Fig. 5: Quantitative proteomic profiling reveals AAV.ULK1.DN-mediated regulation of biological processes and protein interactions.

Lysates obtained from E18 rat cortical neurons on DIV 8 after transduction with AAV.CTRL or AAV.ULK1.DN were subjected to proteomics analysis. a Volcano plot showing all 1988 quantifiable proteins in SWATH-MS, 122 significantly regulated proteins according to two-sided t-test with permutation-based FDR assessment (FDR 0.1, s0 = 0.05) appear in red (n = 2 independent cultures, three technical replicates for each condition for each experiment). b, c Immunoblotting against two selected proteins regulated in quantitative proteomic profiling was performed to validate the results. Representative western blots of PAK2 and TAOK1 are shown at the top, the quantifications of band intensities normalized to GAPDH as loading control are depicted at the bottom (n = 4–5 independent cultures different to those used for the proteomics analysis). Data are presented as single data points and means ± SEM. *P < 0.05 according to one-sample t-test. d Biological processes annotated to significantly regulated proteins by AAV.ULK1.DN according to enrichment analysis of functional annotations in Gene Ontology. The fold enrichment value is given for each biological process. Only significantly regulated biological processes are shown. e Protein network map of all significantly regulated proteins after transduction with AAV.ULK1.DN in comparison with AAV.CTRL showing a significant number of interactions (STRING database enrichment P value = 6.93E−07). Four clusters according to k-Means clustering are highlighted by different colors. f The same protein network map as in e highlighting down- and upregulated proteins.