Engineering Cell Fate: The Roles of iPSC Transcription Factors, Chemicals, Barriers and Enhancing Factors in Reprogramming and Transdifferentiation

Abstract

Direct reprogramming technology has emerged as an outstanding technique for the generation of induced pluripotent stem (iPS) cells and various specialized cells directly from somatic cells of different species. Recent studies dissecting the molecular mechanisms of reprogramming have methodologically improved the quality, ease and efficiency of reprogramming and eliminated the need for genome modifications with integrating viral vectors. With these advancements, direct reprogramming technology has moved closer to clinical application. Here, we provide a comprehensive overview of the cutting-edge findings regarding distinct barriers of reprogramming to pluripotency, strategies to enhance reprogramming efficiency, and chemical reprogramming as one of the non-integrating approaches in iPS cell generation. In addition to direct transdifferentiation, pluripotency factor-induced transdifferentiation or cell activation and signaling directed (CASD) lineage conversion is described as a robust strategy for the generation of both tissue-specific progenitors and clinically relevant cell types. Then, we consider the possibility that a combined method of inhibition of roadblocks (e.g. p53, p21, p57, Mbd3, etc.), and application of enhancing factors in a chemical reprogramming paradigm would be an almost safe, reliable and effective approach in pluripotent reprogramming and transdifferentiation. Furthermore, with respect to the state of native, aberrant, and target gene regulatory networks in reprogrammed cell populations, CellNet is reviewed as a computational platform capable of evaluating the fidelity of reprogramming methods and refining current engineering strategies. Ultimately, we conclude that a faithful, highly efficient and integration-free reprogramming paradigm would provide powerful tools for research studies, drug-based induced regeneration, cell transplantation therapies and other regenerative medicine purposes.

Chemicals as the Sole Transformers of Cell Fate

“…Another strategy for transdifferentiation is the induction of epigenetic plasticity in donor cells and subsequently providing developmental cues to promote lineage conversion ( 49 ). The findings of Pennarossa et al ( 23 ) and Sayed et al ( 24 ) suggest that experimental techniques of manipulation of innate immune signaling pathways or administration of small-molecule modifiers of epigenome could be used to induce epigenetic plasticity in somatic cells and to engineer cell fate ( 23 , 24 ).…”

“…The findings of Pennarossa et al ( 23 ) and Sayed et al ( 24 ) suggest that experimental techniques of manipulation of innate immune signaling pathways or administration of small-molecule modifiers of epigenome could be used to induce epigenetic plasticity in somatic cells and to engineer cell fate ( 23 , 24 ). This form of chemical transdifferentiation strategy is similar to the CASD lineage conversion, which uses iPSC transcription factors for induction of a plastic state ( 49 ). However, in contrast to the direct reprogramming technology and the CASD paradigm, these chemical methods do not use any genetic modification; this potentially allows their clinical application ( 23 , 24 ).…”

“…The late transdifferentiation technique was named cell-activation and signaling-directed (CASD) lineage conversion ( 48 ). In this paradigm, a brief expression of pluripotency transcription factors dedifferentiates the starting cells into an unstable and plastic state (cell-activation) and then lineage-specific differentiation signals direct them toward a specific fate ( 49 ). This transdifferentiation technique still utilizes forced expression of transgenes.…”