Figure 2.

GDF5-Induced Changes in the Proteome in SH-SY5Y Cells and Gene Co-expression Analysis of Data from the Human SN Identifies Correlated Patterns of STRAP and NME1 Expression

(A) Schema showing the experimental workflow using to identify changes in the proteome induced by GDF5 in SH-SY5Y cells.

(B) Volcano plots of the -log₁₀p values and the log₂Fold change of proteins that were altered in SH-SY5Y cells following treatment with 100 ng/mL GDF5 for 240 min.

(C–E) (C) Table showing the co-expression scores for genes associated with STRAP in STRING with a medium confidence threshold, which identified NME1 (highlighted in red), which was also found in the proteomic analyses. Graphs showing the LFQ intensities from the proteomics screen at 240 min for (D) STRAP and (E) NME1. Data are mean ± SEM from three independent samples per group (n = 3) (∗p < 0.05, ∗∗∗p < 0.001 versus control; Student's t test).

(F) Linear regression showing the correlation between STRAP and NME1 in the human SN (n = 101). The r and Bonferroni-corrected p values are shown on the graph. All transcriptome data are 2log expression values. Raw data was obtained from the Gene expression Omnibus GSE60863 and analyzed using the R2: Genomics analysis and visualization platform (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi).

(G) Graph showing NME1 expression in the SN of adult rats that had received AAV-Control (“Cont”) or AAV-GDF5 (“GDF5”), as a percentage of that on the contralateral side. Data are mean ± SEM from n = 4 rats (∗p < 0.05 versus control; unpaired Student's t test).

(H) Representative photomicrograph of NME1 (green) and TH (red) expression in the SN of AAV-Cont and AAV-GDF5 animals. Scale bar, 50 μm.