Development of a new genotype–phenotype linked antibody screening system

  1. Takashi Watanabe  Is a corresponding author
  2. Hikaru Hata
  3. Yoshiki Mochizuki
  4. Fumie Yokoyama
  5. Tomoko Hasegawa
  6. Naveen Kumar
  7. Tomohiro Kurosaki
  8. Osamu Ohara
  9. Hidehiro Fukuyama
  1. Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Japan
  2. Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Japan
  3. Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences, Japan
  4. Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Japan
  5. Department of Applied Genomics, Kazusa DNA Research Institute, Japan
  6. Division of Immunology, Near-InfraRed Photo-Immunotherapy Research Institute, Kansai Medical University, Japan
  7. INSERM EST, France
3 figures, 2 tables and 2 additional files

Figures

Figure 1 with 3 supplements
System to link the antigen-binding feature with the Ig repertoire genetic information.

(A) Single cell-sorted B cells were subjected to two processes: Ig-seq database building and Ig-expressing transformant library preparation. Antigen-binding Ig transformants were collected by …

Figure 1—figure supplement 1
The Ig repertoires are visualized using the in-house software.

Overview of heavy (V–D–J) and light (V–J) chain usages (A), and the repertoire clonality (B) is shown. (C) The mutation rates and their positions of heavy chains in three cell populations (PR8+, …

Figure 1—figure supplement 2
Progression flowchart.

The process for efficiently isolating influenza cross-reactive antibodies from mouse germinal center B cells with high affinity is shown. Experiment outcome flow numbers of clones in each step are …

Figure 1—figure supplement 3
Sorting strategy.

CD43 MACS B cells from the spleen purified using negatively charged beads were sorted for IgG1 + cells and then separated into H2 and PR8. The majority of cross-reactive IgG1 + cells (red box) were …

Figure 2 with 3 supplements
Isolation of H2 and H1-reactive B cells.

(A) Mixture of Ig-expressing transformant libraries stained with HA probes. (B) Three strong HA-binding populations, H1+H2+ (cross), H2+ (H2), and H1+ (H1), were sorted and collected in a bulk …

Figure 2—figure supplement 1
SPR profiles of kinetics analysis of nine clones, A6p4, B10p2, C10p2, A2p1, D11p4, E11p2, G6p2, D4p4, and G12p4 using a BIAcore 3000 machine (GE Healthcare).
Figure 2—figure supplement 2
Two hundred and eighty-four clones are plotted in a two-dimensional map of phylogeny trees for heavy and light chain genes.

Nine mAb clones are overlaid in green. Six ‘cross’ clones are located in a major cluster. B10p2 and C10p2 are co-localized and distant from the cluster. A6p4 is uniquely located in the map.

Figure 2—figure supplement 3
The affinity of antigen-antibody binding (in this case, probe and membrane-bound antibody expressing cell) can be inferred from the population shift (flow cytometry analysis).
Competition assay of ‘cross’ Ig-transformants using C179, a broadly-reactive mAb binding to the Stem region of HA, and NSP2 (Narita strain-specific mAb), a strain-specific mAb that binds to the head region of HA.

On the right panel, two stem-reactive clones (see Table 1) were examined reciprocally with combination of transformant and recombinant antibodies.

Tables

Table 1
Affinities (Kd) of the antibodies to six HA antigens from strains A/Okuda/1957(H2N2), termed H2, A/Puerto Rico/8/1934(H1N1), termed PR8, A/California/2009 (X-179A) [H1N1] Pdm09, termed Cal, A/Texas/50/2012 (X-223) [H3N2], termed H3, A/Egypt/N03072/2010(H5N1), termed H5, and A/Brisbane/59/2007 (H1N1), termed Stem, were determined using surface plasmon resonance analysis.

H2, PR8, Cal, and H5 belong to group 1, and H3 belongs to group 2. High (red), Middle (orange), and Low (blue).

Group111211
H2PR8CalH3H5Stem
A6p44.51E-081.41E-061.14E-052.91E-051.59E-08
B10p26.75E-092.3E-093.29E-09
C10p21.66E-091.29E-095.66E-104.26E-08
A2p12.49E-061.42E-071.14E-051.25E-041.91E-05
D11p47.93E-071.72E-061.04E-061.36E-051.05E-11*
E11p24.4E-081.86E-081.67E-062.92E-072.37E-07
G6p23.51E-083.53E-081.44E-081.78E-053.05E-08
D4p41.1E-051.78E-056.4E-054.38E-052.47E-05
G12p41.45E-071.52E-075.7E-079.44E-071.58E-07
  1. Surface plasmon resonance (Biacore) KD (M).

  2. *

    The affinity of D11p4 for H5 was low and inaccurate (Figure 2—figure supplement 1).

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Gene (Aequorea coerulescens)venusRIKEN BRC; Nagai et al., 2002
Strain, strain background (Escherichia coli)DH5αThermo Fisher ScientificEC0112competent cells
Genetic reagent (F’ Episome)ccdBThermo Fisher ScientificV79020pcDNA3.1 (+) Mammalian Expression Vector
Cell line (Homo sapiens)FreeStyle 293Thermo Fisher ScientificR79007
Transfected construct (M. musculus)Antibody expression vectorThis paperPlasmid construct to transfect and express the antibody.
Biological sample (M. musculus)Mouse splenocytesThis paperCLEA Japan, Inc.
AntibodyAnti-CD43 MicroBeads (Mouse monoclonal)Miltenyi Biotec, Inc.130-049-801Add 10 μL of Anti-CD43 (Ly-48) MicroBeads (mouse) per 10⁷ total cells (1:1000 dilution)
Recombinant DNA reagentpcDNA3.4-mIgG1 (plasmid)This paperTo obtain a large amount of secretory antibodies
Recombinant DNA reagentpcDNA3.4-kappa (plasmid)This paperTo obtain a large amount of secretory antibodies
Sequence-based reagentBsaI_IL6sp_LThis paperPCR primersCTAGGGTCTCAAGCAGATGAACTCCTTCTCCACAAGCG
Sequence-based reagentmC_G_new2_BsaIThis paperPCR primersTCCTAGGTCTCCCACACACAGGGGCCAGTGGATAGAC
Peptide, recombinant proteinAnti-HA antibodiesThis paperNine cross reactive antibodies
Commercial assay or kitBsaI-HFv2New England BiolabsNEB #R3733
Commercial assay or kitT4 DNA ligaseNew England BiolabsM0202T
Chemical compound, drugAddaVaxInvivoGenvac-adx-10adjuvant
Software, algorithmBONSCIin-house softwareIg database construction and visualization of the Ig repertoire
OtherCM5 sensor chipGE Healthcare TechnologiesBR1005303 sensor chips

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