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Quantitative molecular analysis of polyclonal memory B cell responses

English title Quantitative molecular analysis of polyclonal memory B cell responses
Applicant Reddy Sai
Number 143869
Funding scheme Project funding (Div. I-III)
Research institution Computational Systems Biology Department of Biosystems, D-BSSE ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Immunology, Immunopathology
Start/End 01.06.2013 - 31.05.2016
Approved amount 529'800.00
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All Disciplines (2)

Discipline
Immunology, Immunopathology
Molecular Biology

Keywords (5)

antibody repertoire; bioinformatic; B cells; high-throughput; humoral immunity

Lay Summary (English)

Lead
Applying systems biology study humoral immunity
Lay summary

Memory B cells play an indispensible role in preserving long-term immunological defense against pathogens, despite their importance, several aspects related to memory B cell and plasma cell differentiation and development remain unknown. In this proposal, we describe a systems-immunology-based approach to quantitatively analyze the polyclonal memory B cell response following immunization. We will use very novel methods of high-throughput repertoire analysis to study the polyclonal antibody immune response in a quantitative manner. The work described here will answer long-standing questions related to the differentiation pathway of memory B cells and plasma cells and their corresponding antibody repertoire. Moreover, a wealth of quantitative information will be gained on aspects of antibody repertoire clonal frequency and distribution, germline usage, molecular evolution, and specificity and affinity towards antigens. We will use very novel methods of high-throughput repertoire analysis to study the polyclonal antibody response; this will lay the foundation for future studies that can expand study of immune responses in a quantitative manner. This comprehensive understanding of the memory B cell response will also provide valuable knowledge that will aid in the design and development of novel vaccines and immunotherapeutics. 


Direct link to Lay Summary Last update: 08.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting.
Khan Tarik A, Friedensohn Simon, Gorter de Vries Arthur R, Straszewski Jakub, Ruscheweyh Hans-Joachim, Reddy Sai T (2016), Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting., in Science advances, 2(3), 1501371-1501371.
A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status.
Greiff Victor, Bhat Pooja, Cook Skylar C, Menzel Ulrike, Kang Wenjing, Reddy Sai T (2015), A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status., in Genome medicine, 7(1), 49-49.
Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.
Greiff Victor, Miho Enkelejda, Menzel Ulrike, Reddy Sai T (2015), Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires., in Trends in immunology, 36(11), 738-49.
Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing.
Menzel Ulrike, Greiff Victor, Khan Tarik A, Haessler Ulrike, Hellmann Ina, Friedensohn Simon, Cook Skylar C, Pogson Mark, Reddy Sai T (2014), Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing., in PloS one, 9(5), 96727-96727.
High-throughput sequencing of human immunoglobulin variable regions with subtype identification.
Schanz Merle, Liechti Thomas, Zagordi Osvaldo, Miho Enkelejda, Reddy Sai T, Günthard Huldrych F, Trkola Alexandra, Huber Michael (2014), High-throughput sequencing of human immunoglobulin variable regions with subtype identification., in PloS one, 9(11), 111726-111726.
Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice.
Greiff Victor, Menzel Ulrike, Haessler Ulrike, Cook Skylar C, Friedensohn Simon, Khan Tarik A, Pogson Mark, Hellmann Ina, Reddy Sai T (2014), Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice., in BMC immunology, 15, 40-40.
Using next-generation sequencing for discovery of high-frequency monoclonal antibodies in the variable gene repertoires from immunized mice.
Haessler Ulrike, Reddy Sai T (2014), Using next-generation sequencing for discovery of high-frequency monoclonal antibodies in the variable gene repertoires from immunized mice., in Methods in molecular biology (Clifton, N.J.), 1131, 191-203.

Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Quality control for genetic sequencing ETH News International 2016

Associated projects

Number Title Start Funding scheme
170110 The structure and evolution of immunoglobulin repertoires 01.01.2017 Project funding (Div. I-III)

Abstract

The memory B cell response recognizes and responds to pathogens by initiating a series of molecular and cellular reactions, which culminate in the generation of antigen-specific polyclonal antibodies; therefore memory B cells plays an indispensible role in maintaining immunological protection. Following initial encounter and stimulation by antigen, naïve B cells differentiate into either short-lived plasma cells or form germinal centers (GC), which result in the further differentiation of memory B cells or long-lived antibody-secreting plasma cells. Despite their immense importance to immunity, there are still many unknowns related to the differentiation and development of memory B cells. For example, most previous studies have relied on transgenic mouse models and analysis of monoclonal-like B cell responses. Consequentially, such approaches were not able to capture the complexities and repertoire diversity present in a more “natural” immune response, one that leads to the generation of a polyclonal population of antibodies against antigen. The overall goal of this proposal is to provide a quantitative molecular analysis of polyclonal memory B cell responses in wild-type mice following immunization with protein antigens, which will enable us to elucidate mechanisms governing differentiation and development of memory B cells and plasma cells. Our analysis will be conducted with a systems immunology-based approach; specifically this will consist of magnetic-associated sorting coupled to flow cytometry for isolation of antigen-specific IgG+ memory B cells and plasma cells (Aim 1). Next we will use the Illumina miSeq platform for high-throughput DNA sequencing of antibody variable genes from the isolated antigen-specific cells; this will be followed by extensive bioinformatic and statistical analysis for the characterization and quantification of several features related to polyclonal antibody repertoires (Aim 2). In addition to a comprehensive genetic analysis, we will also perform a thorough investigation of the polyclonal antibodies on a protein-based level. This will include recombinant expression of several high-frequency antibodies from each memory B cell and plasma cell subset followed by biophysical characterization of binding affinity towards antigen (Aim 3). The major outcome of all of these aims will be to gain substantial insight into the differentiation and development of memory B cells and plasma cells. For example, we will be able to address whether memory B cells and plasma cells follow a bifurcative or linear differentiation program. Additionally, we will also quantify the clonal diversity of each antigen-specific memory repertoire. We will also determine the relationship between high frequency of antibody expression in a repertoire and it’s binding affinity towards antigen. Importantly, since all of these studies will be performed on a quantitative and systems-based manner, we will be able to generate an unprecedented depth of information on the antigen-specific polyclonal memory B cell and plasma cell response, which will provide valuable insight in the design and development of vaccines and immunotherapeutics.
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