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Supplementary Figures S1-8. Figure S1 - Analysis of nonlinear blending synergy for the pairs of antibodies that constitute Pan-HER. Figure S2 - In vitro comparison of Pan-HER and a combination of cetuximab, trastuzumab and MM-121. Figure S3 - In vivo assessment of nonlinear blending synergy for the target specificities in the Pan-HER mixture. Figure S4 - Dose titration of Pan-HER in the BxPC3 xenograft model. Figure S5 - IHC analysis of Calu-3 tumors. Figure S6 - Assessment of cell death and cell cycle arrest. Figure S7 - Assessment of ADCC in a panel of cell lines. Figure S8 - Analysis of the effect of receptor internalization on effector functions.

Supplementary Methods. Description of methods used for assessment of synergy, immunohistochemistry, cell death, cell cycle arrest, ADCC and CDC.

Supplementary Tables S1-2. Table S1 - Source, origin, subtype and growth medium for each cell line. Table S2 - Characteristics of tested patient-derived xenograft models.

Purpose: Accumulating evidence indicates a high degree of plasticity and compensatory signaling within the human epidermal growth factor receptor (HER) family, leading to resistance upon therapeutic intervention with HER family members.Experimental Design/Results: We have generated Pan-HER, a mixture of six antibodies targeting each of the HER family members EGFR, HER2, and HER3 with synergistic pairs of antibodies, which simultaneously remove all three targets, thereby preventing compensatory tumor promoting mechanisms within the HER family. Pan-HER induces potent growth inhibition in a range of cancer cell lines and xenograft models, including cell lines with acquired resistance to therapeutic antibodies. Pan-HER is also highly efficacious in the presence of HER family ligands, indicating that it is capable of overcoming acquired resistance due to increased ligand production. All three target specificities contribute to the enhanced efficacy, demonstrating a distinct benefit of combined HER family targeting when compared with single-receptor targeting.Conclusions: Our data show that simultaneous targeting of three receptors provides broader efficacy than targeting a single receptor or any combination of two receptors in the HER family, especially in the presence of HER family ligands. Pan-HER represents a novel strategy to deal with primary and acquired resistance due to tumor heterogeneity and plasticity in terms of HER family dependency and as such may be a viable alternative in the clinic. Clin Cancer Res; 21(18); 4110–22. ©2015 AACR.See related commentary by Yarden and Sela, p. 4030

Therapeutic monoclonal antibodies (mAbs) are mainly produced by heterologous expression in Chinese hamster ovary (CHO) cells. The glycosylation profile of the mAbs has major impact on the efficacy and safety of the drug and is therefore an important parameter to control during production. In this study, the effect on IgG N-glycosylation from feeding CHO cells with eight glycosylation precursors during cultivation was investigated. The study was conducted in fed-batch mode in bioreactors with biological replicates to obtain highly controlled and comparable conditions. We assessed charge heterogeneity and glycosylation patterns of IgG. None of the eight feed additives caused statistically significant changes to cell growth or IgG productivity, compared to controls. However, the addition of 20 mM galactose did result in a reproducible increase of galactosylated IgG from 14% to 25%. On the other hand, addition of 20 mM N-acetyl-D-glucosamine (GlcNAc) reduced relative abundance of galactosylated IgG by 4%. Additionally, supplementation with 10 mM mannose slightly reduced GlcNAc occupancy of IgG. Overall, comparing the effects of IgG glycosylation, by supplementing the cell culture medium with glycosylation precursors during cultivation, revealed an application of these glycosylation precursors for modulating N-glycosylation of IgG.

Disease-specific alterations in proteins and peptides such as the appearance of new isoforms, changed relative concentrations of known isoforms, or changed catabolism characterize the group of protein precipitation disorders collectively known as amyloidoses. The goal of this study was to develop an approach for isolating and characterizing the pool of isoforms of a polypeptide of interest from biological fluids for use in development of diagnostic markers and elucidation of pathogenesis. For this purpose, we employed an on-line immunoaffinity-liquid chromatography-mass spectrometry (IA-LC-MS) modular approach using antibodies binding populations of protein isoforms. In this system, crude biological samples, e.g., serum, may be injected and subjected to fast hands-off analysis. The setup consists of an optional preclear column for removal of unspecific binding components, an immunoaffinity column, a short cartridgelike reversed-phase column, and an electrospray time-of-flight mass spectrometer. We have tested the system for the automated analysis of three amyloid-related polypeptides, serum amyloid P component, amyloid beta-peptide, and beta2-microglobulin, and we show the feasibility of detection of altered isoforms or determination of relative abundance of isoforms of the proteins from serum or cerebrospinal fluid samples. For each new protein investigated, the only change needed in the system is a new antibody or antibody mixture and the selection of a reversed-phase cartridge of appropriate hydrophobicity.

Synthetic peptides based on amino-acid residues 27-38 of human serum amyloid P component represent a novel type of heparin binders as they do not contain clusters of basic amino acids or other known features associated with protein or peptide heparin binding. Here, we characterize the binding using capillary electrophoresis (CE), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). By CE, heparin-binding activity was readily apparent for both a regular peptide and a slightly N-terminally modified form, while a sequence-scrambled peptide had no measurable binding. Dissociation constants in the 1-15 microm range were estimated, but only a minor part of the binding isotherm was covered by the experiments. SPR measurements using immobilized peptides verified heparin binding, the range of the binding constants, and the reduced binding of the sequence-scrambled peptide. Structurally defined heparin oligosaccharides were used to establish that while the tetrasaccharide is too small to exhibit strong binding, little difference in binding strength is observed between hexa- and tetradeca-saccharides. These experiments also confirmed the almost complete lack of activity of the sequence-scrambled peptide. The amino-acid sequence-dependent binding and the importance of a disulfide bond in the peptide were verified by ITC, but the experimental conditions had to be modified because of peptide precipitation and ITC yielded significantly weaker binding constants than the other methods. While the precise function of the peptide in the intact protein remains unclear, the results confirm the specificity of the glycosaminoglycan interaction with regard to peptide sequence by applying two additional biophysical techniques and showing that the N-terminal part of the peptide may be modified without changing the heparin binding capabilities.

The amyloidogenic protein beta-microglobulin was characterized by affinity capillary electrophoresis (CE). CE could separate conformational variants of beta2-microglobulin and with the amyloid-specific dye Congo red as a buffer additive it was possible to measure different Congo red-affinities of native and abnormally folded beta2-microglobulin. We find that native beta2-microglobulin has an intermediate affinity for Congo red at pH 7.3 and that binding involves electrostatic interactions. The conformational variant of beta2-microglobulin that appears in acetonitrile solutions binds Congo red more strongly. Affinity CE using Congo red as a buffer additive is a new, simple, fast, and quantitative micromethod for the characterization of soluble conformational intermediates of amyloidogenic proteins.

Tyrosine O-sulfation was first described about 50 years ago as a post-translational modification of fibrinogen. In the following 30 years it was considered to be a rare modification affecting only a few proteins and peptides. However, in the beginning of the 1980s tyrosine (Tyr) sulfation was shown to be a common modification and since then an increasing number of proteins have been identified as sulfated. The target proteins belong to the classes of secretory, plasma membrane, and lysosomal proteins, which reflects the intracellular localization of the enzymes catalyzing Tyr sulfation, the tyrosylprotein sulfotransferases (TPSTs).Traditionally, Tyr sulfation has been analyzed by incorporation of radiolabeled sulfate into target cells followed by purification of the target protein. Subsequently, the protein is degraded enzymatically or by alkaline hydrolysis followed by thin-layer electrophoresis to demonstrate the presence of radioactively labeled tyrosine. These techniques have been described in detail previously. The aim of this chapter is to present alternative analytical methods of Tyr sulfation than radioisotope incorporation before analysis.

Tyrosine O-sulfation was first described about 50 years ago as a post-translational modification of fibrinogen. In the following 30 years it was considered to be a rare modification affecting only a few proteins and peptides. However, in the beginning of the 1980s tyrosine (Tyr) sulfation was shown to be a common modification and since then an increasing number of proteins have been identified as sulfated. The target proteins belong to the classes of secretory, plasma membrane, and lysosomal proteins, which reflects the intracellular localization of the enzymes catalyzing Tyr sulfation, the tyrosylprotein sulfotransferases (TPSTs).Traditionally, Tyr sulfation has been analyzed by incorporation of radiolabeled sulfate into target cells followed by purification of the target protein. Subsequently, the protein is degraded enzymatically or by alkaline hydrolysis followed by thin-layer electrophoresis to demonstrate the presence of radioactively labeled tyrosine. These techniques have been described in detail previously. The aim of this chapter is to present alternative analytical methods of Tyr sulfation than radioisotope incorporation before analysis.

Tyrosine O-sulfation is a posttranslational modification of secretory and membrane proteins transported through the Golgi apparatus, which is widespread among higher eukaryotes. O-Sulfated tyrosines are not immediately identified during sequencing of peptides and proteins, because the sulfate ester is acid labile and rapidly hydrolyses to tyrosine in strong acidic solutions. Little is known about the hydrolysis at mildly acidic solutions, which are used during several protein purification and analysis procedures. We have examined the stability of tyrosine sulfate using sulfated gastrin-17, caerulein, and drosulfokinin as models for tyrosine O-sulfated peptides. The peptides were incubated in acidic solutions in a pH range of 1 to 3 at different temperatures and time spans. Only marginal hydrolysis of gastrin-17 was observed in triflouroacetic acid at room temperature or below. Comparison of the acid hydrolysis of the three peptides showed that hydrolysis rate depends mainly on the primary amino acid composition of the peptide. The activation energy (E(a)) for the hydrolysis of sulfated gastrin-17 was found to be E(a)=98.7+/-5 kJ mol(-1). This study serves as a general reference for handling tyrosine sulfated peptides in aqueous acidic solutions. We conclude that tyrosine sulfate is more stable under normal protein purification conditions than previously assumed.

Transthyretin (TTR) is a small serum protein that is involved in distinct phenotypes of amyloidosis with different tissue localization, age of onset, and rate of progression. Some types of TTR-amyloidosis (such as familial amyloid polyneuropathy) are associated with various amino acid point mutations, while cardiac amyloid myopathy may also be associated with precipitation of the wild-type molecules, e.g., in senile systemic amyloidosis. Because of the unsettled relationship between circulating and precipitated TTR we here explore on-line immunoaffinity (IA) chromatography-MS and immunoprecipitation (IP)-MS methods for characterizing the circulating TTR population in normal individuals and in patients with known TTR-amyloidosis. It was found necessary to reduce the samples, e.g., with DTT, prior to ESI-TOF-MS. This reversed oxidative modifications to sufficiently resolve the two mass peaks isolated from sera of heterozygous patients. A simple IP technique without the use of centrifugal filtration was found to be convenient for the assessment of the TTR population in serum as demonstrated for both normal and variant (the Met111Leu mutation) TTR. This approach also readily allowed the identification of oxidation, S-sulfation, and S-cysteinylation in unreduced samples, while these modifications were less well resolved in the on-line IA chromatography-MS approach.

Background: Patients on chronic hemodialysis are prone to develop amyloid deposits of misfolded β2-microglobulin (β2M) in osteoarticular tissues. β2M with various deletions/truncations and chemical modifications has been found together with structurally intact β2M in extracts of β2M amyloid fibrils. The state of the circulating population of β2M molecules has not been characterized previously with high-resolution methods.Methods: We used immunoaffinity–liquid chromatography–mass spectrometry analysis of serum samples to examine whether structurally modified β2M is generated in the circulation. In addition, we developed an immunoassay for the quantification of a cleaved β2M variant in biological fluids based on novel monoclonal antibodies and applied this assay to patient and control sera.Results: A specific alteration compatible with the generation of lysine-58–cleaved and truncated β2M (ΔK58-β2M) was found in the sera of many (20%–40%) dialysis patients but not in control sera or sera from patients with cerebral amyloidosis (Alzheimer disease). Applied to patient sera, specific immunoassays revealed that dialysis, as expected, significantly lowered the total β2M concentration, but the concentrations of ΔK58-β2M remained unchanged after dialysis. The results also show that patients dialyzed with less biocompatible membranes have higher serum concentrations of cleaved β2M (mean, 8.5, 1.8, and 0.7 mg/L in cuprophane membrane-dialyzed, polysulfone membrane-dialyzed, and control sera, respectively).Conclusions: This study for the first time demonstrates and assigns the structure of a specific β2M variant in sera from dialysis patients. Because this variant is conformationally unstable in vitro, it may be involved in in vivo amyloidogenesis.

Aggregation and fibrillation of beta(2)-microglobulin are hallmarks of dialysis-related amyloidosis. We characterize perturbations of the native conformation of beta(2)-microglobulin that may precede fibril formation. For a beta(2)-microglobulin variant cleaved at lysine 58, we show using capillary electrophoresis that two conformers spontaneously exist in aqueous buffers at neutral pH. Upon treatment of wild-type beta(2)-microglobulin with acetonitrile or trifluoroethanol, two conformations were also observed. These conformations were in equilibrium dependent on the sample temperature and the percentage of organic solvent present. Circular dichroism showed a loss of beta-structures and gain of alpha-helices. Reversal to the native conformation occurred when removing the organics. Affinity capillary electrophoresis experiments showed increased specific interactions of the nonnative beta(2)-microglobulin conformation with the dyes 8-anilino-1-naphthalene sulfonic acid and Congo red. The observations may relate to early folding events prior to amyloid fibrillation and facilitate the development of methods to detect and inhibit pro-amyloid protein and peptide conformations.