Extended Data Fig. 8: ICB does not differentially impact viral reservoir content between lymphoid and myeloid lineages, and vDNA content correlates with intact proviral genomes.

(a) The number of LN vRNA⁺ cells per 10⁵ cells were quantified by RNAscope before (d-29) and after ICB therapy (d28 p.t.). All RMs are color-coded and grouped based on ICB therapy as follows with population sizes as indicated for RNAscope analyses: controls (n=6), black; αCTLA-4 (n=6), blue; αPD-1 (n=6), pink; combined blockade (n=7), red; and BsAb (n=8), purple. In the LN B cell follicle (BCF) and T cell zone (TCZ), the number of (b) vDNA or (c) vRNA cells per 10⁵ cells were measured based on their co-expression of CD3 (lymphoid) or CD68/CD163 (MØ; myeloid) in a subset of ICB-responsive RMs (n=19). (d) In situ immunofluorescence staining for CD3 (green), CD68/CD163 (blue), and DAPI (grey) combined with hybridization for SIV vDNA (red) in LN TCZ or BCF (annotated at upper right) prior to or following ICB in representative RMs (3 of 38 unique samples; up to two tissue sections were analyzed). vDNA positive cells are annotated with a white arrow and successive magnification within the indicated boxed area (white) are shown below. (e) From LN at d28 p.t., the log-transformed frequency of vDNA⁺ cells per 10⁶ cells were correlated against the contemporaneous frequency of log-transformed intact proviral genomes per 10⁶ CD4⁺ cells (n=29). Averaged data are presented as the mean ± s.e.m. and were analyzed with (a,b,c) a two-sided Wilcoxon matched-pairs signed rank test relative to baseline or (e) a Pearson correlation coefficient.