Fig. 2: Longitudinal plasma proteomic changes following anti-retroviral therapy initiation.

A, D, E Volcano plot of the differentially expressed proteins between paired participants pre- and post-ART initiation in (A) persistent VC (N = 57), (D) transient VC (N = 36), and (E) persistent EC (N = 9) in the discovery cohort. X-axis depicts Log2 fold change of differentially expressed proteins and Y-axis depicts the (A, D) -log10(FDR P value) or (E) -log10(P value). Differential expression analysis was performed using linear mixed models with (A, D) age, sex center and storage time or (E) age and storage time as covariates. See also Supplementary Data 3,5,6. B Correlation plot between the effect of ART and time of the differentially expressed proteins across paired persistent VC pre- and post-ART initiation from A. X-axis depicts Log2 fold change of differentially expressed proteins before and after ART in 57 persistent VC. Y-axis depicts Log2 fold change of differentially expressed proteins between two ART-naïve time points in 23 persistent VC. Only one of differentially expressed proteins after ART was also nominally significant for a change over time (blue dot). Grey line depicts linear correlation line (pearson coefficient). No statistical testing was done. C Network of functional pathways based on enrichment analysis of downregulated differentially expressed proteins in post-ART samples of persistent VC (N = 57). Circular nodes represent pathways, with the colors showing a gradient of the enrichment FDR P values; node size represents the number of genes in the pathway; weighted edges represent the degree of gene overlap score between pathways. Only pathways with P value < 0.05 were depicted in the figure. See also Supplementary Data 4.