Multifaceted B-cell response to transient HIV viraemia in elite controllers

Chronic HIV infection drives B-cell dysfunction associated with the accumulation of tissue-like memory (TLMs) and activated memory B cells (MBCs) but decline in resting memory B cells. TLMs express multiple inhibitory receptors and lack response to soluble antigens. However, their origin and the mechanisms driving their expansion in HIV infection remain unclear. By using bulk BCR sequencing of memory B cell subsets from elite HIV controllers and an ART-controlled cohort, we revealed that TLMs (CD21- CD27- B cells) were significantly less mutated but also less diverse than other MBCs, suggesting an enrichment for innate-like B cells or that they belong to a less mature subset. Subsequent detailed multi-omics study of an immune response in an elite controller to a transient HIV viraemia demonstrated a functional increase in Env-reactive IgG and MBCs with non-TLM phenotype. Single-cell RNA/BCR sequencing of PMBCs enriched for B cells revealed an orchestrated TNF-alpha response followed by interferon alpha and gamma response across all B cells subsets. We noted an emergence of innate-like extrafollicular PLD4+ plasmablasts and previously undepreciated heterogeneity of a stable TLM population. We identified two distinct TLM subsets: TLM1 (T-betlow) and TLM2 (T-bethi) that differed in their differentiation stage, isotype use and mutational burden. Surprisingly, both subsets (TLM1 more than TLM2) were enriched for IGHV4-34 segment use (associated with self-reactivity) and displayed a persistent activation and BCR signalling signature, indicating (with other BCR indices) a strong presence of innate-like B cells. However, pseudotime analyses revealed that TLMs contained not only innate-like B cells but also cells from the conventional memory B cell lineages, further highlighting the complexity of the whole TLM compartment. This study provides a new insight into multifaceted functional B-cell response to transient HIV viraemia as likely happens during the early phase of anti-retroviral therapy cessation, highlighting the TLM heterogeneity and the contribution of innate-like B cells which might have important clinical implications for anti-HIV vaccine and therapy design.