Technical Development Project 1: Measuring the Immunome: Genomic Approaches to B Cell Repertoire. In this project, we propose to develop new technological applications of next generation DNA sequencing, high throughput PCR chips, and microfluidic single cell processors to perform systemic analyses of the human B cell repertoire. Using B cells purified from human peripheral blood, we will apply these technologies to try to understand the effects of three phenomena on immune repertoire: aging, genetic background and vaccination history. Four groups of subjects will be studied: 1. age groups - children, young adults and elderly;2. genetic background - identical twins vs fraternal twins vs not-related subjects;3. vaccination history - pre, post and multiple immunizations;4. vaccination type - the trivalent inactivated influenza vaccine (TIV) and the live attenuated influenza vaccine (LAIV). This study will provide the first comprehensive and systematic measurements of B cell repertoire at three different anatomic levels, V/D/J/C exon usage, immunoglobulin (Ig) gene deep sequencing, and single cell gene expression analysis.
Our specific aims are:
Aim 1. Develop a quick and quantitative assay to measure the V, D J, and C exon usage landscape.
Aim 2. Develop a high throughput sequencing protocol to perform deep sequencing of Ig heavy chain gene diversity.
Aim 3. Develop a microfluidic parallel processor for single cell analysis of B cell repertoire.
Aim 4. Dissect the influences of aging, genetic background, and vaccination history on the human B cell repertoire.

Public Health Relevance

Data generated from this study will advance our understanding of the B cell repertoire in response to influenza vaccine, which in turn will increase our knowledge of how influenza interacts with the immune system. In addition, technologies developed here may prove useful to advance clinical diagnostics for influenza and other pathogens.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
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Special Emphasis Panel (ZAI1-KS-I)
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Stanford University
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Krishnaswamy, Smita; Spitzer, Matthew H; Mingueneau, Michael et al. (2014) Systems biology. Conditional density-based analysis of T cell signaling in single-cell data. Science 346:1250689
Bendall, Sean C; Davis, Kara L; Amir, El-Ad David et al. (2014) Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157:714-25
Gaudillière, Brice; Fragiadakis, Gabriela K; Bruggner, Robert V et al. (2014) Clinical recovery from surgery correlates with single-cell immune signatures. Sci Transl Med 6:255ra131
Sen, Adrish; Rott, Lusijah; Phan, Nguyen et al. (2014) Rotavirus NSP1 protein inhibits interferon-mediated STAT1 activation. J Virol 88:41-53
Furman, David; Hejblum, Boris P; Simon, Noah et al. (2014) Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination. Proc Natl Acad Sci U S A 111:869-74
Sen, Nandini; Mukherjee, Gourab; Sen, Adrish et al. (2014) Single-cell mass cytometry analysis of human tonsil T cell remodeling by varicella zoster virus. Cell Rep 8:633-45
Pernas, Lena; Ramirez, Raymund; Holmes, Tyson H et al. (2014) Immune profiling of pregnant Toxoplasma-infected US and Colombia patients reveals surprising impacts of infection on peripheral blood cytokines. J Infect Dis 210:923-31
Bruggner, Robert V; Bodenmiller, Bernd; Dill, David L et al. (2014) Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci U S A 111:E2770-7
Chang, Serena; Kohrt, Holbrook; Maecker, Holden T (2014) Monitoring the immune competence of cancer patients to predict outcome. Cancer Immunol Immunother 63:713-9
Birnbaum, Michael E; Mendoza, Juan L; Sethi, Dhruv K et al. (2014) Deconstructing the peptide-MHC specificity of T cell recognition. Cell 157:1073-87

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