Functional characterisation of rare variants in genes encoding the MAPK/ERK signalling pathway identified in long-lived Leiden Longevity Study participants

Human longevity, which is coupled to a compression of age-related disease, has been shown to be heritable. However, the number of identified common genetic variants linked to this trait remains small. This may indicate that longevity is, at least to some extent, determined by rare genetic variants that are potentially family-specific. We therefore investigated whole-genome sequencing data of long-lived families from the Leiden Longevity Study for family-specific variants. We identified variants residing in genes involved in the mitogen-activated protein kinase (MAPK) cascade, a lifespan-associated and evolutionarily conserved pathway emerging from studies in model organisms. We subsequently generated mouse embryonic stem cells (mESCs) harbouring these variants and conducted in vitro functional characterisation. Two variants, located in NF1 (Phe1112Leu) and RAF1 (Asp633Tyr), reduce MAPK/extracellular signal-regulated kinase (ERK) signalling pathway activity in mESCs. At the proteomic and transcriptomic level, we observed prominent changes that were shared (e.g. up-regulation of the ribosome) and opposing between the variants (e.g. down-regulation of mTORC1 signalling in the RAF1 Asp633Tyr variant cell line versus up-regulation in the NF1 Phe1112Leu variant cell lines). These metabolic changes were accompanied by an opposing effect of the variants on proliferation. Moreover, the RAF1 Asp633Tyr variant improved resistance to replication stress, while this was not the case for the NF1 Phe1112Leu variant. In conclusion, we identified two rare genetic variants in long-lived families that influence MAPK/ERK signalling in a manner that has previously been linked to increased lifespan in model organisms. Interestingly, we also observe some opposing and diverging effects between the variants, which indicates that they may either have some pleiotropic effects that are not relevant to longevity or that they target slightly different mechanisms to elicit their effects in mESCs. Our findings suggest that mESCs offer a good starting point for in vitro characterisation of rare genetic variants linked to human longevity and can be used to assess which of these variants to take forward to in vivo studies in model organisms.