Get Help Sign In

Antigen-specific B cell enrichment for faster, more efficient antibody discovery

Mahendra A, Haque A, Prabakaran P, et al. Honing-in antigen-specific cells during antibody discovery: a user-friendly process to mine a deeper repertoire. Commun Biol. 2022;30;5(1):1157.

Antigen-specific B cells are a crucial resource for antibody discovery but represent only a tiny fraction of total B cells. An article published by Mahendra et al. described an improved workflow for efficient purification of these rare but important cells. Using gBlocks™ Gene Fragments to synthesize variable regions of candidate antibodies from the purified B cells, Mahendra et al. expressed antigen-binding antibody fragments (Fabs) for additional testing. By specifically capturing the targeted cell type, the researchers were able to access greater sequence diversity and biologically functional clones to enhance their antibody discovery capabilities.


Antibody discovery research has enabled the identification and development of many important biologic drugs, with >100 therapeutic antibody treatments already approved or under review in the US or EU [1,2]. Many researchers view antigen-specific B cells (AgSCs) as a particularly potent resource when mining for new immunotherapeutic antibodies. Unfortunately, focusing the discovery process solely on AgSCs from immunized individuals poses a huge challenge as they represent only 0.01%–0.1% of the total B cell population. In this article, Mahendra et al. tested a new method of purifying AgSCs from immunized mice. This improved workflow allowed them to quickly eliminate non-relevant cells from the antibody discovery process without damaging the AgSCs, enabling the generation of functional antibody clones from individual B cells. Using gBlocks Gene Fragments from IDT, they were able to express target-specific Fabs for further evaluation as part of a streamlined antibody discovery workflow.


The researchers used a multi-step enrichment workflow for bulk purification of AgSCs from immunized mice lymphoid tissues (spleen and lymph nodes). First, the total B cell population was isolated from other cell types by lysing red blood cells and selecting out unwanted cell types with antigen-coated beads. IgM+ and IgD+ B cells were also removed from the total B cell population, which was enriched for IgG+ B cells. AgSCs were selected out of the IgG+ B cell suspension using magnetic separation and biotinylated target antigen, then single-sorted for further use.

The researchers prepared cDNA from the individual B cells to amplify genes encoding IgG variable chains (VH and VK). They assessed sequence diversity of the recovered IgG genes using both Sanger and next generation sequencing (NGS). Recombinant antibody fragments (Fabs) from both AgSCs and non-antigen-selected B cells were cloned and expressed using their in-house method for antibody characterization. In brief, the variable regions of functional antibodies were synthesized as gBlocks Gene Fragments, cloned into an expression vector, then expressed and purified on an automated platform. Properties of the Fabs, including melting temperatures and antigen affinity, were measured using various assays.


Antigen-specific B cell (AgSC) bulk purification workflow produced viable AgSCs with minimal “escape” in flow-through population

The researchers used their multistep enrichment process to purify AgSCs from the initial suspension of dissociated cells from the harvested lymph node and spleen tissue. The collected AgSCs, which represented 0.19–1.12% of total B cells, were ~95% viable after the enrichment process. This represents a large improvement over another common method of antigen-specific B-cell enrichment, FACS, which sorts the fragile cells at such high speeds that it often causes significant damage and cell mortality. Importantly, IgG genes crucial for the antibody discovery process (VH and VK chains) were able to be efficiently recovered from single-sorted AgSCs for all 5 antigens (81%–99%), then expressed as recombinant IgGs (rIgGs) in a high-throughput system [3] for subsequent antigen binding tests.

The researchers investigated antigen binding of individual antibodies from three B-cell populations: the purified AgSCs, total B cell (TBC) population, and non-selected flow-through. 51–88% of rIgGs from the AgSC population bound to their target antigens, compared to only 1–8% of rIgGs from the TBC population and 0–2% from the flow-through population. The small percentage of target-specific rIgGs in the flow-through population suggests that few, if any, antigen-specific B cells escaped selection during the bulk purification process.

Greater variable gene segment diversity and enrichment of biologically functional clones

To demonstrate the utility of bulk purified AgSCs during the antibody discovery process, the researchers made Fab-based phage display libraries from the AgSC and IgG+ TBC pools for two antigens. Using both Sanger and NGS, the researchers evaluated the sequence diversity of variable gene segments from the two libraries. AgSC library clones displayed higher number of unique VH sequences compared to TBC library clones (57 vs. 13, respectively) and 4–6-fold greater complementarity-determining region (CDR) diversity. Number of unique VK sequences was similar between clones from AgSC and TBC libraries (147 vs. 115, respectively). In addition to greater VH sequence diversity, the researchers also found that monoclonal antibodies derived from antigen-selected B cells were more likely to be biologically functional than monoclonal antibodies from TBC library clones.


Mahendra et al. demonstrated an improved enrichment workflow for the bulk purification of antigen-specific B cells. This was accomplished through the stepwise exclusion of non-relevant cells and resulted in a pool of viable AgSCs competent for recovery of IgG VH and VK genes and the generation of phage display libraries. The researchers selected variable regions of biologically functional antibodies identified in their antibody discovery process to be synthesized as gBlocks Gene Fragments and subsequently expressed and purified as recombinant Fabs. The successful expression and purification of these Fabs allowed for downstream characterization of their biophysical properties, such as thermal stability and affinity for target antigens. In addition to improved efficiency when generating functional clones, the demonstrated AgSC purification process resulted in greater sequence diversity compared to clones from total B cell libraries. This AgSC bulk purification workflow, as described by Mahendra et al., represents a time-saving and resource-maximizing improvement over FACS isolation or total B cell populations for antibody discovery.


1. Lu RM, Hwang YC, Liu IJ, et al. Development of therapeutic antibodies for the treatment of diseases. J Biomed Sci. 2020;27(1):1.

2. The Antibody Society. Therapeutic monoclonal antibodies approved or in review in the EU or US. Accessed November 14, 2022.

3. Ramasubramanian A, Tennyson R, Magnay M, et al. Bringing the Heavy Chain to Light: Creating a Symmetric, Bivalent IgG-Like Bispecific. Antibodies (Basel). 2020;9(4):62.

4. Mahendra A, Haque A, Prabakaran P, et al. Honing-in antigen-specific cells during antibody discovery: a user-friendly process to mine a deeper repertoire. Commun Biol. 2022;30;5(1):1157.

For research use only. Not for use in diagnostic procedures. 
Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations. RUO22-1610_001

Published Jan 9, 2023