Combining deep mutational scanning to heatmap of HLA class II binding of immunogenic sequences to preserve functionality and mitigate predicted immunogenicity

Removal of CD4 T cell epitopes from therapeutic antibody sequences is expected to mitigate their potential immunogenicity, but its application is complicated by the location of their T cell epitopes, which mainly overlap with complementarity-determining regions. We therefore evaluated the flexibility of antibody sequences to reduce the predicted affinity of corresponding peptides for HLA II molecules and to maintain antibody binding to its target in order to guide antibody engineering for mitigation of predicted immunogenicity. Permissive substitutions to reduce affinity of peptides for HLA II molecules were identified by establishing a heatmap of HLA class II binding using T-cell epitope prediction tools, while permissive substitutions preserving binding to the target were identified by means of deep mutational scanning and yeast surface display. Combinatorial libraries were then designed to identify active clones. Applied to adalimumab, an anti-TNFα human antibody, this approach identified 200 mutants with a lower HLA binding score than adalimumab. Three mutants were produced as full-length antibodies and showed a higher affinity for TNFα and neutralization ability than adalimumab. This study also sheds light on the permissiveness of antibody sequences with regard to functionality and predicted T cell epitope content.

Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology.

Combinatorial biology methods such as phage and yeast display, suitable for the generation and screening of huge numbers of protein fragments and mutated variants, have been useful when dissecting the molecular details of the interactions between antibodies and their target antigens (mainly those of protein nature). The relevance of these studies goes far beyond the mere description of binding interfaces, as the information obtained has implications for the understanding of the chemistry of antibody-antigen binding reactions and the biological effects of antibodies. Further modification of the interactions through combinatorial methods to manipulate the key properties of antibodies (affinity and fine specificity) can result in the emergence of novel research tools and optimized therapeutics.

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies.

BACKGROUND: Anti-CD3 immunotherapy was initially approved for clinical use for renal transplantation rejection prevention. Subsequently, new generations of anti-CD3 antibodies have entered clinical trials for a broader spectrum of therapeutic applications, including cancer and autoimmune diseases. Despite their extensive use, little is known about the exact mechanism of these molecules, except that they are able to activate T cells, inducing an overall immunoregulatory and tolerogenic behavior. To better understand the effects of anti-CD3 antibodies on human T cells, PBMCs were stimulated, and then, we performed RNA-seq assays of enriched T cells to assess changes in their gene expression profiles. In this study, three different anti-CD3 antibodies were used for the stimulation: two recombinant antibody fragments, namely, a humanized and a chimeric FvFc molecule, and the prototype mouse mAb OKT3. RESULTS: Gene Ontology categories and individual immunoregulatory markers were compared, suggesting a similarity in modulated gene sets, mainly those for immunoregulatory and inflammatory terms. Upregulation of interleukin receptors, such as IL2RA, IL1R, IL12RB2, IL18R1, IL21R and IL23R, and of inhibitory molecules, such as FOXP3, CTLA4, TNFRSF18, LAG3 and PDCD1, were also observed, suggesting an inhibitory and exhausted phenotype. CONCLUSIONS: We used a deep transcriptome sequencing method for comparing three anti-CD3 antibodies in terms of Gene Ontology enrichment and immunological marker expression. The present data showed that both recombinant antibodies induced a compatible expression profile, suggesting that they might be candidates for a closer evaluation with respect to their therapeutic value. Moreover, the proposed methodology is amenable to be more generally applied for molecular comparison of cell receptor dependent antibody therapy.

Characterization of Monoclonal Antibodies against Bovine herpesvirus type 1 selected by Phage Display Technology / Caracterização de Anticorpos Monoclonais reativos ao Herpesvírus bovino tipo 1 selecionados por Phage Display

The specificity of monoclonal antibodies (mAbs) to desired targets makes these molecules suitable for therapeutic and diagnostic uses against a wide range of pathogens. Phage display antibody libraries offer one method by which mAbs can be selected for, without the use of conventional hybridoma technology. In this work, phage display technology was used to construct, select and characterize a combinatorial single chain fragment variable (scFv) antibody library against bovine herpesvirus type 1 (BoHV-1) from the immune repertoire of chickens immunized with the virus. In silico analysis of the hypervariable domains of the antibody heavy chains revealed a high frequency of scFv fragments with low variability, suggesting that selection had probably been carried out and favored by a few im-munogenic viral antigens. The reactivity of the scFv fragments selected against BoHV-1 was demon-strated by Phage-ELISA. A significant increase in antibody reactivity to the target was observed after six rounds of library selection, showing its potential use as a molecule for BoHV-1 diagnosis. The strategy described here opens up a field for the use of phage display as a tool for selection of mono-clonal antibodies that could be used for theranostic applications against infectious and parasitic dis-eases of veterinary interest.(AU)

A especificidade dos anticorpos monoclonais (mAb) aos alvos desejados torna estas moléculas ade-quadas para uso em diagnóstico ou terapia de uma vasta gama de agentes patogênicos. Biblioteca de anticorpos apresentados em fagos filamentosos é uma metodologia para a produção de mAbs, poden-do ser utilizada como alternativa à tecnologia de hibridoma convencional, tradicionalmente empregada para este fim. Neste trabalho, a tecnologia de Phage display foi usada para construir, selecionar e ca-racterizar uma biblioteca combinatorial de fragmentos de anticorpos de cadeia única (scFv) contra o Herpesvírus bovino tipo 1 (BoHV-1) a partir do repertório imune de galinhas imunizadas com o vírus. A análise in silico dos domínios hipervariáveis das cadeias pesadas dos anticorpos revelou uma alta frequência de fragmentos scFv com baixa variabilidade, sugerindo que a seleção foi provavelmente conduzida e favorecida por poucos antígenos virais mais imunogênicos. A reatividade dos fragmentos scFv selecionados contra BoHV-1 foi demonstrada por Fago-ELISA. Observou-se um aumento signi-ficativo da reatividade dos anticorpos após seis ciclos de seleção, evidenciando sua utilização como molécula para o diagnóstico de BoHV-1. A estratégia aqui descrita abre a possibilidade do uso da tec-nologia de Phage display como ferramenta na seleção de anticorpos monoclonais com potencial uso tanto para o diagnóstico quanto para terapia de doenças infecciosas e/ou parasitárias de interesse veterinário.(AU)

Characterization of Monoclonal Antibodies against Bovine herpesvirus type 1 selected by Phage Display Technology / Caracterização de Anticorpos Monoclonais reativos ao Herpesvírus bovino tipo 1 selecionados por Phage Display

The specificity of monoclonal antibodies (mAbs) to desired targets makes these molecules suitable for therapeutic and diagnostic uses against a wide range of pathogens. Phage display antibody libraries offer one method by which mAbs can be selected for, without the use of conventional hybridoma technology. In this work, phage display technology was used to construct, select and characterize a combinatorial single chain fragment variable (scFv) antibody library against bovine herpesvirus type 1 (BoHV-1) from the immune repertoire of chickens immunized with the virus. In silico analysis of the hypervariable domains of the antibody heavy chains revealed a high frequency of scFv fragments with low variability, suggesting that selection had probably been carried out and favored by a few im-munogenic viral antigens. The reactivity of the scFv fragments selected against BoHV-1 was demon-strated by Phage-ELISA. A significant increase in antibody reactivity to the target was observed after six rounds of library selection, showing its potential use as a molecule for BoHV-1 diagnosis. The strategy described here opens up a field for the use of phage display as a tool for selection of mono-clonal antibodies that could be used for theranostic applications against infectious and parasitic dis-eases of veterinary interest.

A especificidade dos anticorpos monoclonais (mAb) aos alvos desejados torna estas moléculas ade-quadas para uso em diagnóstico ou terapia de uma vasta gama de agentes patogênicos. Biblioteca de anticorpos apresentados em fagos filamentosos é uma metodologia para a produção de mAbs, poden-do ser utilizada como alternativa à tecnologia de hibridoma convencional, tradicionalmente empregada para este fim. Neste trabalho, a tecnologia de Phage display foi usada para construir, selecionar e ca-racterizar uma biblioteca combinatorial de fragmentos de anticorpos de cadeia única (scFv) contra o Herpesvírus bovino tipo 1 (BoHV-1) a partir do repertório imune de galinhas imunizadas com o vírus. A análise in silico dos domínios hipervariáveis das cadeias pesadas dos anticorpos revelou uma alta frequência de fragmentos scFv com baixa variabilidade, sugerindo que a seleção foi provavelmente conduzida e favorecida por poucos antígenos virais mais imunogênicos. A reatividade dos fragmentos scFv selecionados contra BoHV-1 foi demonstrada por Fago-ELISA. Observou-se um aumento signi-ficativo da reatividade dos anticorpos após seis ciclos de seleção, evidenciando sua utilização como molécula para o diagnóstico de BoHV-1. A estratégia aqui descrita abre a possibilidade do uso da tec-nologia de Phage display como ferramenta na seleção de anticorpos monoclonais com potencial uso tanto para o diagnóstico quanto para terapia de doenças infecciosas e/ou parasitárias de interesse veterinário.

Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach.

Phage-display technology facilitates rapid selection of antigen-specific single-chain variable fragment (scFv) antibodies from large recombinant libraries. ScFv antibodies, composed of a VH and VL domain, are readily engineered into multimeric formats for the development of diagnostics and targeted therapies. However, the recombinant nature of the selection strategy can result in VH and VL domains with sub-optimal biophysical properties, such as reduced thermodynamic stability and enhanced aggregation propensity, which lead to poor production and limited application. We found that the C10 anti-epidermal growth factor receptor (EGFR) scFv, and its affinity mutant, P2224, exhibit weak production from E. coli. Interestingly, these scFv contain a fusion of lambda3 and lambda1 V-region (LV3 and LV1) genes, most likely the result of a PCR aberration during library construction. To enhance the biophysical properties of these scFvs, we utilized a structure-based approach to replace and redesign the pre-existing framework of the VL domain to one that best pairs with the existing VH. We describe a method to exchange lambda sequences with a more stable kappa3 framework (KV3) within the VL domain that incorporates the original lambda DE-loop. The resulting scFvs, C10KV3_LV1DE and P2224KV3_LV1DE, are more thermodynamically stable and easier to produce from bacterial culture. Additionally, C10KV3_LV1DE and P2224KV3_LV1DE retain binding affinity to EGFR, suggesting that such a dramatic framework swap does not significantly affect scFv binding. We provide here a novel strategy for redesigning the light chain of problematic scFvs to enhance their stability and therapeutic applicability.

Engineering antibody fragments: replicating the immune system and beyond / La ingeniería de fragmentos de anticuerpos: imitando y expandiendo el sistema inmune

Since genetic engineering of humanized murine monoclonal antibodies was first demonstrated over two decades ago, antibody engineering technologies have evolved based upon an increasing understanding of the mechanisms involved in antibody generation in vivo, and a constant search for alternative routes to evolve and exploit the characteristics of antibodies. As a result, antibody engineers have devised innovative strategies for the rapid evolution and selection of antibodies and novel antibody designs (i.e., antibody fragments). Phage display, cell display and ribosome display technologies, which comprise the core of the currently available technologies for the discovery and preparation of such antibodies, are reviewed herein. This article intends to communicate the state-of-the-art technology available for the engineering of antibodies to a general readership interested in this important field. Therefore, important immunology concepts are introduced before detailed descriptions of the three antibody engineering technologies are presented in later sections. A comparison of these methodologies suggests that despite the predominance of phage display for the engineering of antibody fragments in the past 20 years, cell display and ribosome display will likely gain importance in the selection and discovery of the antibody fragments in the future. Finally, these technologies are likely to play an important role in the production of the next generation of antibody-based therapeutics.

Las tecnologías para la ingeniería de anticuerpos han evolucionado durante las últimas dos décadas, desde la demostración de la posibilidad de humanizar anticuerpos monoclonales de ratón mediante ingeniería genética, apoyadas en el creciente entendimiento de los mecanismos involucrados en la generación de anticuerpos in vivo, y en una búsqueda constante de rutas alternativas para evolucionar y explotar sus características. Es así como los ingenieros de anticuerpos han desarrollado estrategias innovadoras para la evolución y selección de anticuerpos y de novedosos diseños de anticuerpos conocidos como fragmentos de anticuerpos. Esta revisión se enfoca en tres tecnologías que comprenden el núcleo de las tecnologías actualmente disponibles para el descubrimiento y preparación de tales anticuerpos: la presentación en fagos, la presentación en células, y la presentación en ribosomas. Este artículo busca presentar el estado del arte de estas tecnologías a un grupo general de lectores interesados en este campo, por lo que inicialmente se introducen importantes conceptos de inmunología requeridos para comprender en detalle las tecnologías discutidas. Una comparación de estas metodologías para la ingeniería de anticuerpos sugiere que a pesar del dominio de las tecnologías basadas en la presentación en fagos durante los últimos 20 años, en los próximos años la presentación en células y la presentación en ribosomas probablemente ganarán importancia para la selección y descubrimiento de fragmentos de anticuerpos. Finalmente, es probable que estas tecnologías jueguen un papel importante en la producción de la siguiente generación de terapéuticos basados en anticuerpos.

Engineering antibody fragments: replicating the immune system and beyond: [review] / La ingeniería de fragmentos de anticuerpos: imitando y expandiendo el sistema inmune: [revisión]

Since genetic engineering of humanized murine monoclonal antibodies was first demonstrated over two decades ago, antibody engineering technologies have evolved based upon an increasing understanding of the mechanisms involved in antibody generation in vivo, and a constant search for alternative routes to evolve and exploit the characteristics of antibodies. As a result, antibody engineers have devised innovative strategies for the rapid evolution and selection of antibodies and novel antibody designs (i.e., antibody fragments). Phage display, cell display and ribosome display technologies, which comprise the core of the currently available technologies for the discovery and preparation of such antibodies, are reviewed herein. This article intends to communicate the state-of-the-art technology available for the engineering of antibodies to a general readership interested in this important field. Therefore, important immunology concepts are introduced before detailed descriptions of the three antibody engineering technologies are presented in later sections. A comparison of these methodologies suggests that despite the predominance of phage display for the engineering of antibody fragments in the past 20 years, cell display and ribosome display will likely gain importance in the selection and discovery of the antibody fragments in the future. Finally, these technologies are likely to play an important role in the production of the next generation of antibody-based therapeutics.

Las tecnologías para la ingeniería de anticuerpos han evolucionado durante las últimas dos décadas, desde la demostración de la posibilidad de humanizar anticuerpos monoclonales de ratón mediante ingeniería genética, apoyadas en el creciente entendimiento de los mecanismos involucrados en la generación de anticuerpos in vivo, y en una búsqueda constante de rutas alternativas para evolucionar y explotar sus características. Es así como los ingenieros de anticuerpos han desarrollado estrategias innovadoras para la evolución y selección de anticuerpos y de novedosos diseños de anticuerpos conocidos como fragmentos de anticuerpos. Esta revisión se enfoca en tres tecnologías que comprenden el núcleo de las tecnologías actualmente disponibles para el descubrimiento y preparación de tales anticuerpos: la presentación en fagos, la presentación en células, y la presentación en ribosomas. Este artículo busca presentar el estado del arte de estas tecnologías a un grupo general de lectores interesados en este campo, por lo que inicialmente se introducen importantes conceptos de inmunología requeridos para comprender en detalle las tecnologías discutidas. Una comparación de estas metodologías para la ingeniería de anticuerpos sugiere que a pesar del dominio de las tecnologías basadas en la presentación en fagos durante los últimos 20 años, en los próximos años la presentación en células y la presentación en ribosomas probablemente ganarán importancia para la selección y descubrimiento de fragmentos de anticuerpos. Finalmente, es probable que estas tecnologías jueguen un papel importante en la producción de la siguiente generación de terapéuticos basados en anticuerpos.