Contribution of VH replacement products to the generation of anti-HIV antibodies

VH replacement occurs through RAG-mediated secondary recombination to change unwanted IgH genes and diversify antibody repertoire. The biological significance of VH replacement remains to be explored. Here, we show that VH replacement products are highly enriched in IgH genes encoding anti-HIV antibodies, including anti-gp41, anti-V3 loop, anti-gp120, CD4i, and PGT antibodies. In particular, 73% of the CD4i antibodies and 100% of the PGT antibodies are encoded by potential VH replacement products. Such frequencies are significantly higher than those in IgH genes derived from HIV infected individuals or autoimmune patients. The identified VH replacement products encoding anti-HIV antibodies are highly mutated; the VH replacement “footprints” within CD4i antibodies preferentially encode negatively charged amino acids within the IgH CDR3; many IgH encoding PGT antibodies are likely generated from multiple rounds of VH replacement. Taken together, these findings uncovered a potentially significant contribution of VH replacement products to the generation of anti-HIV antibodies.

► VH replacement products are enriched in IgH genes encoding anti-HIV antibodies.
► VH replacement footprints encode negatively charged residues in CD4i Ab CDR3.
► The PGT Abs are likely generated from multiple rounds of VH replacement.