Multi-omic rejuvenation of human cells by maturation phase transient reprogramming

Abstract

Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first “maturation phase transient reprogramming” (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells reacquire their fibroblast identity following MPTR, possibly as a result of persisting epigenetic memory at enhancers. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. The magnitude of rejuvenation instigated by MTPR is substantially greater than that achieved in previous transient reprogramming protocols. MPTR fibroblasts produced youthful levels of collagen proteins, suggesting functional rejuvenation. Overall, our work demonstrates that it is possible to separate rejuvenation from pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.HighlightsWe developed a novel method by which human fibroblasts are reprogrammed until the maturation phase of iPSCs and are then returned to fibroblast identityDNA methylation memory in fibroblast enhancers may allow recovery of cell identity when fibroblast gene expression programmes are already extinctMolecular measures of ageing including transcriptome and DNA methylation clocks and H3K9me3 levels reveal robust and substantial rejuvenationFunctional rejuvenation of fibroblasts by MPTR is suggested by reacquisition of youthful levels of collagen proteins

Cellular reprogramming and epigenetic rejuvenation

“…Another important question was whether the partially reprogrammed cells would retain their lower eAge and show a stable rejuvenated phenotype after reversion to somatic state, or would they quickly revert back to their original eAge? A recent preprint by Gill et al addressed these questions using a similar in vitro reprogramming system with fibroblasts from middle aged donors and discontinuing OSKM expression after days 10, 13, 15 or 17 [73]. Importantly, the study confirmed a rejuvenated phenotype of the transiently reprogrammed cells, which is maintained upon reversion to somatic state at least four weeks after OSKM withdrawal.…”

“…B OSKM treatment increased lifespan of progeria mice, improved the regenerative capacity of muscle and pancreas, as well as glucose tolerance [74]. C Overlaid summary of iPSC reprogramming time-course experiments by [118] and [73]. Upper panel: Horvath multi-tissue age predictor applied to OSKM-expressing adult fibroblasts [118] partially dedifferentiating and producing a rejuvenative effect to surrounding cells by being more stem-like?…”

“…(b) gene transcription; analysis of key age-associated genes that increase or decrease in transcription with age and are associated with age-related outcomes [61][62][63][64][65][66][67][68][69][70][71][72]. A number of gene transcriptionbased clocks have been created in a similar manner to epigenetic clocks, but very few of them have been validated in other studies [68,[71][72][73]. (c) amelioration of physiological (e.g.…”

Epigenetic predictors of maximum lifespan and other life history traits in mammals

“…Many authors have suggested that epigenetic mechanisms may play a role in controlling lifespan and aging [7][8][9][10][11][12][13][14][15] . The role of epigenetics in mammalian aging is underscored by recent studies demonstrating age reversal through (transient) epigenetic reprogramming with Yamanaka factors [16][17][18][19][20][21] .…”

Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging

“…It is made The copyright holder for this preprint this version posted March 12, 2021. ; https://doi.org/10.1101/2021.03.11.435028 doi: bioRxiv preprint and growth hormone receptor knockout (30)(31)(32)(33)(34)(35)(36). Most importantly, the clocks developed based on aging patterns of mostly adult tissues report the effects of cell rejuvenation upon complete-or partial reprogramming of adult fibroblasts into induced pluripotent stem cells (iPSCs) as demonstrated in both human and mouse (33,35,(37)(38)(39). Even though iPSCs correspond to an embryonic state and the transition to these cells involves major molecular changes, including changes in the epigenome, this rejuvenation event can be assessed by epigenetic clocks.…”