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 temporarily lose and then reacquire their fibroblast identity during MPTR, possibly as a result of epigenetic memory at enhancers and/or persistent expression of some fibroblast genes. 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 appears substantially greater than that achieved in previous transient reprogramming protocols. In addition, MPTR fibroblasts produced youthful levels of collagen proteins, and showed partial functional rejuvenation of their migration speed. Finally, our work suggests that more extensive reprogramming does not necessarily result in greater rejuvenation but instead that optimal time windows exist for rejuvenating the transcriptome and the epigenome. Overall, we demonstrate that it is possible to separate rejuvenation from complete pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.

Universal DNA methylation age across mammalian tissues

“…Epigenetic clocks such as the pan-tissue clock for humans 4 indicate that cellular reprogramming based on the Yamanaka factors (OSKM) leads to age reversal 4,26 . To assess whether the universal clocks exhibit the same age reversal pattern during reprogramming, we applied Clock 2 and Clock 3 to a previously published reprogramming dataset in human dermal fibroblasts (HDFs) (Ohnuki et al, 2014).…”

Progeria and Aging - Omics Based Comparative Analysis

“…They also reported that some of these changes could be reversed [88] interpreting "aging as a disease", a notion that has already been proposed in ancient times [89] and has recently garnered attention [89,90]. Regardless of whether aging should be seen as a disease or not, extending not only the lifespan but also the health span [1,89,90] and possibly even rejuvenation [27] are of great interest. In this study, we analyzed a publicly available RNA Seq dataset using bioinformatic tools.…”

“…The dataset contains RNA-Seq data of dermal fibroblasts donated by ten progeria patients and 133 "apparently healthy" individuals (aged 1 to 96 years according to their metadata) [16,17]. Their dataset is publicly available on the Gene Expression Omnibus (GEO) database [18] under accession number GSE113957 [16,17] Since its publication in November 2018, the article by Fleischer et al has been cited 37 times in PubMed (until May 2022), with 13 of the citing papers mentioning the use of the GSE113957 dataset from the Fleischer et al paper [19][20][21][22][23][24][25][26][27][28][29][30][31] (as described in Table 1). According to the publications in PubMed, the dataset alone contributed to 8 studies investigating aging [20,[22][23][24][25][26][27][28].…”

Human age reversal: Fact or fiction?

“…In a separate cohort of patients with severe obesity, a decrease in epigenetic ∆age was observed 12 months after bariatric surgery (Fraszczyk et al, 2020). human dermal fibroblasts (Gill et al, 2022).…”

“…A final point of consideration is the reversal of an aging clock, which has been reported in vivo in mice (Browder et al, 2022;Y. Lu et al, 2020) and in vitro in human cells (Gill et al, 2022) in response to reprogramming. As shown in Table 1, epigenetic age can also be reversed in response to different interventions.…”