Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan

Abstract

Summary The VH1-2 restricted VRC01-class of antibodies targeting the HIV envelope CD4 binding site are a major focus of HIV vaccine strategies. However, a detailed analysis of VRC01-class antibody development has been limited by the rare nature of these responses during natural infection and the lack of longitudinal sampling of such responses. To inform vaccine strategies, we mapped the development of a VRC01-class antibody lineage (PCIN63) in the subtype C infected IAVI Protocol C neutralizer PC063. PCIN63 monoclonal antibodies had the hallmark VRC01-class features and demonstrated neutralization breadth similar to the prototype VRC01 antibody, but were 2- to 3-fold less mutated. Maturation occurred rapidly within ∼24 months of emergence of the lineage and somatic hypermutations accumulated at key contact residues. This longitudinal study of broadly neutralizing VRC01-class antibody lineage reveals early binding to the N276-glycan during affinity maturation, which may have implications for vaccine design.

Comparisons of the antibody repertoires of a humanized rodent and humans by high throughput sequencing

“…The resulting amplicons were subjected to high throughput sequencing in conjunction with preprocessing and annotation by the AbStar analysis pipeline 17 (Methods) which resulted in a mean of ∼3 x 10 6 processed heavy chain sequences and ∼1.5 x 10 6 processed kappa chain sequences per transgenic animal (Table S1). Two previously published datasets 13,18 of the same 10 humans which together contain a mean of ∼3.6 x 10 7 processed heavy chain sequences and ∼1.5 x 10 6 processed kappa chain sequences per individual were used for comparison.…”

B cells expressing authentic naive human VRC01-class BCRs can be primed and recruited to germinal centers in multiple independent mouse models

“…HuGL16 (KD 18.5 M) was chosen for its use of VK1-33, which is capable of Env N276 glycan-accommodating glycine mutations in L-CDR1 rather than deletions. HuGL17 (Kd 1.3 M) uses VK1-5, which should similarly be able to accommodate the N276 glycan by L-CDR1 point mutations based on similarity with bnAb lineage PCIN63 (34). HuGL17 and HuGL18 have an L-CDR3 sequence of CQQYETF, only 1 aa different than mature VRC01.…”

“…Mutations were observed in HuGL18 BGC cells at Y107 (100b), including Y→P or Y→W ( Fig S3A). VH1-2 positions known to be important for VRC01-class broad neutralization capacity were mutating, including M34L/I in H-CDR1, as well as K63Q/R and Y95F ( Fig 5B-C, Fig S3A) (9,34). We next determined how many VRC01-class mutations existed in each HC sequence (excluding the H-CDR3, which cannot be computationally assessed) and compared that to the total overall mutations to ascertain whether HuGL18 B cells were capable of maturing along a desired affinity maturation pathway in response to eOD-GT8 60mer.…”

“…Interestingly, all of the clones that contained deletions had an accompanying V29G mutation. V29G is present in the mature VRC01 and appears to be important based on the minimally mutated VRC01 bnAb construct (9,34). Both of these observations are of considerable interest, as L-CDR1 deletions are critical for most VRC01-class Abs to develop breadth, to circumvent clashing with the Env N276 glycan.…”

“…To develop neutralizing breadth, VCR01-class Abs also require acquisition of a small L-CDR1 deletion or other accommodation to avoid a clash with the Env glycan at N276 (9,19,33). VRC01-class B cells undergo 19-40% aa somatic hypermutation (SHM) from germline to develop into bnAbs in HIV + individuals (32)(33)(34)(35)(36). Germinal centers (GCs) are the anatomical site in which antigen-activated B cells undergo SHM, clonal competition, and Darwinian selection by T follicular helper (TFH) cells for survival (37)(38)(39)(40).…”