Quantitative proteomic analysis reveals protein expression changes in the murine neuronal secretome during apoptosis

Neurodegenerative diseases often lack early and specific diagnostic and prognostic biomarkers. Many studies are focusing on the cerebrospinal fluid (CSF) proteome to identify relevant biomarkers and therapeutic targets for these disorders. An alternative approach consists in comparing proteins secreted by healthy neurons and neurons degenerating by apoptosis, one of the mechanisms underlying neuronal death in neurodegenerative diseases. Here, we adapted the stable isotope labeling by amino acids in cell culture (SILAC) technology to primary cultures of mouse cerebellar granule neurons (CGNs), a well-characterized in vitro model of neuronal apoptosis, in order to identify variations in protein release by neurons during apoptosis. Using two different heavy isotope labels followed by liquid chromatography coupled with Fourier transform tandem mass spectrometry, we directly compared the secretome of apoptotic and surviving CGNs. A total of 1375 proteins were identified in CGN-conditioned media. Among these proteins, 47 were differentially expressed in the supernatants of apoptotic and surviving neurons. About 50% of them have been previously identified in human CSF and some are involved in neuronal death or neuroprotection. This list of apoptosis-regulated proteins should be considered when using targeted quantitative proteomics approaches to characterize or validate CSF biomarkers of neurodegenerative disorders.