Researchers from Monash University in Melbourne and The University of Western Australia have demonstrated how a reprogramming method imitates embryonic epigenetic reset. Transient naive treatment (TNT) reprogrammed human induced pluripotent stem (hiPS) cells that are molecularly and functionally more similar to human embryonic stem (hES) cells than primed hiPS cells, which are more like cells in the post-implantation embryo. This research suggests that TNT reprogramming has the potential to set a new standard for therapeutic and biomedical uses.

The research article “Transient naive reprogramming corrects hiPS cells functionally and epigenetically” was published online today in Nature.

“Our work shows that TNT reprogramming is a practical and scalable approach to overcome these intrinsic characteristics of hiPS cells, which is important for the clinical delivery of this technology,” stated the authors. “We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications.”

A substantial epigenome reorganization is necessary to transform cells into hiPS cells. However, the epigenomes of hiPS and hES cells differ noticeably, which affects how hiPS cells function. Because these differences can be transferred to differentiated cells, using hiPS cells as disease models, drug testing models, or cell therapies is not the best option. It is still unknown, however, by what mechanisms aberrant epigenetic states arise during reprogramming.

Somatic cells can now be reprogrammed to become naive pluripotent stem cells (naive-hiPS cells) with low global DNA methylation and look like epiblasts before implantation. However, it is still unknown if naive-hiPS cell reprogramming leads to epigenetic memory and abnormalities.

In the new study, a quartet of co-lead authors—Jia Ping Tan, Daniel Poppe, Sam Buckberry, and Xiaodong Liu—set out to investigate the dynamics, causes, and mechanisms of epigenetic abnormalities in primed and naive reprogramming to gain a thorough understanding of the reprogramming process.

The report says that TNT reprogramming effectively removes epigenetic memory, especially in places where chromatin and lamina interact, and fixes overexpression of transposable elements and gene expression. If a cell’s response to signals for differentiation depends on how chromatin is arranged in space to make loci available for transcription factor binding, then the authors think that the differentiation bias in primed-hiPS cells may be caused by heterochromatic memory changing the dynamics of transcription factor binding. These domains are reconfigured to resemble hES cells through TNT reprogramming, which preserves genomic imprinting.

TNT-reprogrammed hiPS and hES cells exhibit comparable differentiation efficiencies. Additionally, TNT reprogramming improves the differentiation of hiPS cells derived from various cell types. Therefore, TNT reprogramming corrects aberrations and epigenetic memory, resulting in hiPS cells that are more functionally and molecularly similar to hES cells than traditional hiPS cells.

According to their theory, there may be similarities between the more thorough epigenome reset attained through TNT reprogramming and the epigenetic reset during human preimplantation development. TNT reprogramming, which also takes place during the early stages of embryonic development, first modifies a well-known epigenetic mark on histone H3, H3K9me3 (prior to the establishment of lineage-specific H3K9me3 following implantation). Second, TNT reprogramming promotes transient demethylation throughout the genome, akin to pre-implantation development. Third, genomic imprints are kept from being erased during preimplantation epigenome resetting, and the data show that the temporary nature of TNT reprogramming can help prevent loss of imprinting since the loss of imprinting seems to be a sign of long-term culture in a naive medium.

By leveraging the TNT reprogramming system, this study has demonstrated the functional benefit of completely resetting the epigenome. Before this work, SCNT reprogramming was the only method shown to improve DNA methylation anomalies. However, SCNT-reprogrammed cells can still feature persistent cell-of-origin H3K9me3 heterochromatin, and the technique is difficult and unfeasible to scale.

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