The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing

Kodangattil, Sreekumar; Huard, Christine; Ross, Cindy; Li, Jian; Gao, Huilan; Mascioni, Alessandro; Hodawadekar, Santosh; Naik, Snehal; Min-debartolo, Jessica; Visintin, Alberto; Almagro, Juan C.

doi:10.4161/mabs.28059

Cited by 31 publications

(31 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…BnAbs isolated from chronic infection have a number of unusual features that have been selected to cope with the glycan shield including much longer than average HCDR3 loops 10–12 . HCDR3s in most vertebrates have restricted lengths that predominantly encode loops of 12–16 amino acids upon VDJ recombination 9,13–15 . Therefore, in many species, relatively few antibody precursors can be affinity-matured to HIV bnAbs.…”

Section: Main Textmentioning

confidence: 99%

Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows

Sok

Vadnais

et al. 2017

Nature

156

198

View full text Add to dashboard Cite

No immunogen to date has reliably elicited broadly neutralizing antibodies (bnAbs) to HIV in humans or animal models. Advances in the design of immunogens (BG505 SOSIP) that antigenically mimic the HIV envelope glycoprotein (Env)1 have improved the elicitation of potent isolate-specific Ab responses in rabbits2 and macaques3, but so far failed to induce bnAbs. One possible contributor to this failure is that the relevant antibody repertoires are poorly suited to target somewhat occluded conserved epitope regions on Env relative to exposed variable epitopes. To test this hypothesis, we immunized four cows with BG505 SOSIP. The antibody repertoire of cows contains long third heavy chain complementary determining regions (HCDR3) with an ultralong subset that can reach over 70 amino acids in length4–9. Remarkably, BG505 SOSIP immunization resulted in rapid elicitation of broad and potent serum antibody responses in all four cows. Longitudinal serum analysis for one cow showed the development of neutralization breadth (20%, n = 117 cross-clade isolates) in 42 days and 96% breadth (n = 117) at 381 days. A monoclonal antibody (mAb) isolated from this cow harbored an ultralong HCDR3 of 60 amino acids and neutralized 72% of cross-clade isolates (n = 117) with a potent median IC50 of 0.028 μg/ml. We note that breadth was elicited with a single trimer immunogen and did not require additional envelope diversity. Immunization of cows may provide an avenue to rapidly generate antibody prophylactics and therapeutics to address disease agents that have evolved to avoid human antibody responses.

show abstract

Section: Main Textmentioning

confidence: 99%

Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows

Sok

Vadnais

et al. 2017

Nature

156

198

View full text Add to dashboard Cite

show abstract

“…So far, ~50 functional Vκ genes have been identified. 76, 95 Recently, using next-generation sequencing of rabbit antibody repertoires, Kodangattil et al 96 demonstrated that light-chain rearrangements are significantly more diverse than heavy-chain rearrangements in rabbits. In addition, the imprecise junction of VL and JL genes in rabbits encompasses particularly long stretches of N-nucleotides, resulting in, on average, longer LCDR3s (12±2 amino acids; mode=12) compared to mouse and human (9±1 amino acids; mode=9; Figure 4).…”

Section: Ontogeny Of Rabbit B-cell and Antibody Repertoiresmentioning

confidence: 99%

From rabbit antibody repertoires to rabbit monoclonal antibodies

2017

View full text Add to dashboard Cite

In this review, we explain why and how rabbit monoclonal antibodies have become outstanding reagents for laboratory research and increasingly for diagnostic and therapeutic applications. Starting with the unique ontogeny of rabbit B cells that affords highly distinctive antibody repertoires rich in in vivo pruned binders of high diversity, affinity and specificity, we describe the generation of rabbit monoclonal antibodies by hybridoma technology, phage display and alternative methods, along with an account of successful humanization strategies.

show abstract

“…RNA was extracted from PBMCs, spleen, and bone marrow samples stored in RNALater. RNA were enriched for Ig transcripts by multiplex PCR as performed in [40,19]. Gene-specific primers were designed in Ig leader and constant region to ensure full transcript sequencing.…”

Section: Ig Transcript Sequencingmentioning

confidence: 99%

“…In therapeutics, rabbits have been used to improve HIV-1 vaccine design [2], and humanized rabbit mAbs developed by Apexigen Inc. are undergoing clinical trials to treat immuno-oncology and ocular diseases [25]. Interest in rabbit antibodies is due to their reported higher affinities and unique specificity [19,38]. Although, Landry et al [20] reported the improvement may only be slight, with rabbit mAbs generated against linear peptides having on 20-200 pM binding (across 1450 rabbit mAbs), compared to mouse mAbs with 30-300pM binding (across 46 mouse mAbs).…”

Section: Introductionmentioning

confidence: 99%

Serum proteomics expands on high-affinity antibodies in immunized rabbits than deep B-cell repertoire sequencing alone

Bonissone

Lima

K³

et al. 2019

Preprint

View full text Add to dashboard Cite

Rabbits are a model for immunology studies, and monoclonal antibodies developed from rabbits have been highly sought after to empower immunoassays in a variety of other applications. Highthroughput characterization of circulating serum antibodies in response to specific antigens is highly impactful for both immunology studies and antibody development. A combination of high throughput sequencing of antibody transcripts from B cells and proteomic analysis of serum antibodies, referred to as immunoproteogenomics, is applied to profile the immune response of rabbits to β-galactosidase (Beta-gal) in both recombinant antigen and peptide antigen immunization formats. The use of recombinant antigen resulted in observing 56.3% more heavy chains clones in serum than immunization with peptide antigens. Additionally, sampling peripheral blood mononuclear cells (PBMCs) for B-cell repertoire sequencing at different time points throughout the immunization was found to capture 47.8%-72.8% of total proteomically observed heavy chain clones, and would serve well in replacing sequencing the B cell rich, but more difficult to access spleen or bone marrow compartments. Despite B-cell repertoire sequencing to depths of 2M to 10M reads, we found proteomic evidence supporting at least 10% of serum antibodies are still missed. Further improvements to proteomic analysis techniques would enable more precise characterization of antibodies circulating in serum and better estimates of antibodies missed by repertoire sequencing.

show abstract

The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing

Abstract: (2014) The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing, mAbs, 6:3, 628-636,

Cited by 31 publications

References 33 publications

Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows

Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows

From rabbit antibody repertoires to rabbit monoclonal antibodies

Serum proteomics expands on high-affinity antibodies in immunized rabbits than deep B-cell repertoire sequencing alone

Contact Info

Product

Resources

About