Embryonic stem (ES) cells have the ability to maintain pluripotency and self-renewal during in vitro maintenance, which is a key to their clinical applications. ES cells are a model in developmental biology studies due to their potential to differentiate in vitro. Understanding critical pathways of pluripotency, self-renewal, and differentiation during early embryonic development is important for the evaluation of the therapeutic potential of ES cells because of their ability for tumor transformation due to genetic and epigenetic instability acquired during in vitro culture maintenance. Single tandem repeats are sequences of DNA that have been implicated in the deregulation of gene expression in different human conditions. Understanding the origin of repetitive sequence instability and functions in the genome allow characterization of early genomic instability signals in ES cell pluripotency, differentiation, and tumor transformation pathways. The hypothesis of this study was that genetic stability, in repetitive sequences, located near embryonic developmental genes is responsible for pluripotency, self-renewal, differentiation, and chromatin assembly and could be a signal for adaptation, differentiation, or transformation of ES cells in vitro. Our result showed instability in specific repetitive sequences which increased during ES cell passages and embryoid body differentiation in vitro. ES cells displayed significant mean frequencies of genomic instability in repetitive regions that lead to ES cells pluripotency, self-renewal maintenance, or cell lineage specialization. The present study reports potentially biomarkers for identifying accumulation of genomic instability in specific genes that may contributes to adaptation of ES cells and could be the switch that initiates early ES cell lineage commitment in vitro. Determining genetic and epigenetic modifications, including single tandem repeat instability, gene expression changes, and chromatin modifications, is essential for elucidating possible molecular mechanisms of genomic instability and determining novel molecular characterization for diagnostic purposes to ensure ES cell stability and integrity that could potentially lead to use of ES cell derivatives that could then be a safe source needed for regenerative medicine application
