Cell-extrinsic barriers of cellular plasticity: contribution of natural killer cells, T lymphocytes and vitamin B12 to in vivo reprogramming

Abstract

The ectopic expression of transcription factors Oct4, Sox2, Klf4 and Myc (OSKM) enables the conversion of differentiated cells into pluripotent stem cells, a process known as “reprogramming”. Methods based on in vivo reprogramming are a promising strategy for tissue regeneration and rejuvenation. However, this process is inefficient, and little is known about the barriers that limit reprogramming in an in vivo context.

Here we have explored how the immune system affects cellular reprogramming. We report that natural killer (NK) cells significantly limit reprogramming. Cells in the process of reprogramming upregulate the expression of NK-activating ligands, such as Mult1, Icam1 and Cd155. NK cells recognize and kill cells undergoing reprogramming in a degranulation-dependent manner that is partially blocked by antibodies against the NK- activating receptor NKG2D. In mice, transient depletion of NK cells using antibodies significantly improves the efficiency of reprogramming, as determined by the emergence of dysplastic cells and NANOG+ cells. Finally, organoids derived from NK-depleted reprogrammed pancreata are remarkably large, suggesting that NK cells preferentially target those cells with high organoid-formation capacity. Other cell types from the innate immune system also contribute to the modulation of in vivo reprogramming efficiency. In particular, Gr1+ cells, which include neutrophils and myeloid-derived suppressor cells (MDSCs), favour reprogramming, which is in contrast to the negative effect of NK cells. We have also explored the adaptive immune system. Interestingly, CD4+ and CD8+ T cells restrict reprogramming, thereby suggesting that reprogramming elicits an antigenic response to self-antigens. As a first step to study this notion, we have obtained the MHC-I immunopeptidome of partially reprogrammed fibroblasts. Intriguingly, we have found novel peptides not known to be presented by normal cells and tissues and, therefore, with the potential to be self-antigenic. We have also studied the role of vitamin B12 in reprogramming. Genomic analysis of stool bacteria led us to identify vitamin B12 as a limiting metabolite for reprogramming. Remarkably, vitamin B12 supplementation significantly improves the efficiency of the process both in vivo and in vitro. This finding has led us to uncover the limiting role of the one-carbon metabolism during reprogramming.

We conclude that NK cells are a main barrier for in vivo reprogramming, and their transient depletion facilitates the generation of cells with progenitor properties. Partial reprogramming elicits an adaptive immune response that may involve the presentation of peptides that are not presented by normal cells and tissues. Furthermore, vitamin B12 can act as a safe and easily administered metabolite to improve in vivo reprogramming. Our current findings may apply to other contexts of tissue regeneration.