Fig. 6: Transcriptomic programs in LN cells from SHIV_AD8-EO-challenged monkeys on or off early bNAb therapy.

Heatmaps showing the modulation of pathways in sorted LN monocytes (A), NK cells (B), and T cell subsets (C) from untreated and bNAb-treated monkeys at week 2 or 8 post-SHIV_AD8-EO challenge when compared to pre-challenge or week 2 post-challenge, as determined by transcriptomic analysis. Monkeys were either left untreated or were treated at days 3, 10, and 17 post-SHIV_AD8-EO challenge with either VRC07-523-LS and PGT121 or VRC07-523-LS/DEL and PGT121/DEL. Pathways are indicated in rows (database: MSigDB Hallmark) and the comparisons of interest (monkey group & timepoint 1 – monkey group & timepoint 2) in columns. Red cells indicate significant enrichment of a pathway among genes induced in monkey group & timepoint 1 (GSEA nominal p ≤ 0.05 and NES > 0); blue cells indicate significant enrichment of a pathway among genes downregulated in monkey group & timepoint 1 (GSEA nominal p ≤ 0.05 and NES < 0); and gray cells correspond to non-significant enrichment in monkey group & timepoint 1 (GSEA nominal p > 0.05), when compared to monkey group & timepoint 2. A two-sided permutation test was used to calculate the nominal p-value and the Benjamini-Hochberg procedure was used to calculate the adjusted p-value (A–C). Source data are provided in the Source Data file. CM central memory, EM effector memory, fCD8⁺ follicular CD8⁺, GC germinal center, mem. memory, NES normalized enrichment score, pre pre-challenge, Tfh T follicular helper, UnTx untreated, wk week.