Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Area of Science:

• Epigenetics
• Stem Cell Biology
• Reprogramming Technologies

Background:

• Human induced pluripotent stem cells (hiPS cells) undergo significant epigenome changes but retain differences from human embryonic stem (hES) cells.
• These epigenetic discrepancies, including memory and aberrations, impact hiPS cell function, with underlying mechanisms largely unknown.

Purpose of the Study:

• To characterize the emergence and persistence of epigenetic differences during hiPS cell reprogramming.
• To develop a novel reprogramming strategy that emulates the embryonic epigenetic reset and corrects hiPS cell epigenetic defects.

Main Methods:

• Genome-wide DNA methylation profiling during primed and naive reprogramming.
• Development and application of a transient-naive-treatment (TNT) reprogramming strategy.
• Isogenic system analysis to assess epigenetic correction and functional outcomes.

Main Results:

• Reprogramming-induced epigenetic aberrations arise mid-primed reprogramming; DNA demethylation initiates early in naive reprogramming.
• TNT reprogramming reconfigures cell of origin-dependent repressive chromatin (H3K9me3, lamin-B1, CpH methylation) to an hES cell-like state.
• TNT-reprogrammed hiPS cells show corrected transposable element expression, improved gene expression, and enhanced differentiation efficiency compared to conventional hiPS cells.

Conclusions:

• TNT reprogramming effectively corrects epigenetic memory and aberrations, yielding hiPS cells molecularly and functionally akin to hES cells.
• This strategy does not disrupt genomic imprinting and improves differentiation across various cell types.
• TNT reprogramming offers a potential new standard for biomedical and therapeutic applications and a tool for studying epigenetic memory.