Fig. 5: Spatial transcriptomics reveals treatment- and time-dependent effects after implantation.
Transcriptomic data composing the full AOI of the implant site (within 270 µm from the implant site). Volcano plots are shown evaluating gene expression at 4- and 12-weeks post-implantation. Unadjusted p-values are plotted and shown. The black dotted line indicates significance (pvalue = 0.05). Each point on the volcano plot indicates a singular gene. There were A 490 differentially expressed (DE) genes at the 4-week time point between antibiotic and control, which increased to B 1375 DE genes at the 12-week time point. Some pathways of note that were impacted by the antibiotic treatment at C 4-weeks post-implantation include the ribosomal subunit structure and neurodegeneration pathways, with changes occurring temporally as seen D in the 12-week time point. Each gene’s raw data / count underwent Q3 normalization followed by statistical analysis using a custom MATLAB R2021a script to perform unpaired t-tests between samples. Unadjusted p-values were used for all further comparisons in the iPathways software suite. At 4-weeks post-implantation, n = 4 for antibiotic-treated and n = 3 for control, and at 12-weeks post-implantation, n = 3 for antibiotic-treated and n = 3 for control. Created in BioRender. Capadona, J. (2025) https://BioRender.com/p93j360.
