Fig. 2

Temporal proteomic and phospho-proteomic analysis in the total lysates of M83 neurons with α-syn aggregation. A-D α-syn PFF mediated changes in protein expression in total lysates of M83 neurons were evaluated at 7-, and 14-days post-treatment using TMT-MS. Changes were plotted on a volcano plot with log fold changes on x-axis and negative log of p values on y-axis. Statistically significant changes were determined based on a false discovery rate of 0.05. Red dots indicate proteins significantly decreasing, green dots indicate proteins significantly increasing, and black dots indicate proteins that did not change. On day 7, no significant changes were noted in protein expression in proteomics (A) or phospho-proteomics (C). At day 14, a total of 135 proteins in the proteomics (B) and 633 phosphopeptides in the phospho-proteomics (D) showed statistically significant changes (E-F) Enrichment analysis using Metascape was performed based on the proteomics and phospho-proteomics data from the DIV14 post-PFF treatment timepoint. Processes related to RNA metabolism and microtubule organization were identified based on upregulated proteins (E) and HSF1 and actin-based processes were identified in the analysis of downregulated proteins (F). G-J Overlap evaluation with 1542 manually curated RNA binding proteins led to identification of 64 upregulated and 36 downregulated proteins. Subnetworks were created using String database based on these upregulated (G) or downregulated (I) proteins. Identification of mRNA splicing, transport, and metabolism was found in proteins that were upregulated (H). Identification of mRNA processing, mRNA metabolic process, and ribonucleoprotein complex biogenesis and translation was found in the proteins that were downregulated (J)