Fig. 4: Spatial proteomic response is treatment dependent at 4-Weeks post-implantation.
Volcano plots showing neural proteomic panel evaluation of 4-week antibiotic (n = 4) compared to 4-week control (n = 3) across the entire AOI (within 270 μm from the implant), the inner ring of the AOI (within 0–90 μm), the middle ring of the AOI (90–180 μm), and the outer ring (180–270 μm) for all cells, all neuron-specific cells (stained using an NeuN antibody), and all astrocyte-specific cells (stained using a GFAP antibody). Proteins with a negative Log2FC indicate downregulation (blue points) in antibiotic compared to control, while a positive Log2FC indicates upregulation (green points) in antibiotic compared to control. Unadjusted p-values are plotted and shown, but all statistical comparisons were done using adjusted p-values. The black dotted line indicates significance (padjusted = 0.05). Each point on the volcano plot indicates a singular protein, with select proteins shown in the text. Comparisons with no cell specificity were made on the A entire AOI, B inner ring, C middle ring, and D outer ring. Neuron-specific comparisons were made on the E entire AOI, F inner ring, G middle ring, and H outer ring. Astrocyte-specific comparisons were made on the I entire AOI, J inner ring, K middle ring, and L outer ring. After normalization, an unpaired t-test was performed across respective groups for comparison. Unadjusted p-values were corrected using the Benjamini-Hochberg false discovery rate method to account for random significance. A few insignificant proteins were excluded from the plots due to high log2FC values, causing skewing and making visual representation difficult. Five significantly differentially expressed proteins were labeled due to space. Refer to Table 2 for the full list of significantly differentially expressed proteins. Created in BioRender. Capadona, J. (2025) https://BioRender.com/p93j360.
