Macaque study finds CD4 binding site antibodies close to inferred unmutated ancestor

ematsen · February 21, 2016, 3:47pm

ncbi.nlm.nih.gov

HIV-1 Vaccine-elicited Antibodies Reverted to Their Inferred Naive Germline Reveal Associations between Binding Affinity and in vivo Activation.

K Dai, SN Khan, Y Wang, L He, J Guenaga, J Ingale, C Sundling, S O'Dell, K McKee, G Phad, M Corcoran, R Wilson, JR Mascola, J Zhu, Y Li, GB Karlsson Hedestam and RT Wyatt, Scientific reports, Feb 2016 16

The elicitation of HIV-1 broadly neutralizing antibodies following envelope glycoprotein (Env) vaccination is exceedingly difficult. Suboptimal engagement of naïve B cells is suggested to limit these low frequency events, especially at the conserved CD4bs. Here, we analyzed CD4bs-directed monoclonal antibodies (mAbs) elicited by YU2 gp140-foldon trimers in a non-human primate by selective sorting using CD4bs "knock out" trimers. Following two inoculations, the CD4bs-directed mAbs efficiently recognized the eliciting immunogen in their affinity-maturing state but did not recognize CD4bs-defective probes. We reverted these mAbs to their most likely inferred germline (igL) state, leaving the HCDR3 unaltered, to establish correlates of in vitro affinity to in vivo activation. Most igL-reverted mAbs bound the eliciting gp140 immunogen, indicating that CD4bs-directed B cells possessing reasonable affinity existed in the naïve repertoire. We detected relatively high affinities for the majority of the igL mAbs to gp120 and of Fabs to gp140, which, as expected, increased when the antibodies 'matured' following vaccination. Affinity increases were associated with slower off-rates as well as with acquisition of neutralizing capacity. These data reveal in vitro binding properties associated with in vivo activation that result in functional archiving of antigen-specific B cells elicited by a complex glycoprotein antigen following immunization.

The surprising thing for me is that the naive precursors for these CD4 binding site antibodies bound well. This is in contrast to the V1-V2 binding human bNAbs found, say, in Doria-Rose et al 2014 and other papers. Different animal and different antibodies.

They inferred unmutated ancestors (UAs), which for some reason they call igLs, by taking a consensus of similar-looking sequences: “Based on HCDR3 length and homology, as well as by use of the same V and J germlines, we identified related sibling clones.” They could not find anything close to the UA in the pre-vaccination repertoire.

Rather than just doing ELISAs, they also did Biolayer Light Interferometry with Octet, which IIUC directly measures binding through time to get a clearer picture of on and off rates.

As a reminder, here’s a map of the various binding sites from a nice review.