Introduction

Technical improvements in the rapid isolation of monoclonal antibodies (mAbs) are critical for their diagnostic and therapeutic development. This need became apparent to the general public during the COVID-19 pandemic. Antibodies isolated from convalescent COVID-19 patients are valuable resources for the development of mAb therapeutics and rapid diagnostic tools. Human antibodies can be administered to other patients without the need to humanize in an emergency and with a slight modification of Fc receptor binding (1) to increase the half-life or reduce the risk of antibody-dependent enhancement. Although production costs remain high, the efficiency of generating recombinant antibodies has dramatically improved with the use of mammalian cell lines, and the application of therapeutic antibodies is likely to expand in the near future (2).

The gold standard method for isolating mAbs is the hybridoma technology developed by Kohler and Milstein in 1975 (3), in which antibody-producing B cells are fused with immortal B cells, called myelomas, to produce long-lasting antibody-producing B cells. In addition to hybridoma technology, new methods have been developed to increase mAb screening efficiency. These include direct immortalization of B cells by gene reprogramming using the Epstein–Barr virus (4) or retrovirus-mediated gene transfer (5), cloning of variable region-encoding genes by single-cell PCR (6,7), single-cell culture screening (8), and in vitro screening of recombinant antibody libraries (9–13). Some of these methods successfully yield high-affinity antibodies in various formats, including single variable domain on a heavy chain or single-chain fragment variable antibodies. Although hybridoma technology is highly reliable for the isolation of valuable antibodies from animal models, such as mice, rats, and hamsters, it is time-consuming and requires technical skill. The development of a new fusion partner cell line, SPYMEG, has enabled the production of human hybridomas and opened a new direction for the isolation of human mAbs (14). Although many of these new technologies have increased the throughput of mAb isolation, the procedure still requires significant resources and time.

To dramatically enhance the efficiency of mAb isolation, we used next-generation sequencing (NGS) technology, which has changed the method for sequencing immunoglobulin (Ig) variable-region genes. For instance, tens of thousands of Ig genes specific to certain antigens can be identified by combining droplet-based single-cell isolation with DNA barcode antigen technology, followed by NGS (15). Although Ig genes can be sequenced at a high throughput, there is no method for screening antibodies in a high-throughput format that is compatible with NGS technology.

In this study, we developed a new functional screening method that is compatible with NGS to rapidly identify antigen-specific clones. We first generated an Ig dual-expression vector using Golden Gate Cloning (16), which enabled the linkage of heavy-chain variable and light-chain variable DNA fragments obtained from a single-sorted B cell, followed by the expression of membrane-bound Ig. This single-step procedure enabled the enrichment of antigen-specific, high-affinity Igs by flow cytometry, which was significantly faster than conventional cloning-based methods that require sequential steps. To demonstrate the efficiency of our new method, we screened for potent broadly reactive antibodies (17–19) against the influenza virus in an experimental mouse model using our technology. Broad reactivity allows for influenza vaccines that work across seasonal variations in influenza strains, which can only be accomplished by screening a large number of candidate antibodies. We first raised cross-reactive B cells against various hemagglutinin (HA) antigens from the influenza virus by sequential immunization with heterotypic HA antigens from group 1 influenza. Using this technology, we obtained several mAbs that bind to other group 1 HA antigens and even to group 2 HA antigens of the influenza virus. Our technology can also be applied to human antibody screening and represents a new line of mAb screening that accelerates the isolation of therapeutic and diagnostic mAbs.

Results

Rapid membrane-bound dual Ig expression screening system

Cloning-based Ig screening involves several steps: cloning two Ig gene fragments encoding heavy and light chains independently from a single cell, co-expressing these Ig chains, and purifying individual recombinant antibodies. These steps are labor intensive. We established a new antibody screening system for the isolation of valuable mAbs (details in the method). Eventually, the antigen-binding Ig transformants were collected by sorting in a bulk fashion, and the unique CDR3 region and clones of interest were identified using the Ig-seq database (Fig. 1A).

Figure 1.

We generated a dual-expression vector to express both Ig heavy and kappa/lambda in a single-expression vector (Fig. 1B). These plasmids were individually transfected transiently to the floating human FreeStyle 293 cell line. Igs were expressed on the cell surface in 2 days; their expression could be confirmed and normalized by Venus expression, since the Ig heavy chain is fused with Venus at the cytoplasmic domain tail (Fig. 1C). The advantage of this system is the rapid enrichment of clones of interest through bulk screening. In the current single-cell-based cloning/screening, plasmid DNA extracted from the collected antigen-binding bulk transformants was sequenced for the heavy chain CDR3 region. The CDR3 region is unique and can be used for the identification of a clone (20,21). This membrane-bound Ig expression system links antigen-binding features and genetic information of the Ig repertoire.

Building the Ig-seq database and analysis

As a model experiment, we obtained broadly reactive antibodies against influenza viruses using multiple HA probes. We prepared two HA proteins as probes: A/Puerto Rico/8/1934 (H1N1), designated as PR8, and A/Okuda/1957 (H2N2), designated as H2. A total of 380 IgG1⁺ germinal center B cells of either PR8⁺ (204 cells), H2⁺ (99 cells), or PR8⁺H2⁺ (77 cells) were collected in a single-cell fashion. We obtained sequences of 284 independent clones. The success rate of cloning the paired Ig fragments was 75.9%. An overview of heavy chain V-D-J and light chain V-J usage and repertoire clonality is shown in Supplementary Fig. 1A and B. Mutation rates and CDR3 lengths of the heavy chains of the three cell populations (PR8⁺, H2⁺, and PR8⁺H2⁺) were comparable (Supplementary Fig. 1C and D). These results indicate that broadly reactive antibodies do not require unique genetic traces to obtain breadth in our experimental setup.

Isolation of H2- and H1-reactive B cells

On day 2 after transfection, 287 transformants (Ig-expressing transformant libraries) were stained with HA probes (Fig. 2A). As shown in Fig. 2B, we selected three prominent populations, H1⁺H2⁺ (cross), H2⁺ (H2), and H1⁺ (H1), and collected them in bulk. In contrast to bacterial transfection, mammalian cell lines, such as FreeStyle 293 cells, can contain multiple plasmids in a cell and ectopically express multiple proteins. Therefore, we decided to mix the transformants instead of plasmids. We sorted 2,981 cells from these three populations and performed sequencing. Bulk Ig-seq data are referred to as Ig-seq data, as described above. All the transformants were examined individually. A total of 90 clones from the three populations were verified for their sequences and HA binding by flow cytometry analysis, as shown in Fig. 2. Among these, 110 “H1⁺,” 67 “H2⁺,” and 13 “cross” clones were successfully isolated. Then, 138 transformants were verified for their binding to HAs by flow cytometry. Of these, 81 “H1⁺,” 48 “H2⁺,” and nine “cross” clones were successfully isolated. Finally, 8 of the 13 “cross” clones obtained in bulk were included in this group; the binding of one clone (D11p4) was so weak that it was not included in the gates sorted in bulk. Thus, we established a high-throughput method for sorting “cross” clones.

Figure 2.

Characterization of “cross” clones for broad reactivity against the influenza virus

By generating a secretory form of mAbs for these nine cross clones, including C10p2, we characterized their affinity and broadness using six different HA antigens from strains A/Okuda/1957 (H2N2) named for H2, A/Puerto Rico/8/1934 (H1N1) for PR8, A/California/2009 (X-179A) [H1N1] Pdm09 for Cal, A/Texas/50/2012 (X-223) [H3N2] for H3, A/Egypt/N03072/2010(H5N1) for H5, and A/Brisbane/59/2007 [H1N1] (19) for Stem. We determined the affinities (K_d) of the antibodies for the six HA antigens using surface plasmon resonance analysis (Table 1 and Supplementary Fig. 2), which ranged from 500 to 100 nM. With the highest affinity among them, the C10p2 antibody bound to Cal at K_d ≃ 5.66 × 10^­10 (M). Surprisingly, the antibodies showed a broader spectrum of HA binding among the influenza strains. Seven of the nine mAbs bound to HA from the highly pathogenic avian influenza strain H5N1. Furthermore, the six antibodies that bound to H3 were categorized into group 2 (22). In addition, we observed that two of the broadly reactive antibodies recognized the stem region of the HA of A/Brisbane/59/2007. A possible scenario for other stem cell-negative antibodies is that they may either bind to the stem region of other strains or to the head region of HA. We tested whether some of these antibodies shared features with classic broadly neutralizing antibodies. C179, the first broadly neutralizing mouse antibody isolated in 1993 (17), reacts with the stem region of HAs from group 1 influenza virus strains (22). C179 binds to HAs from group 1 influenza viruses, including H1N1, H2N2, and H5N1. A competition assay for the binding of H2 and PR8 revealed that A6p4 competes with C179 (Fig. 3). In addition, our two-dimensional phylogeny map indicated that A6p4 was unique to all clones (Supplementary Fig. 3). Note that we used NSP2 as a negative control antibody, which binds specifically to the HA from A/California/2009 (X-179A) [H1N1] Pdm09 (23). These results demonstrate that we were able to isolate a broadly reactive mAb with an affinity comparable to that of a classic broadly reactive mAb (C179) using our technology.

Figure 3.

Table 1.

Discussion

The discovery of therapeutic antibodies is accumulating, and their demand is increasing (24). Efficiently isolating one biologically significant antibody from the 10¹³ antibody repertoire is challenging. The hybridoma method has long been used for this purpose and remains reliable. However, the fusion rate of B and myeloma cells is < 0.001% in this method; therefore, the number of hybridomas obtained from one individual B cell is limited to several hundred clones, limiting its use in the production of mAbs. As an alternative choice, cloning-based antibody screening has gained popularity, especially for human antibody discovery, because of the lack of a human myeloma cell line similar to that used for murine cell fusion partners. The SPYMEG cell line can generate antigen-specific antibody-producing cells by fusing the murine SP2/0 myeloma cell line and human megakaryoblastic leukemia cell line MEG-01 with human PBMCs (14, 25). In addition to gene expression profiling, NGS facilitates antibody repertoire analysis. However, despite breakthroughs in sequencing technology, the process of linking antibody function and its genes is still long and labor intensive. To overcome this issue, we developed a new antibody screening system to directly link antigen–antibody binding (as a function) with a gene encoding the antibody by expressing its membrane-bound form. Among conventional cloning-based mAb isolation methods, this system demonstrates several advantages. 1) Membrane Ig expression can link the antigen-binding feature of membrane-expressed Ig, which can be linked to Ig DNA sequence information using our plasmid construct. Similar to the panning procedure used in phage display (26), antigen-binding cells carry the plasmid encoding the Ig genes through surface Ig so that the selection process in bulk format enriches the relevant plasmids for use in further experiments. 2) The dual Ig expression vector links heavy- and light-chain genes, which reduces the plasmid preparation time and stock by half. 3) Highly reliable Golden Gate Cloning technology using type IIs restriction enzymes can readily generate plasmid clones. This reduced the time required to generate an Ig plasmid library. 4) The population profile, defined by the fluorescence intensity during flow cytometry, directly reflected the affinity of a clone (Supplementary Fig. 4). Collectively, our technology has streamlined the isolation of mAbs for therapy and diagnosis.

Conclusion

Our findings indicate that the developed antibody presentation system facilitates antibody functional analysis and is well suited for the discovery of antibodies important for infectious diseases when combined with conventional NGS-based antibody repertoire analysis. Compared with droplet-based experimental systems, well-based systems are limited in the number of cells they can process. Furthermore, experiments involving infectious bacteria and viruses have imposed limitations on human experimentation. To solve these problems, the automation of experiments will become important in the future. By combining our screening system with robotic automation of experiments, it will be possible to obtain useful mAbs for various diseases quickly and in large quantities, which has broad implications for the development of vaccines against various diseases.

Materials and Methods

Protein purification of influenza HAs (H1 and H2) as antigens

A mixture of 25.7 µg of HA, comprising H1 strain A/Puerto Rico/8/1934 (PR8), H1 strain A/California/7/2009 (X-179A), H2 strain A/Okuda/1957 (H2), H3 strain A/Texas/50/2012 (X-223), or H5 strain A/Egypt/N03072/2010], 1.3 µg of NA (Strain-matched), and 3 µg of BirA-expressing plasmids were transfected into Expi293 cells using the Expifectamine 293 transfection kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. The cells were then cultured in Expi293 Expression Medium (Thermo Fisher Scientific) supplemented with D-biotin at a final concentration of 100 µM for in vivo BirA biotinylation in a humidified incubator containing 8% CO₂ at 37°C and 125 rpm. If biotinylation was not necessary, transfection was performed without BirA, and cell culture was carried out without D-biotin. Culture supernatants were harvested at 3 days post-transfection and filtered through a 0.45 μm filter (Merck Millipore, Burlington, MA, USA). All proteins were purified with a Talon metal affinity resin (Takara Bio USA, Mountain View, CA, USA) and dialyzed against pyrogen-free PBS. The oligomeric state and purity were determined at 25°C by size-exclusion chromatography on a Superdex 200 10/300GL column (GE Healthcare Technologies, Chicago, IL).

HA (H1 and H2) protein immunization

Two individual BALB/c mice were intraperitoneally immunized sequentially, 2 weeks apart, with 15 µg of H1 (PR8) HA followed by 15 µg of H2 HA protein as an antigen and supplemented with AddaVax adjuvant (InvivoGen, San Diego, CA, USA). BALB/c mice were purchased from CLEA Japan (CLEA Japan, Inc., Tokyo, Japan) All animal experiments were performed using protocols approved by the Institutional Animal Care and Use Committee (IACUC) of the RIKEN Yokohama Branch.

Fluorescence-activated cell sorting

CD43-negative B cells were collected using AutoMACS (Miltenyi Biotec, Inc., Bergisch Gladbach, North Rhine-Westphalia, Germany) and stained with IgG1 (Bv510), non-biotinylated His-tagged purified recombinant H1 (PR8) protein, and biotinylated purified recombinant H2 protein on ice for 30 min. After washing three times, the cell suspension was incubated with Alexa Fluor 488-labeled anti-His antibodies on ice for 30 min. After washing three times, the cell suspension was incubated with Brilliant Violet 421-conjugated streptavidin on ice for 3 min. Next, the B cells were subjected to single-cell sorting using a BD FACSAria III (BD Biosciences, Franklin Lakes, NJ, USA) and collected into 96-well plates pre-loaded with lysis buffer. The single cells in the lysis buffer were immediately snap-frozen on powdered dry ice and stored at ­80°C.

Amplification of a paired B cell repertoire amplicon from a single cell

Single cells were dropped into pre-loaded plates containing 4 µL/well of lysis buffer (2 U/µL RNase inhibitor, 0.5× PBS, 10 mM DTT) and 1 µL of 10 µM Oligo(dT)18 Primer. Cell lysates were incubated at 70°C for 90 s, followed by 35°C for 15 s, and then placed on ice for 2 min. For first-strand cDNA synthesis, 5 µL of RT mix (2× PCR buffer, 5 mM DTT, 2 mM dNTP Mix, 10 U RNase inhibitor, 100 U SuperScript III Reverse Transcriptase) was added to the cell lysate and incubated consecutively at 35°C for 5 min, 45°C for 20 min, 70°C for 10 min, and 4°C for chilling. For primer digestion, 5 µL of the primer digestion mix (1× ExoI Buffer, 7.5 U Exonuclease I) was prepared and incubated at 37°C for 30 min, 80°C for 20 min, and 4°C for chilling. For the poly-A tailing reaction, 5 µL of the poly-A tailing reaction mix (4× PCR buffer, 5 mM dATP, 0.1 U RNase H, 60 U Terminal transferase) was prepared and incubated at 37°C for 50 s, 65°C for 10 min, and 4°C for chilling. For the 2nd strand cDNA synthesis, 25 µL of the amplification mix (1× KAPA HiFi HotStart ReadyMix, 400 nM SMART_dT primer, 10 µL of poly-A tailing product, 1.5 µL of nuclease-free H₂O) was prepared and incubated at 95°C for 3 min, 40°C for 1 min, 65°C for 10 min, and 72°C for 5 min and chilled. For the cDNA amplification using an Ig-specific outer primer set, 20 µL of the outer amplification mix (1× KOD FX Neo buffer, 400 µM dNTPs, 1× UPM, 300 nM outer primer, 3.5 µL of the SMART product, 0.5 U KOD FX Neo polymerase) was prepared and incubated at 94°C for 2 min, followed by 25 cycles of 98°C for 10 s, 60°C for 30 s, and 68°C for 45 s and then chilled. For cDNA amplification with an Ig-specific inner primer set, 20 µL of the inner amplification mix (1× KOD FX Neo buffer, 400 µM dNTPs, 500 nM 5’ matrix primer mix, 500 nM 3’ matrix primer mix, 3.5 µL of the outer cDNA amplified product, 0.5 U KOD FX Neo polymerase) was prepared and incubated at 94°C for 2 min, followed by 25 cycles of 98°C for 10 s, 60°C for 30 s, and 68°C for 45 s and then chilled. Finally, 3 µL of the amplified inner cDNA product was used for further plate indexing by amplification. Then, 20 µL of the plate-indexing amplification mix (1× KOD FX Neo buffer, 400 µM dNTPs; 500 nM i5-Fwd or i7-Fwd, 500 nM i7-Rev or i5-Rev; 2 µL of the inner cDNA amplified product; 0.5 U KOD FX Neo polymerase) was prepared and incubated at 94°C for 2 min, followed by 25 cycles at 98°C for 10 s, 60°C for 30 s, and 68°C for 45 s and then chilled. All primers used are listed in Supplementary Table 1 and Supplementary Table 2.

Paired-end Illumina sequencing strategy and analysis

The libraries were sequenced on a MiSeq instrument (Illumina, San Diego, CA, USA) following the manufacturer’s protocol. As the sequencing length was limited to 2 × 300 bp, we used the following strategy. Amplicons in both orientations were generated using an Illumina adapter sequence. Then, asymmetric 400+100 nt paired-end sequencing was performed to obtain high-quality 400 + 400 nt paired-end sequences of the original cDNA molecule. This approach provided a sufficient sequencing length to capture extra-long Ig variants. We followed Turchaninova’s method (27). Only reads that met the following four conditions were used as the resulting Ig sequences: 1) reads with a length of 260 nt or more; 2) cumulative clustered reads representing the top 5% of the entire reads; 3) 5’- and 3’-reads overlapping a length of 20 bases or more; and 4) a total length of 460 ± 50 bp for heavy chain or 390 ± 40 bp for light chain. All resulting sequence data were analyzed using IMGT/High V-QUEST (http://www.imgt.org/IMGT_vquest/vquest) for annotation (28). Using the sequences and annotations, Ig database construction and visualization of the Ig repertoire were performed using the in-house BONSCI software.

Construction of a mouse IgG/IgK expression plasmid

The BsaI restriction sites were inserted into the paired B cell repertoire amplicon from a single cell using PCR. The destination vector contained the IL6 signal peptide, EF1a promoter, ccdB gene, and mouse IgK Fc region. The donor vector contained the mouse IgG1 Fc region, the Venus gene, and the EF1a promoter. The paired B cell repertoire amplicons, destination vector, and donor vector containing BsaI restriction sites were assembled using our assembly method. For this step, 10 μL of the assembly mix (1× T4 DNA ligase buffer, 1× BSA, 1 U BsaI restriction enzyme, 40 U T4 DNA ligase, 100 ng heavy chain amplicon, 100 ng light chain amplicon, 100 ng destination vector, and 100 ng donor vector) was prepared and incubated for 25 cycles at 37°C for 3 min, 16°C for 4 min, 50°C for 5 min, and 80°C for 5 min, and then chilled. The antibody sequence that entered the construct was fused to the Venus sequence and expressed in membrane form.

Antibody display on FreeStyle 293 cultured cells

A mixture of 1 μg of antibody-expressing plasmid was transfected into FreeStyle 293 cells using the 293fectin Transfection Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions and cultured in FreeStyle 293 Expression Medium (Thermo Fisher Scientific) in a humidified incubator with 8% CO₂ at 37°C and 125 rpm. Antibodies were displayed on the surface of cultured cells, which enabled the determination of antigen specificity. Furthermore, the antibody-display cells were tested for binding activity with Alexa647-labeled H1 and Alexa568-labeled H2 using a BD FACSAria III (BD Biosciences).

Antibody production

To obtain a large amount of secretory antibodies, PCR fragments from the antibody-expressing plasmid were cloned into the pcDNA3.4-mIgG1 or pcDNA3.4-kappa vectors. A mixture of 15 μg of pcDNA3.4-V-gene-mIgG1 vector and 15 μg of pcDNA3.4-V-gene-kappa vector were transfected into Expi293 cells using the ExpiFectamine 293 Transfection Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions, and cultured in Expi293 Expression Medium (Thermo Fisher Scientific) in a humidified 8% CO₂ incubator at 37°C and 125 rpm. Then, 5 days post-transfection, the culture supernatants were harvested, and all proteins were purified with PureSpeed IMAC resin (Mettler Toledo, Columbus, OH, USA), according to the manufacturer’s instructions.

Surface plasmon resonance

Kinetic analyses were performed at 25°C using a BIAcore 3000 machine (GE Healthcare Technologies). A2p1, B10p2, C10p2, E11p2, G6p2, A6p4, D4p4, D11p4, or G12p4 antibodies were immobilized on a CM5 sensor chip (GE Healthcare Technologies) with an amine-coupling kit according to the manufacturer’s instructions. HA probes were serially diluted at five different concentrations and injected at a flow rate of 30 µL/min for 3 min with a dissociation time of 7 min in HBS–EP buffer (10 mM HEPES, pH 7.4, 150 mM NaCl, 3.4 mM EDTA, and 0.005% Surfactant P20). The chip was regenerated using 10 mM glycine (pH 2.5) as an HA probe.

Data access

All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE140720.

Acknowledgements

We thank Mr. Atsuo Kobayashi, Ms. Chieko Okamura, Dr. Seok-Won Kim, Mr. Maxime Hebrard, Dr. Todd D Taylor, and the RIKEN IMS Genome Platform for their technical support, and Dr. Christopher Nicholas for critical reading and English editing of the manuscript. We would like to thank Editage (www.editage.jp) for English language editing.

Funding

This study was supported in part by research grants from the RIKEN Research Program ‘Single cell Project’ (O.O., T.W., T.K., and H.F.) and Grants-in-Aid for Scientific Research (S) [26221306 to T.K. and H.F.]. The funding sources were not involved in the study design, data collection and interpretation, or paper submission decisions.

Conflict of interest

None declared.

Author contributions

T.W. and H.F. designed the study, the main conceptual ideas, and the proof outline. H.H., Y.M., F.Y., T.H., and N.K. collected the data. O.O. and T.K. supervised the project. T.W. wrote the manuscript with support from H.F. All authors discussed the results and commented on the manuscript.

Supplementary Tables

Supplementary Table 1.

Supplementary Table 2.

Supplementary Figures

Supplementary Figure 1.

Supplementary Figure 2.

Supplementary Figure 3.

Supplementary Figure 4.