Phage display aided improvement of a unique prostate-specific antigen (PSA) antibody unreactive with Lys145–Lys146 internally cleaved forms

Combinatorial mutagenesis with alternative CDR-L1 and -H2 loop lengths contributes to affinity maturation of antibodies

Loop length variation in the complementary determining regions (CDRs) 1 and 2 encoded in germline variable antibody genes provides structural diversity in naïve antibody libraries. In synthetic single framework libraries the parental CDR-1 and CDR-2 length is typically unchanged and alternative lengths are provided only at CDR-3 sites. Based on an analysis of the germline repertoire and structure-solved anti-hapten and anti-peptide antibodies, we introduced combinatorial diversity with alternative loop lengths into the CDR-L1, CDR-L3 and CDR-H2 loops of anti-digoxigenin and anti-microcystin-LR single chain Fv fragments (scFvs) sharing human IGKV3-20/IGHV3-23 frameworks. The libraries were phage display selected for folding and affinity, and analysed by single clone screening and deep sequencing. Among microcystin-LR binders the most frequently encountered alternative loop lengths were one amino acid shorter (6 aa) and four amino acids longer (11 aa) CDR-L1 loops leading up to 17- and 28-fold improved affinity, respectively. Among digoxigenin binders, 2 amino acids longer (10 aa) CDR-H2 loops were strongly enriched, but affinity improved anti-digoxigenin scFvs were also encountered with 7 aa CDR-H2 and 11 aa CDR-L1 loops. Despite the fact that CDR-L3 loop length variants were not specifically enriched in selections, one clone with 22-fold improved digoxigenin binding affinity was identified containing a 2 residues longer (10 aa) CDR-L3 loop. Based on our results the IGKV3-20/IGHV3-23 scaffold tolerates loop length variation, particularly in CDR-L1 and CDR-H2 loops, without compromising antibody stability, laying the foundation for developing novel synthetic antibody libraries with loop length combinations not existing in the natural human Ig gene repertoire.

Clinical Utility of Mutant Antibody-Based Assays for Determination of Internally Cleaved and Intact Forms of Free Prostate-Specific Antigen

BACKGROUND

Subforms of prostate-specific antigen (PSA) have been a subject of intensive research, and use of multikallikrein immunoassays can add clinical value to the early detection of prostate cancer, overcoming known limitations of PSA. In this study, we evaluated mutant 4D4 (L3-2) antibody-assisted assay constructs against reference wild-type (wt)-4D4-based assays for determination of intact PSA (iPSA) and nicked PSA (nPSA) in plasma samples.

METHODS

Perioperative plasma samples obtained from 105 men who underwent biopsy (73 cancer, 32 noncancer) were analyzed with sandwich immunoassays for total PSA (tPSA), free PSA (fPSA), iPSA (3 constructs), and measured nPSA (2 constructs). Calculated nPSA (CN) was obtained from total fPSA - iPSA.

RESULTS

Mutant-assisted iPSA assays measured lower concentrations than the reference in both patient groups. CN separated the 2 groups with the iPSA using the mutant for capture (I-MC) performing the best (P = 0.008). In prostate volume group > median, only measured nPSA provided significant discrimination [area under the curve (AUC), 0.71; P = 0.016] but equally using mutant and wt antibodies. In the whole cohort, all ratios to tPSA performed well (AUC, 0.819-0.870; P ≤ 0.0001) with CN based on I-MC scoring highest (AUC, 0.870). Importantly, in the ≤ median volume group, the I-MC/F and CN(I-MC)/T ratios stand out as the best performing parameters (AUC, 0.825 and 0.861; P = 0.001 and P = 0.0003, respectively).

CONCLUSIONS

The new assay construct using the mutant 4D4 (L3-2) as a capture provides clear improvement in separating cancer from noncancer in all subgroups analyzed but especially in patients with prostate volume ≤ median.Clinical Trial Registration: ClinicalTrials.gov Identifier NCT01864135.

Use of computational and recombinant technologies for developing novel influenza vaccines

Influenza vaccine design has changed considerably with advancements in bioinformatics and computational biology. Improved surveillance efforts provide up-to-date information about influenza sequence diversity and assist with monitoring the spread of epidemics and vaccine efficacy rates. The advent of next-generation sequencing, epitope scanning and high-throughput analysis all help decipher influenza-associated protein interactions as well as predict immune responsiveness based on host genetic diversity. Computational approaches are utilized in nearly all aspects of vaccine design, from modeling, compatibility predictions, and optimization of antigens in various platforms. This overview discusses how computational techniques strengthen vaccine efforts against highly diverse influenza species.