Research Article: The emerging role of alternative splicing in senescence and aging

Date Published: July 13, 2017

Publisher: John Wiley and Sons Inc.

Author(s): Mathieu Deschênes, Benoit Chabot.

http://doi.org/10.1111/acel.12646

Abstract

Deregulation of precursor mRNA splicing is associated with many illnesses and has been linked to age‐related chronic diseases. Here we review recent progress documenting how defects in the machinery that performs intron removal and controls splice site selection contribute to cellular senescence and organismal aging. We discuss the functional association linking p53, IGF‐1, SIRT1, and ING‐1 splice variants with senescence and aging, and review a selection of splicing defects occurring in accelerated aging (progeria), vascular aging, and Alzheimer’s disease. Overall, it is becoming increasingly clear that changes in the activity of splicing factors and in the production of key splice variants can impact cellular senescence and the aging phenotype.

Partial Text

Aging is defined as a progressive decline of fitness over time, ultimately leading to death (Kirkwood & Holliday, 1979; Kirkwood, 2005). This decline is associated with several changes such as tissue deterioration and disorganization, organ dysfunction, and loss of stem cell renewal, the latter contributing to age‐associated immunodeficiency. At the cellular and molecular levels, the aging phenotype varies between tissues but can include common hallmarks such as genomic and epigenetic instability, mitochondrial dysfunction, telomere attrition, and the accumulation of senescent cells (Kirkwood & Holliday, 1979; Kirkwood, 2005; López‐Otín et al., 2013). Considered as one of the causes of age‐related tissue degeneration, cellular senescence is an irreversible and programmed cell‐cycle arrest that occurs in most diploid cell types (Hayflick & Moorhead, 1961). Senescence is associated with large‐scale changes affecting a variety of processes such as cytokine secretion through the senescence‐associated secretory phenotypes (SASPs), alterations in gene expression, and alternative splicing, as well as chromatin remodeling that includes senescence‐associated heterochromatin foci (SAHF) (Narita et al., 2003; Rodier et al., 2009; Kuilman et al., 2010; Campisi, 2013; Holly et al., 2013). Senescence is also seen as a mechanism that prevents tumorigenesis (Serrano et al., 1997). The upregulation of tumor suppressors, such as p16INK4A, p21, and p53, as well as the activation of RB, is common in senescent cells, contributing to irreversible cell‐cycle arrest (Beausejour, 2003; Sage et al., 2003; Kuilman et al., 2010; Campisi, 2013). Although replicative senescence is linked to telomere attrition (Allsopp et al., 1992; Bodnar et al., 1998), telomere shortening is not necessarily required for the onset of senescence, implying the existence of different senescent programs (van Deursen, 2014; Sharpless & Sherr, 2015). Consistent with this view, telomere‐independent senescence can be controlled by pathways triggered by insults (stress‐induced senescence), as well as by other intrinsic signals that occur during embryonic development and tissue repair (Von Zglinicki, 2002; Baker et al., 2008; Krizhanovsky et al., 2008; Schmidt et al., 2010; Nardella et al., 2011; Storer et al., 2013). Notably, senescence can also be engaged by the hyperactivation of factors, such as RAS, that promote cell growth, a process known as oncogene‐induced senescence that may be linked to telomere dysfunction (Courtois‐Cox et al., 2008; Günes & Rudolph, 2012). While the exact connection between senescence and organismal aging is still much debated (Sharpless & Sherr, 2015), it has become increasingly clear that cellular senescence plays a role in some age‐related diseases and in tissue degeneration associated with aging (Baker et al., 2008; Günes & Rudolph, 2012; van Deursen, 2014). Senescent cells progressively accumulate in the tissues and organs of aging mammals including humans (Herbig et al., 2006; Ressler et al., 2006; Jeyapalan et al., 2007; Kreiling et al., 2011). This accumulation of senescent cells may be due in part to a decreased ability of the immune system at removing them (Nikolich‐Zugich, 2008; Wang et al., 2011a). In addition, SASPs have been linked with aging organs and tissue degeneration (Parrinello et al., 2005; Coppé et al., 2008), where they are thought to enhance significantly the senescence of neighboring cells by a mechanism called paracrine senescence (Nelson et al., 2012; Acosta et al., 2013) (Fig. 1). Consistent with a role for senescence in aging, reducing the level of senescent cells is associated with a significant decrease in the incidence of age‐related disorders (Baker et al., 2008, 2011; Zhu et al., 2015), and was shown recently to improve homeostasis and extend lifespan in mouse models (Baker et al., 2016; Baar et al., 2017). While nonreplicating cells in aging tissues such as muscle harbor senescent markers and can become senescent, they may, in general, be more resistant to senescence. However, muscle replicative stem cells and satellite cells likely undergo senescence and may contribute more importantly to aging. Altogether, the accumulation of senescent cells in tissues and organs suggests that this process contributes to the progressive deterioration that irremediably associates with aging (van Deursen, 2014).

The vast majority of precursor mRNAs (pre‐mRNAs) produced by mammalian cells are made of exons separated by introns. Introns are normally removed leaving joined exons that form the mature mRNA. Splicing is carried out by the spliceosome, a massive complex that includes hundreds of proteins and five small nuclear ribonucleoproteins (snRNPs) named U1, U2, U4, U5, and U6 (Matera & Wang, 2014). The U1 and U2 snRNPs, respectively, recognize the 5′ splice site and the branch site near the 3′ splice site, making these two snRNPs important in defining intron borders. While many introns are removed constitutively, a large fraction of splicing signals are not always used leading to alternative splicing (Fig. 2). Alternative splicing occurs in transcripts produced by more than 95% of human genes (Pan et al., 2008; Wang et al., 2008), including ones implicated in senescence, apoptosis, and DNA repair (Schwerk & Schulze‐Osthoff, 2005; Kelemen et al., 2013; Tang et al., 2013).

With such a complex regulatory machinery controlling splicing decisions, the molecular changes that occur with aging are therefore likely to impact the activity of factors that control splicing. A gene ontology analysis in both human and mouse reported that changes in pathways such as mRNA binding, RNA processing, and RNA splicing are strongly associated with age (Southworth et al., 2009; Harries et al., 2011). Age‐related splicing changes in the human brain affect pathways such as sugar metabolism and DNA repair (Tollervey et al., 2011), both relevant to aging (Colman et al., 2009; López‐Otín et al., 2013).

Several genes produce transcripts whose alternative splicing changes in aging tissues or during prolonged cell passages in culture. An important question is whether those changes are the causes or the consequences of aging. Although recent studies have reported splicing changes in transcripts encoding proteins involved in processes that are intimately associated with aging, such as DNA damage sensing, DNA repair, and telomere biogenesis (Tollervey et al., 2011; Rodríguez et al., 2016), we currently do not know if these switches produce splice variants with distinct functional properties. Here we will restrict our discussion to splice variants for which experimental evidence support a role in aging or senescence.

A number of human diseases known as progeroid syndromes provoke phenotypic alterations that resemble those noted during normal aging. These include Hutchinson–Gilford Progeria syndrome (HGPS or progeria), Werner syndrome, and Cockayne syndrome. The study of HGPS has revealed that alternative splicing defects are responsible for some of its distinctive features.

Given the challenges associated with maintaining homeostasis in cells and tissues subjected to constant internal and external insults, we can anticipate that a subset of mutations and epigenetic changes may alter the expression or activity of spliceosome components and splicing regulatory factors. These changes may, in turn, alter the splicing profile in several transcripts, resulting in a cascade of alterations that may either activate senescence, promote apoptosis, or elicit tumor formation. Although senescence and apoptosis may protect against tumor formation, the gradual accumulation of senescent cells will elicit tissue degeneration and organ dysfunction. While progressive age‐related disturbances in homeostasis do indeed correlate with a broad range of alterations in alternative splicing, the current challenge is to determine whether a specific splicing change contributes to the aging phenotype or is simply a consequence with little or no functional impact. In this review, we have focused on altered alternative splicing events whose contributions to age‐related phenotypes are experimentally supported. These events occur in genes known for their implication in mechanisms that are relevant to cell senescence and organismal aging. Although we reviewed the impact of selected splice variants on aging, regulatory networks likely coordinate the production of splice variants from different genes to maximize functional outcomes that determine cell fate, and ultimately the aging phenotype. Consistent with this proposition, the activity of p53 in senescence and apoptosis can be modulated by SIRT1 and ING1, in turn affecting ING1 signaling and SIRT1 activity. Extending these relationships to the full repertoire of splice variants for all the components of the extended p53 regulatory network may be required to determine how important is the level of coordination and feedback involved in the production of splice variants contributing to aging. Already, the splicing regulatory proteins SRSF1, SRSF2, SRSF3, and SRSF6 are emerging as central players coordinating multiple splicing decisions in age‐relevant and senescent transcripts (Fig. 8). Future studies will likely investigate in more details how defects in the expression or activity of these proteins, as well as hnRNP proteins and core spliceosomal components, affect senescence and aging. Another group of potentially relevant regulatory molecules are noncoding RNAs. Some display age‐dependent changes in expression (e.g., see Gruner et al., 2016), and recent studies have implicated microRNAs, large noncoding RNAs, and circular RNAs in senescence and SASP (Abdelmohsen & Gorospe, 2015; Panda et al., 2017a). Specifically, the circular RNA CircPVT1, whose expression is reduced in senescent cells, is produced by circularization of an exon of the PVT gene through RNA splicing. CircPVT sequesters let‐7 RNA and its depletion triggers senescence (Panda et al., 2017b). There is clearly a need to investigate further how splicing regulation is altered to affect the production of circular RNA molecules during senescence and aging. To help clarify the contribution of an expanding list of splice variants and regulators associated with aging, it would be useful to combine expression assays with the monitoring of phenotypes like cell growth and the production of senescent markers. Likewise, it would be informative to determine whether and how SASP components produced by senescent cells reprogram the splicing profiles of neighboring cells.

The work in the laboratory of BC is supported by the Canadian Institutes of Health Research (grant MOP‐136948). BC is the Pierre C. Fournier Chair in Functional Genomics.

None declared.

 

Source:

http://doi.org/10.1111/acel.12646

 

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