Cysteine-SILAC Mass Spectrometry Enabling the Identification and Quantitation of Scrambled Interchain Disulfide Bonds: Preservation of Native Heavy-Light Chain Pairing in Bispecific IgGs Generated by Controlled Fab-arm Exchange

Bispecific antibodies (bsAbs) are one of the most versatile and promising pharmaceutical innovations for countering heterogeneous and refractory disease by virtue of their ability to bind two distinct antigens. One critical quality attribute of bsAb formation requiring investigation is the potential randomization of cognate heavy (H) chain/light (L) chain pairing, which could occur to a varying extent dependent on bsAb format and the production platform. To assess the content of such HL-chain swapped reaction products with high sensitivity, we developed cysteine-stable isotope labeling using amino acids in cell culture (SILAC), a method that facilitates the detailed characterization of disulfide-bridged peptides by mass spectrometry. For this analysis, an antibody was metabolically labeled with ¹³C₃,¹⁵N-cysteine and incorporated into a comprehensive panel of distinct bispecific molecules by controlled Fab-arm exchange (DuoBody technology). This technology is a postproduction method for the generation of bispecific therapeutic IgGs of which several have progressed into the clinic. Herein, two parental antibodies, each containing a single heavy chain domain mutation, are mixed and subjected to controlled reducing conditions during which they exchange heavy–light (HL) chain pairs to form bsAbs. Subsequently, reductant is removed and all disulfide bridges are reoxidized to reform covalent inter- and intrachain bonds. We conducted a multilevel (Top-Middle-Bottom-Up) approach focusing on the characterization of both “left-arm” and “right-arm” HL interchain disulfide peptides and observed that native HL pairing was preserved in the whole panel of bsAbs produced by controlled Fab-arm exchange

Biophysical characterization of antibody hexamerization in solution.

<p>(A) Native MS analysis of solutions of IgG1-005 and mutant antibodies at 2 μM. IgG1-005-RGY (RGY), a previously described triple mutant, is used as a positive control. The charge envelope of the IgG monomers appears around <i>m/z</i> 5,500 (~ 147 kD Mw) and that of the IgG hexamers around <i>m/z</i> 12,500 (~890 kD Mw). The signals of the hexameric species are displayed at a 100-fold or 10-fold (RGY only) amplification. (B–C) Dynamic light scattering analysis of 7D8 and mutant solutions formulated in PBS pH 7.4. Three independent experiments are shown. (B) Linear regression of diffusion coefficient versus Ab concentration. (C) Hydrodynamic radii (Rhs) of mutants measured by dynamic light scattering (DLS) were divided by Rh of wild-type 7D8 to correct for viscosity without masking the contribution of Fc:Fc self-association. (D) HP-SEC analysis of 100 mg/mL 7D8 and mutant antibody solutions formulated in PBS, incubated for three months at 5°C. Multimer detection limit of 1% is indicated by a dashed line.</p

E345 and E430 limit Fc:Fc interactions.

<p>(A) Left: overview of the IgG1 antibody hexamer observed in the IgG1-b12 crystal structure (PDB access code 1HZH [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002344#pbio.1002344.ref020" target="_blank">20</a>]). Right: zoomed-in view of two neighboring Fc domains with enhancing amino acid positions highlighted. (B) Summary of CDC inhibition data. The surface view is rotated 90° relative to panel A to show the Fc:Fc interface. Daudi cells were opsonized with mutants of anti-CD38 mAb IgG1-005 (1.0 μg/mL) and assessed for CDC. Light and dark grey colors indicate the unmodified amino acids of the two heavy chain regions composing a single Fc domain. All mutants assessed were ranked by efficiency per amino acid position, and the resulting median lysis efficacy is indicated by coloring per position; orange and red colors indicate positions with reduced lysis. Blue: >60% lysis; orange: 30%–60% lysis; red: <30% lysis. (C) Summary of CDC enhancement data. Wien 133 cells were opsonized with mutants of anti-CD38 mAb IgG1-005 (1.0 μg/mL) and assessed for CDC. Light and dark grey colors indicate unmodified amino acids as described under (B). The maximal lysis of the most efficient mutant per amino acid position is displayed with green indicating positions for which CDC was enhanced. Blue: <20% lysis; light green: 20%–40% lysis; dark green: >40% lysis. (D) Dose response in CDC of Wien 133 cells by IgG1-005 and selected mutants. A representative of 3 replicate experiments is shown. (E) Dose response in CDC of Ramos cells induced by RTX and selected mutants. A representative experiment of 3 replicates is shown. (F) Structural view zoomed to residue E345. Amino acids facing E345 at the Fc:Fc interface are indicated in blue and named with apostrophe. (G) Structural view zoomed to residue E430, forming a salt bridge with K338 at the intramolecular C_H2–C_H3 domain interface.</p

Promoting Fc:Fc interactions alleviates CDC sensitivity to target and mCRP expression.

<p>(A) Cell lines were opsonized with saturating amounts of wild-type or mutated RTX and analyzed by CDC assay. Left panel: cell lines with increasing CD20:mCRP ratio (left to right); right panel: cell lines with decreasing CD20:mCRP ratio (left to right). (B) In vivo analysis of subcutaneous tumor growth in a severe combined immunodeficiency (SCID) xenograft model. SCID mice were injected with luciferase-expressing Raji cells. Eight days after tumor cell injection, mice were randomized at an average tumor volume of 85 mm³ per group and treated with 50 μg IgG1 antibody. Tumor volumes were monitored over time and depicted as average tumor volume ± standard error of the mean (SEM) (left panel), and as Kaplan-Meier curves with time to progression cutoff set at a tumor volume of >700 mm³ (right panel).</p

CDC enhancement by promoting Fc:Fc interactions is broadly applicable.

<p>A representative example of three replicates is shown. Each graph compares CDC in dose response for the wild-type and E345R-mutated mAb. (A) CDC of Wien 133 (left) and Daudi cells (right) opsonized with anti-CD20 mAbs RTX and 11B8. (B) CDC of Wien 133 (left) and Raji cells (right) opsonized with anti-CD52 mAb ALM. (C) CDC of Wien 133 cells (left) and Daudi cells (right) opsonized with anti-CD38 mAbs IgG1-003 and IgG1-005. (D) CDC assay of A431 cells opsonized with anti-EGFR mAb 2F8.</p

Specific IgG mutations retain fluid phase complement suppression and regular pharmacokinetics.

<p>(A) C4d ELISA of IgG1-005 mutants detecting solution-phase complement activation in serum. The background (BKG) C4d level in serum is indicated with a dashed line. Results were averaged over three experiments. (B) PK analysis of IgG1-005 mutants in SCID mice, using three mice per group. Clearance of a single 500 μg dose of mAb was monitored for three weeks and is expressed as 1,000 * Dose / area under the curve (AUC); dashed line: clearance of wild-type IgG1-005.</p

Efficient lysis of CLL patient tumor cells.

<p>Peripheral B cells isolated from the blood of six CLL patients were opsonized with wild-type or mutant, 7D8, RTX or control (IgG1-b12) antibody and tested in CDC assays. The CLL cells of patient 4 were highly refractory to CDC due to their very low CD20 expression.</p