolations from other organisms, such as the mouse, might be misleading when applied to human studies. To address these challenges, proposed criteria to define the naive state of hESCs have established a common framework for researchers to evaluate their own cells against. The criteria include transcriptional profiles, metabolic activity, cell-surface protein expression and signaling responses [3,12,13]. Reassuringly, naive hESC-associated pluripotency factors are detected in human and primate preimplantation epiblast cells, providing support that naive hESC lines maintained in certain conditions can recapitulate the gene expression program of epiblast cells in vivo [2,14,15]. Importantly, several epigenomic hallmarks are also used to categorize naive hESCs, such as the presence of two active X-chromosomes in female cells, and global DNA hypomethylation [3,13]. These defining epigenetic characteristics satisfy expectations based on the available human embryo data, and provide exciting opportunities for further study. However, there are also important considerations about what these epigenetic hallmarks actually indicate and how we can interpret them, which I will discuss below.