The aging synapse: an integrated proteomic and transcriptomic analysis

An important hallmark of aging is the loss of proteostasis, which can lead to the formation of protein aggregates and mitochondrial dysfunction in neurons. Although it is well known that protein synthesis is finely regulated in the brain, especially at synapses, where mRNAs are locally translated in activity-dependent manner, little is known as to the changes in the synaptic proteome and transcriptome during aging. Therefore, this work aims to elucidate the relationship between transcriptome and proteome at soma and synaptic level during aging. Cerebral cortices were isolated from 3 weeks-old mice, 5 months-old and 18 months-old mice and synaptosomal fraction was extracted by ultracentrifugation on discontinuous sucrose gradient. The fraction was then analyzed by Data Independent Analysis (DIA) Mass Spectrometry and the resulting data were analyzed using Spectronaut software. RNA was also extracted and analyzed by ribo-zero RNA-seq. Data were analyzed and combined with R software. Proteomic and transcriptomic data analysis revealed that, in young animals, proteins and transcripts are correlated and synaptic regulation is driven by changes in the soma. During aging, there is a decoupling between transcripts and proteins and between somatic and synaptic compartments. For example, there is an increase of ribosomal proteins at synapses that is not mirrored by a concomitant increase at somatic level. Furthermore, soma-synapse gradient of ribosomal genes changes upon aging, i.e. ribosomal transcripts are less abundant and ribosomal proteins are more abundant in synaptic compartment of old mice with respect to younglings. Mass spectrometry analysis of synaptic protein aggregates revealed that they are particularly rich in ribosomal proteins and also of some components of lysosomes and proteasome, suggesting that loss of proteostasis and inefficient degradation leads to aggregation of ribosomes in synaptic compartment. Strikingly, Desmoplakin, a structural constituent of desmosomes, was also highly abundant in synaptic aggregates. This study suggests that aging affects both the local translational machinery and the trafficking of transcripts and proteins.