eLife assessment: Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

Full text Figures and data Peer review Side by side Abstract eLife assessment Introduction Results Discussion Materials and methods Data availability References Article and author information Abstract Partial reprogramming(definition) by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock(definition)-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal. eLife assessment This important study reports comprehensive multi-omics data on the changes induced in young and aged male mouse dermal fibroblasts after treatment with chemical reprogramming factors. The authors provide solid evidence to support their claim that chemical reprogramming factors induce changes consistent with a reduction of cellular 'biological' age (e.g., correlations with established aging markers in whole tissues). https://doi.org/10.7554/eLife.90579.3.sa0 About eLife assessments Introduction Cellular aging is accompanied by various features, such as epigenetic changes, upregulation of inflammation, metabolic dysfunction, decreased proteostatic clearance, and increased DNA damage (Schumacher et al., 2021; Hipp et al., 2019; Ferrucci and Fabbri, 2018; Amorim et al., 2022; Kane and Sinclair, 2019). However, while all these hallmarks consistently show changes during aging, there are only limited insights into their potential causative roles. Additionally, many therapies that have targeted single 'hallmarks' of aging have failed to increase lifespan or improve biological functions in vivo (Gems and de Magalhães, 2021; Keshavarz et al., 2023). An alternative way to discover therapies for targeting biological age is to develop tools to quantify it, and then screen interventions for their effect on biological age reduction. Several methods currently exist for quantifying cell aging, such as epigenetic clocks that use mean methylation levels of CpG sites that change during aging (Horvath, 2013), transcriptomic clocks that rely on age-associated changes in gene expression (Choukrallah et al., 2020; Buckley et al., 2023), clocks that rely on age-dependent telomere(definition) attrition (Vaiserman and Krasnienkov, 2020), and various proteomic, metabolomic, and glycomic clocks (Jansen et al., 2021; Pearce et al., 2022; Johnson et al., 2020; Krištić et al., 2014). The development of tools that aim to quantify biological aging have undergone significant improvements over the years. Most notably, second-generation epigenetic clocks trained to predict phenotypic measures and mortality instead of chronological age have been shown to outperform many of these aforementioned clocks in their ability to predict lifespan and healthspan(definition) (Lu et al., 2019). Using various methods for biological age prediction, several intervention strategies have recently been shown to slow down and/or reverse biological aging. These include pharmacological interventions such as mTOR(definition)-inhibiting drug studied for extending healthspan and lifespan." style="text-decoration:underline dotted; text-underline-offset:2px; cursor:help;">rapamycin(definition) and metformin (Sharp and Strong, 2023; Shindyapina et al., 2022; Juricic et al., 2022; Kulkarni et al., 2020), genetic interventions (Petkovich et al., 2017), heterochronic parabiosis (Zhang et al., 2021; Ma et al., 2022), and partial reprogramming by doxycycline-induced expression of Yamanaka factors (Yang et al., 2023; Lu et al., 2020; Kriukov et al., 2022). A natural rejuvenation process during early development has also been described (Kerepesi et al., 2021; Gladyshev, 2021). Although partial reprogramming of somatic cells has been shown to lead to improvements in biological function lost during aging (Ocampo et al., 2016; Browder et al., 2022), the effective in vivo delivery of the transgenic cassettes and precise control of the expression of Yamanaka factors present challenges. To date, only one peer-reviewed study has demonstrated lifespan increase of wild type animals upon the treatment (Macip et al., 2024). Recently, administration of cocktails of small-molecule compounds have been shown to reprogram somatic cells back to pluripotency (Guan et al., 2022; Hou et al., 2013); moreover, short-term administration of two chemical cocktails (7c and 2c) has demonstrated efficacy at ameliorating several senescence(definition))." style="text-decoration:underline dotted; text-underline-offset:2px; cursor:help;">hallmarks of aging(definition) in human fibroblasts, while simultaneously preserving cellular identity (Lucas and Paine, 2022). Thus, partial reprogramming by short-term administration of chemicals could represent a more feasible, controllable, and adaptable method for inducing rejuvenation in vivo. However, the effects of short-term chemical reprogramming on biological age and function are currently unknown, and the mechanisms by which these chemical reprogramming cocktails act are not ful