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Epigenetic Reprogramming Reverses Age-related Alterations

By Stuart P. Atkinson, Ph.D.

September 14, 2023

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Introduction: Reprogramming - Feels Like We Only Go Backwards

The forced expression of so-called reprogramming factors – which include OCT4, SOX2, KLF4, and MYC – in somatic cells prompts genome-wide epigenetic and transcriptomic alterations that induce the generation of induced pluripotent stem cells (iPSCs), which possess broad similarities to embryonic stem cells. Excitingly, multiple studies have also sought to harness the ability of these reprogramming factors to induce epigenetic alterations to reverse the multitude of harmful alterations that occur during aging by restoring youthful gene expression profiles, reversing epigenetic aging/slowing epigenetic age acceleration, and reestablishing youthful functions in old/senescent cells and tissues. Here, we bring you two of the most recent studies from the leading laboratories in the fields of epigenetics and aging.

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Part One: Defining (and Reversing) a Cancer-related Epigenetic "Cellular Division and Replication Induced FingerprinT"

Linking Age-related Epigenetic and Replication Changes to Cancer

Increased age in humans entails a considerable increase in the risk of developing multiple cancers (National Cancer Institute, Age and cancer risk), which may derive from the accumulation of mutations in cells as they divide over a lifetime and/or the dramatic epigenetic alterations that occur during aging. Importantly, a wide range of studies have established that similar changes to DNA methylation profiles occur during normal aging, cancer development, and cell proliferation. In their recent Science Advances article, a team of researchers directed by Morgan E. Levine (Yale School of Medicine/Altos Labs) aimed to simultaneously link age-related epigenetic alterations, replication-related alterations, and cancer development. Fascinatingly, their findings suggest that epigenetic remodeling represents a function of DNA replication that may correlate with the tumorigenic transformation of normal tissues; however, the team also notes that the epigenetic changes induced by the expression of reprogramming factors may represent a means to reverse age-related alterations.

CellDRIFT – An Epigenetic Cellular Division and Replication Induced FingerprinT

In their fascinating new study, Minteer et al. revealed that a common epigenetic replication "signature" defined both the processes of normal aging and cancer development. They described the signature or "replication fingerprint" – which they named CellDRIFT (Cellular Division and Replication Induced FingerprinT) – through an analysis of DNA methylation data derived from extensively passaged immortalized human fetal astrocytes and a de novo computational training platform. Signs of the DNA methylation-based CellDRIFT signature accumulated during normal aging in multiple tissues in vivo, which provided evidence that DNA methylation alterations may underlie the age-related transition of youthful normal tissues to tumorigenic transformation. Further analysis indicated that the CellDRIFT signature distinguished tumor tissue (which displayed more notable signs) from normal tissue (less notable signs) and that the normal tissue of breast cancer patients displayed accelerated signs of the CellDRIFT signature.

Reversing CellDRIFT via Reprogramming

Importantly, the researchers revealed that induced cellular reprogramming (Takahashi and Yamanaka) in aged somatic cells could transiently reset the DNA methylation-based CellDRIFT signature, suggesting the potential to reverse age-related alterations (and perhaps cancer risk) via epigenetic reprogramming. Briefly, reprogramming human fibroblasts into iPSCs through the expression of OCT4, SOX2, KLF4, and MYC prompted a dramatic decrease in signs of the CellDRIFT signature during the maturation phase of cellular reprogramming, which coincides with cell dedifferentiation and the transition from the somatic to pluripotent state.

Conclusions: Age-related Replication Can Drive the Epigenetic Alterations that Induce Tumorigenesis

Overall, the findings of this fascinating study suggest that age-related replication drives the alteration of epigenetic profiles (DNA methylation in particular) that can induce the development of a tumorigenic state; however, the development of the CellDRIFT signature allows us to quantify and track the age-related wear and tear that affects us all. While these findings highlight epigenetic reprogramming induced by the forced expression of factors such as OCT4, SOX2, KLF4, and MYC to reverse/ameliorate age-related alterations, this strategy currently remains far from clinical applications; however, new studies (such as that described below) may have made huge strides towards solving this problem.

For more on the definition and potential reversal of a cancer-related epigenetic cellular division and replication induced fingerprinT, see Science Advances, July 2023.

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Part Two: A Chemical-based Alternative to Epigenetic Reprogramming and Reversing Age-related Alterations?

Bypassing the Limitations of Reprogramming Factor-mediated Epigenetic Reprogramming

Proposed approaches for the forced expression of factors such as OCT4, SOX2, KLF4, and MYC to induce epigenetic reprogramming and reverse age-related alterations in vivo currently rely on delivery mechanisms with limitations (including prohibitive costs and safety concerns) that inhibit their broader application. This situation has prompted the development of ingenious studies focusing on alternative chemical-based reprogramming strategies that could lower costs, simplify protocols, and even support whole-body rejuvenation (Du et al. and Mertens et al.). In their recent study reported in Aging, researchers led by David A. Sinclair (Harvard Medical School) developed and utilized a novel screening method to identify various "chemical cocktails" with the potential to quickly and safely induce epigenetic reprogramming and reverse the signs of aging in aged/senescent fibroblasts.

Confirming the Impact of Reprogramming Through Nucleocytoplasmic Compartmentalization Assays

To ensure the reliability and applicability of their fluorescence-based high-throughput system to evaluate chemicals with the potential to reverse aging through epigenetic reprogramming, Yang, Petty, Dixon-McDougall, and colleagues evaluated modifications to "nucleocytoplasmic compartmentalization," a well-conserved physiological hallmark of aging (Mertens et al. and D'Angelo et al.), alongside transcriptomic alterations. The authors first confirmed that the epigenetic reprogramming induced by the short-term expression of OCT4, SOX2, and KLF4 sufficed to reverse the age-related alterations assessed before evaluating a range of chemicals known to have successfully reprogrammed human and mouse somatic cells into iPSCs (Guan et al. and Hou et al.).

Replacing Reprogramming Factors with Chemical Cocktails

A short-term incubation with two basal cocktails comprising either i) valproic acid, CHIR-99021, E-616452, tranylcypromine, ii) and forskolin or ii) CHIR-99021, E-616452, TTNPB, Y-27632, Smoothened Agonist, and ABT-869 reversed age-related alterations, which was further improved through the combination of additional additives (such as bFGF, sodium butyrate, and α-ketoglutarate). Transcriptomic analyses also demonstrated that the epigenetic reprogramming induced by these chemical cocktails reversed age-associated transcriptional alterations (e.g., those involving inflammation, mitochondrial metabolism, lysosomal function, apoptosis, p53, and growth signaling) without inducing the expression of non-specific cell identity markers or pluripotency-associated genes. A subsequent transcriptomic clock analysis (Kriukov et al.) indicated that a short-term incubation with these chemical cocktails prompted significant reductions in biological and chronological age, with the latter result comparable to the total change observed after a year of a regenerative treatment focused on restoring epigenetic information (Fahy et al.). All cocktails induced a similar transcriptomic profile in cells despite their differing chemical components, suggesting they functioned through shared pathways. Importantly, the transcriptomic analysis also highlighted critical roles for upregulated respiration-associated pathways (such as oxidative phosphorylation and mitochondrial translation) and downregulated hypoxia and multiple inflammation-associated pathways (such as interferon and JAK-STAT signaling) in response to chemical cocktail-mediated reprogramming.

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Conclusions: Better Living Through Chemistry?

Overall, the authors identified chemical cocktails that induced epigenetic reprogramming to reverse the transcriptomic age of cells without erasing cell identity or inducing a pluripotent state. The authors hope that said chemical cocktails may support the treatment of aging-related diseases such as amyotrophic lateral sclerosis and frontotemporal dementia, which have been associated with disrupted nucleocytoplasmic compartmentalization during aging. Ongoing research from the laboratory aims to next understand the enduring effects of these chemical cocktails on various cell types from young and old individuals and the mechanisms involved in epigenetic age reversal through chemical cocktail treatment.

For more on how chemical cocktails can induce epigenetic reprogramming and reverse age-related alterations, see Aging, June 2023.

Related Studies of Interest

If this brief foray into the world of epigenetics, cell reprogramming, and aging has piqued your interest, be sure to check out the Epigenetics Blog at Active Motif, including this recent article and the following related studies!

Reporting in Nature, researchers led by Saiyong Zhu (Zhejiang University) report a rapid chemical reprogramming system that promotes cell identity transition through a diapause-like state, which provides critical insights into how environmental cues can influence pluripotency and regeneration (Chen, Lu, and Wang. et al.). Also reporting in Nature, a team led by Jose M. Polo (Monash University) and Ryan Lister (University of Western Australia) describe a "transient-naive-treatment" reprogramming strategy that emulates the epigenetic reset associated with embryonic development to create functionally and epigenetically corrected iPSCs that possess more significant similarities to embryonic stem cells (Buckberry, Liu, and Poppe et al.).

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About the author

Stuart P. Atkinson, Ph.D.

Stuart was born and grew up in the idyllic town of Lanark (Scotland). He later studied biochemistry at the University of Strathclyde in Glasgow (Scotland) before gaining his Ph.D. in medical oncology; his thesis described the epigenetic regulation of the telomerase gene promoters in cancer cells. Following Post-doctoral stays in Newcastle (England) and Valencia (Spain) where his varied research aims included the exploration of epigenetics in embryonic and induced pluripotent stem cells, Stuart moved into project management and scientific writing/editing where his current interests include polymer chemistry, cancer research, regenerative medicine, and epigenetics. While not glued to his laptop, Stuart enjoys exploring the Spanish mountains and coastlines (and everywhere in between) and the food and drink that it provides!

Contact Stuart on Twitter with any questions

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