Senescence and the return of established splicing tech

New evidence brings an already-established alternative splicing mechanism back to light with reignited importance for senescence and human Longevity.

Cellular senescence is currently an inevitable process where cells protect themselves against DNA damage, telomere erosion and other stress factors by irreversibly arresting cell growth. For decades it has been clear that senescence contributes to aging, age-related diseases and anti-tumour properties, yet the mechanisms of just how cells are triggered to enter senescence remain elusive.

Longevity.Technology: Alternative splicing is an RNA mechanism that allows multiple combinations, known as isoforms, from a single gene. In simple terms, multiple proteins can thus be encoded by a single gene. One type of alternative splicing is intron retention (IR), where exons do not surround the intron spliced out.

Deregulation and impairment of splicing mechanisms have been shown to contribute to aging phenotype development in mice and humans, as well as increasing Alzheimer’s disease susceptibility [1,2]. IR specifically has been found to accumulate during general cell development and differentiation [3], blood-cell synthesis [4] and hypoxic tumour cells [5].

A study by Adusumalli et al. in 2019 found that IR deviation can be used as an aging molecular signature [6]. A more detailed look into the biological pathways is needed in order to illuminate the role of IR in aging.

Professor Ting Ni at Fudan University decided to take on the challenge through extensive bioinformatical analysis of poly-adenine RNA-sequencing to see whether IR plays a role in senescence and if so what RNA-binding proteins (RBPs) regulate this phenomenon.

After establishing that IR is prevalent in senescent human foreskin and lung embryonic fibroblast cells, the Shanghai-based team speculated that “dynamic changes of IR driving senescence may fine-tune gene expression.”

In RBP knock-out (KO) experiments, senescence was monitored using the well-established marker senescence-associated beta-galactoside. The splicing factor U2AF1 was pin-pointed and studied further. In various U2AF1-KO cell lines, growth rates decreased and levels of cyclin-dependent kinase inhibitor p15 increased. The results point towards U2AF1 contributing significantly to intron retention and thus senescence.

“On top of furthering understanding of the Longevity field, the fact that the IR transcript can be degraded by the exosome could be developed as a therapeutic target … This study presents a viable, druggable target.”

For further U2AF1 pathway elucidation, a genetic screen was run to find genes affected by the splicing KO model. Out of the six genes identified, CPNE1 showed the highest IR levels. This gene encodes a calcium-dependent membrane-binding protein that activates the AKT cascade which promotes cell survival and growth in response to extracellular stimuli.

Interestingly, IR CPNE1 transcripts were found almost exclusively in the nucleus and thus degraded by the exosome. This forms the following hypothesis: the IR isoform competes for replicative cell machinery leading to senescent phenotypes.

The authors conclude: “Our study revealed a hidden layer of post transcriptional regulation of cellular senescence and may have implications for age-related diseases” [7]. Future studies need to explore the other splicing events affected by U2AF1 and their effect on aging hallmarks.

On top of furthering understanding of the Longevity field, the fact that the IR transcript can be degraded by the exosome could be developed as a therapeutic target.

The removal of senescent cells through senolytic drugs is at the forefront of the Longevity market, yet a less invasive approach lies in senotherapeutic interventions. These aim to reprogramme and prevent cells from entering senescence.

PROTACs, proteolysis targeting chimera, are an established pharmacological approach for specific protein degradation. In the last few years, the exosome has gained attention for RNA degradation [8]. This study presents a viable, druggable target for the exosome. The RNA transcripts and splicing factors that lead to senescent phenotypes could be removed, prolonging Longevity.

Image by Gordon Johnson from Pixabay