A Systems Biology Approach to Manipulating the Biochemistry of Senescent Cells

Cells become senescent in response to reaching the Hayflick limit on replication, or to potentially cancerous mutations, or a toxic environment and consequent cell damage, or signaling from other senescent cells. Senescence is nominally an irreversible state. Replication halts and the cell begins secreting pro-inflammatory signals to attract the attention of the immune system. Senescent cells are normally removed via programmed cell death or the actions of cytotoxic immune cells. With age the rate of creation increases and the rate of removal falls, however, leading to a growing number of senescent cells throughout the body. The signaling of that growing number of senescent cells in aged tissues causes chronic inflammation and disrupts tissue maintenance, leading to age-related disease.

What to do about this? Much of the focus of the research community is on senolytic approaches that force senescent cells into apoptosis and self-destruction, or that provoke the immune system into more efficient clearance of senescent cells. These therapies have achieved impressive results in mice, reversing age-related disease and many measures of aging. Some researchers are interested in the reversal of senescence, however: reprogramming cells in ways that overcome the regulatory processes that normally ensure continuation of the senescent state.

Is reversal of senescence a good idea? It seems likely that at least some senescent cells are senescent for a good reason. That they are damaged, and in some cases that damage is potentially cancerous. Reversing senescence may well produce short term gains that are similar to those of senolytic therapies, since in either case the harmful signaling produced by senescent cells is removed. But a significantly raised risk of cancer may be the cost of that approach.

Systems biology for reverse aging

Although partial reprogramming proved that senescent cells can be reverted, early termination of this reprogramming process is known to cause epigenetic dysregulation, resulting in dedifferentiated dysplastic cells such as renal cancer. Therefore, a novel therapeutic strategy without such critical limitations is highly needed. Cellular senescence is caused by complex interactions among biomolecules that govern cell cycle, DNA damage response, energy metabolism, and cytokine secretion. Recent studies showed that cellular senescence, previously considered as an irreversible biological phenomenon, can be reversed, but due to the nature of such complex interactions governing cellular senescence, the mechanism by which cellular senescence can be reversed has not been revealed.

Researchers reconstructed an ensemble of 5000 Boolean network models that can represent senescence, quiescence, and proliferation phenotypes by integrating information from the literature, network databases and phosphoprotein array data of dermal fibroblasts. In their models, cellular senescence is induced by simultaneous activation of DNA damage signal (doxorubicin) and growth signal (IGF-1 plus serum). They identified 3-phosphoinositide-dependent protein kinase 1 (PDK1) as the optimal protein target that can safely revert senescence to quiescence while avoiding uncontrolled proliferation, through extensive computer simulation analysis of the ensemble model. PDK1 forms a positive feedback structure along with AKT, IKBKB, and PTEN, that simultaneously control both nuclear factor κB, which controls cytokine secretion, and mTOR, which regulates cell growth.

In order to validate the simulation results, researchers conducted in vitro experiments and confirmed that when PDK1 was inhibited, various markers of cellular senescence are returned to normal and proliferation potential is restored. From wound healing assays and 3D reconstructed skin tissue experiments, they also reaffirmed that the reverted cells are able to respond appropriately to external stimuli. In particular, by observing dermal fibroblast within dermis along with keratinocyte within epidermis, 3D reconstructed skin tissue experiments verified that PDK1 inhibition promotes epidermal renewal and restores skin thickness, resulting in reversal of age-related skin degeneration.