Investigating the impact of vaccine formulations on humoral response via single-cell analysis
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Author(s)
Zhang, Yiming
Advisor(s)
Irvine, Darrell J.
Love, J. Christopher
Date Issued
May 2025
Publisher
Massachusetts Institute of Technology
Abstract
Vaccines generate high-affinity protective antibodies against pathogens by activating antigen-specific B cells and helper T cells and inducing germinal center (GC) reactions in the draining lymph nodes. A critical yet poorly understood aspect is how vaccine formulations influence and alter the humoral response, particularly the characteristics of antigen-specific B cells. To address how vaccine formulations modulate B cell activity, we developed B3E-seq, a method that simultaneously profiles the transcriptome and obtains full-length B cell receptor (BCR) sequences from widely adopted 3’-barcoded single-cell RNA sequencing (scRNA-seq) libraries.
We applied B3E-seq to investigate a slow delivery and follicle-targeting HIV vaccine formulation in mice. The most common clinical adjuvant, aluminum hydroxide (alum), can be engineered into a slow-delivery vehicle by tagging immunogens with short phosphoserine (pSer) linkers to achieve pseudo-covalent alum-binding. Upon mixture, the individual alum particles are decorated with pSer-tagged immunogens and mimic virus-like particles. We term this multivalent antigen and alum complex "alum-pSer." We also developed a potent saponin-based adjuvant, SMNP, to modulate the inflammatory response. With flow cytometry, B3E-seq, ELISA, and microscopy, we investigated the impact of vaccine slow delivery with or without the addition of the potent SMNP adjuvant on germinal center responses elicited by a stabilized HIV Env trimer immunogen in mice. We found that the combination of alum-pSer and SMNP demonstrated remarkable synergy, significantly amplifying GC reactions, B cell clonal expansion and diversity, positive selection signals, memory B cell formation, and antigen localization on follicular dendritic cells compared to alum-pSer or SMNP vaccination alone, revealing key mechanisms by which vaccine formulations can shape and optimize the development of humoral immunity.
Our integrated single-cell multi-omic approach offers new insights into the dynamics of B cell responses, particularly in how vaccine formulations drive antigen-specific B cell expansion and development. These findings underscore the utility of B3E-seq in advancing vaccine development, providing a critical tool for studying immune responses to a broad range of pathogens and informing next-generation vaccine design strategies.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
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