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Biology subjects

Smider, V.

Publications and source records attributed to Smider, V..

3 recordsLinked to original sources

Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire

The generation of broadly neutralizing antibodies (bnAbs) to specific HIV epitopes of the HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The current animal models we use have been unable to reliable produce a broadly neutralizing antibody response, with the exception of cows. Cows have rapidly and reliably produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models other engineered immunogens previously have been able to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n=4) with two regiments of V2-apex focusing immunogens to investigate whether antibody responses could be directed to the V2-apex on Env. Group 1 were immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 were immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows respectively. The best bnAbs had both medium breadth and potency. Potent and broad responses developed later than previous CD4bs cow bnAbs and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target multiple broadly neutralizing epitopes on the HIV surface reveals important insight into the generation of immunogens and testing in the cow animal model. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response. Author SummaryThe elicitation of epitope-specific broadly neutralizing antibodies is highly desirable for an HIV vaccine as bnAbs can prevent HIV infection in robust animal challenge models and humans, but to date, cows are the only model shown to reliably produce HIV bnAb responses on Envelope (Env) immunization. These responses involve Abs with ultralong CDRH3s and are all directed to a single site, the CD4 binding site. To determine whether this is a unique phenomenon or whether cow antibodies can target further bnAb sites on Env, we employed an immunization protocol that generated cow bnAbs to a second site, the V2-apex. We conclude that ultralong CDRH3s are well adapted to penetrate the glycan shield of HIV Env and recognize conserved regions and may constitute protein units, either in the context of antibodies or in other engineered proteins, that could be deployed as anti-HIV reagents.

immunology↗

Identification of Potential Antibody Epitopes in MMP-15

Monoclonal antibody therapy is a well-established cancer treatment paradigm that often targets cancers-pecific cell surface proteins. Matrix Metalloproteinase 15 (MMP-15) is a surface protein implicated in metastasis and angiogenesis, however it is not well characterized. Here we use bioinformatics tools to identify epitopes for drug or diagnostic targeting and elucidate features of this potentially important protein in metastatic processes. We identified conserved regions in MMP-15 as well as unique, variable peptide regions compared to other Membrane Type MMPs (MT-MMP). Conservation of catalytic and hemopexin domains in MMP-15 imply functional importance, however, their similarity to other MT-MMPs discourage use as target epitopes. Our analyses also identified an MMP-15 peptide that was highly divergent from other MMPs, suggesting that it may serve as an appropriate specific epitope for a specific antibody drug. Thus, we were able to elucidate features and potential unique epitopes of MMP-15 for use in further antibody discovery and targeting.

molecular biology↗

A selectable system to evaluate synthetic gene optimization features

Heterologous gene expression - transferring genes from a natural cell or origin to another host cell, often across species - is a fundamental technique in biological research as well as biotechnological and pharmaceutical manufacturing. Optimization of gene sequences, therefore, is a critical factor when enhanced protein yield is needed. For any given protein, an enormous diversity of nucleotide sequences comprising the vast combinatorics of possible codon combinations could theoretically be used to encode the same amino acid sequence. The process of "codon optimization" typically replaces certain codons thought to be suboptimal with a more optimal codon encoding the same amino acid. However, such methods cannot address the enormity of possible nucleotide sequences possible to encode a given protein, or to decipher potential factors in addition to codon usage that may affect gene expression. Here we utilize the Sh ble gene encoding zeocin resistance in a system comprising bioinformatic synthetic gene production and an antibiotic selection platform. We find that supposedly codon optimized genes do not produce enhanced antibiotic resistance, suggesting that other factors are more important in synthetic gene optimization and heterologous gene expression.

synthetic biology↗