Eliciting effective affinity maturation is an essential component of efficacious humoral vaccines. Recent findings in vaccine development for influenza and HIV-1 suggest that success in these key areas will depend on the ability to influence affinity maturation to an extent not yet possible. Continuing advances in experimental methods for elucidating cellular interactions in the germinal center reaction now make it possible to understand and model selection in affinity maturation.
The specific aims are organized around the major goal of developing and using a mathematical model through cycles of experimentation, development, prediction and validation. For all research aims, the antibodies and antibody clones used will be selected from among those isolated and characterized in human and murine vaccine studies. The model developed will include an accurate model of somatic hypermutation sequence- specific mutation rate. This model will be made possible through the use of mice engineered to express the same rearranged Ig gene in productive and non-productive, but mutating, forms. The model will contain statistically accurate models of the correspondence between amino acid mutations and changes in affinity due to these mutations. These models will be realized through the use of a novel high-throughput B-cell culture system that allows the isolation of light- chain/heavy-chain pairs from individual B cells as well as measurement of the avidity of the antibody encoded by these genes. Furthermore, we will obtain the structures and detailed kinetic binding parameters for selected clonally related antibodies. The Ig variable-region genes to be used in these studies will be selected from genes isolated in a study of affinity maturation in the human response to seasonal influenza vaccine and in murine studies of influenza virus hemagglutinin or Bacillus anthracis protective antigen immunization. The models and methods obtained in these studies will then be used to study 1) the extent to which important features of affinity maturation are conserved in repeated experiments using controlled mouse studies as well as repeated vaccinations in human subjects; and 2) the effects on affinity maturation of modulating the effective selection intensity in mice engineered to overexpress an anti-apoptotic gene. We will provide cross-disciplinary training in our own laboratories and through summer schools and symposia. All models and software will be shared with the scientific community.
Vaccines work by activating B cells to produce antibodies that recognize and bind to molecules on pathogens and infected cells. Affinity maturation is a key process elicited by vaccines that leads to high-affinity antibodies in the memory cells that provide protection against subsequent pathogen exposure. We propose to develop a detailed computer model of vaccine-induced affinity maturation and perform the essential experiments to ensure the accuracy of the model to make it easier to tackle the outstanding, complex problems in vaccine development. Project 1 - Model Development, Data Analysis, and Simulation for Affinity Maturation Project Leader: Kepler, Thomas DESCRIPTION (as provided by applicant): The elicitation of effective affinity maturation has proven to be an essential component of efficacious humoral vaccines. In fact, recent findings in vaccine development for influenza and HIV-1 suggest that success in these key areas may depend on the ability to enhance affinity maturation to an extent not yet possible. It is the overarching goal of this U19 research project to use highly focused mathematical modeling driven by state-of-the art experimentation to advance our understanding of the interconnected complex processes that together constitute affinity maturation in the humoral response to vaccine immunogens. In this project, we will develop and fit key components of the affinity maturation model including the generation of antibody diversity through somatic hypermutation and the correspondence between antibody amino acid sequence and affinity of the antibody and the eliciting antigen. Somatic hypermutation modeling will be driven by experiments in passenger-transgene engineered mice, which express a single productive antibody gene and contain an identical but transcription-disabled gene on the other chromosome, which mutates without experiencing selection. Affinity modeling will be driven by data generated in project 2 (high-throughput sequence and affinity in a murine system) and project 3 (structure and affinity studies) and pursued using a combination of biophysical and statistical modeling. We have designed and will carry out a study of affinity maturation in the response of human vaccinees to influenza vaccine in two successive years. Sequence and affinity data from these studies will be used to identify antibodies and antibody clones to be studied in detail in the mouse transgene system and in the structural studies. The inter- and intra-clonal dynamics obtained in these studies will in turn be analyzed using the models developed. The research team from this project will participate in statistical data analysis throughout the overall program. The software and methods developed under this program will be made available to the broader research community, and relevant training made available to ensure their effective use. These resources, together with the insights into the mechanics of diversification and selection under affinity maturation that will be forthcoming from our research efforts, promise to bring substantial opportunities for the development of novel approaches in vaccinology.
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