Aging and rejuvenation - a modular epigenome model

Abstract

The view of aging has evolved in parallel with the advances in biomedical sciences. Long considered as an irreversible process where interventions were only aimed at slowing down its progression, breakthrough discoveries like animal cloning and cell reprogramming have deeply changed our understanding of postnatal development, giving rise to the emerging view that the epigenome is the driver of aging. The idea was significantly strengthened by the converging discovery that DNA methylation (DNAm) at specific CpG sites could be used as a highly accurate biomarker of age defined by an algorithm known as the Horvath clock. It was at this point where epigenetic rejuvenation came into play as a strategy to reveal to what extent biological age can be set back by making the clock tick backwards. Initial evidence suggests that when the clock is forced to tick backwards in vivo, it is only able to drag the phenotype to a partially rejuvenated condition. In order to explain the results, a bimodular epigenome is proposed, where module A represents the DNAm clock component and module B the remainder of the epigenome. Epigenetic rejuvenation seems to hold the key to arresting or even reversing organismal aging.

Keywords: DNA methylation; aging; cell reprogramming; epigenetic clock; rejuvenation.

Figure 1

Rejuvenation by cell reprogramming of fibroblasts from healthy centenarian individuals. In culture, fibroblasts from old individuals display a typical transcriptional signature, different of that from young counterparts as well as shortened telomeres, reduced population doubling (PD) potential, dysfunctional mitochondria and higher levels of oxidative stress. When cells were reprogrammed to iPS with a 6-factor cocktail the above alterations were fully reversed. Then iPS cells were differentiated back to fibroblasts by culture in the presence of an appropriate set of differentiation factors. In the resulting cells, all of the above variables had levels typical of fibroblasts taken from young individuals. See [34] for further details.

Figure 2

Modular epigenome model to explain in vivo rejuvenation results. A bimodular epigenome is considered, where Module A represents the DNAm clock component which encompasses all age-dependent DNA methylation epigenetic marks. Module B represents the remainder of the epigenome, including but not limited to cell identity marks. The model does not make further assumptions on the properties of each module. In this context, the existence of, for instance, age-dependent cell identity marks (bivalent marks) is not ruled out. The upper diagram (path 1) proposes that ex vivo, conventional reprogramming erases all age and cell identity marks from both modules, and can turn an old (brown color represents old) neuron or any other cell, into an iPSC that can then be differentiated back to a rejuvenated (blue represents young) neuron. In vivo, continuous expression of the OSKM genes leads to the genesis of multiple teratomas and the death of the animal. The middle diagram (path 2) illustrates the hypothesis that several cycles of partial reprogramming can progressively rejuvenate cells by erasing all epigenetic marks of age without affecting cell type identity marks. This means that in principle, the strategy could lead to major phenotype rejuvenation in vivo. The lower diagram (path 3) illustrates an alternative outcome for partial reprogramming. In this case, partial reprogramming erases age marks from the DNAm clock (module A) but spares age marks of module B. This outcome is compatible with a major resetting of DNAm age but partial rejuvenation of the phenotype.

Figure 3

Morphological changes induced by long-term OSKM gene action in human umbilical cord perivascular cells (HUCPVC). (A) HUCPVC incubated for 7 days with an adenovector expressing a polyscistron harboring OSKM and GFP genes. Phase contrast microscopy; (B) The same field observed under fluorescence microscopy. (C) HUCPVC incubated for 85 days with the above OSKM-GFP adenovector. Phase contrast microscopy; (D) The same field as in C observed under fluorescence microscopy. Inset (E) Control intact HUCPVC on Experimental day 7. Obj X 4 in all panels. (Goya et al., unpublished results).