Supplementary Figure 3: Analysis of mouse chronic neonatal LCMV infection as model for late-stage HIV-infection.

(a) LCMV serum titers in chronic clone 13 LCMV-infected mice (n = 5). (b) ALT serum concentration in control (n = 3) and chronic neonatal LCMV-WE infected mice (cnLCMV-WE, n = 3). (c,d) Flow cytometric analysis of TIM-3, LILRB4, 2B4, CTLA-4, LAG3, PIR-B, BTLA, CD160, and CD200 co-expression on (c) CD4⁺PD-1⁺ and (d) CD8⁺PD-1⁺ T cells from cnLCMV-WE mice (n = 5). (e) Left, sorting strategy to isolate PD-1 expressing CD4⁺ T cells from acute LCMV WE-infected and cnLCMV-WE mice for gene expression analysis. Right, analysis of purities of isolated cell populations. (f) GSEA using genes from the murine chronic clone 13 LCMV-infected gp66⁺CD4⁺ T cell RNA fingerprint²⁵ as the gene set in CD4⁺PD-1⁺ and CD4⁺PD-1⁻ T cells from cnLCMV-WE mice. ES: enrichment score, FDR: false-discovery rate. (g) Prediction probability for each sample being classified as HIV-positive (HIV⁺) or uninfected control (HIV⁻) based on group prediction analysis of the cnLCMV-WE T cell RNA fingerprint using an additional publicly available dataset comparing HIV-infected and uninfected individuals (GSE9927)¹⁶. Colors indicate high (red) and low (blue) probability for the cnLCMV-WE RNA fingerprint.