By Gail Dutton

Although similar, the epigenomes of human induced pluripotent stem cells (hiPSCs) differ from those of the human embryonic stem cells (hESCs) they aim to replicate. These differences include epigenetic memory of their original specialized state and reprogramming aberrations that affect the cells’ functions, adding another challenge for biomanufacturers creating hiPSCs and derived cells for stem cell-based therapeutics.

An innovative approach called Transient Naïve Treatment (TNT) reprogramming abolishes that problem. Ready for commercial use, it “mimics the epigenetic reset that naturally occurs during early embryogenesis and generates cells that more accurately resemble target cell identities,” Ryan Lister, PhD, professor and Howard Hughes Medical Institute international research scholar at the University of Western Australia and the Harry Perkins Institute for Medical Research, and co-lead of the new research, tells GEN.

“This method removes recalcitrant epigenetic memory and aberrations, yielding TNT-hiPSCs that are molecularly and functionally more similar to bona fide human embryonic stem cells,” Lister says. Consequently, they are more consistent, differentiating into specialized cells at a higher efficiency and without the lingering epigenetic memory.

Furthermore, project co-lead, Jose Polo, PhD, professor at the University of Adelaide and Monash University, founder of the cell therapy company Mogrify, adds, “Our experiments show TNT-hiPSCs don’t exhibit genetic changes seen in conventional hiPSCs, and the TNT method corrects the inappropriate expression of genes and potentially mutagenic transposable elements observed in conventional hiPSCs.”

Highly variable and potentially genetically unstable

In contrast, current manufacturing processes create hiPSCs that are highly variable and may be genetically unstable. Consequently, Lister says, “Multiple hiPSC clones generally are made for each donor, reducing efficiency, wasting resources and time, and complicating culture scaleup.”

With the TNT method described in their recent paper in Nature, Lister, Polo, and colleagues report that epigenetic memory in hiPSCs is concentrated in large domains of the genome that show “cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1, and aberrant CpH methylation.” By facilitating a transient wave of epigenome resetting genome-wide, TNT reprogramming remodels these domains to closely resemble hESCs and protects important genomic imprints from erasure during the epigenome resetting.

“A key advantage is that the TNT reprogramming method is very straightforward to incorporate into the current reprogramming process,” Lister says. “It requires only a short transient change in defined culturing conditions.” Recounting the benefits of this approach, Lister says, “We envision the TNT reprogramming will improve hiPSC and derived cell type manufacturing efficiency, uniformity, phenotypic identity, genetic and functional stability, safety, and purity.”

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