Antibody engineering for therapeutics

Antibody-Drug Conjugates: A promising breakthrough in cancer therapy

Antibody-drug conjugates (ADCs) provide effective cancer treatment through the selective delivery of cytotoxic payloads to the cancer cells. They offer unparalleled precision and specificity in directing drugs to cancer cells while minimizing off-target effects. Despite several advantages, there is a requirement for innovations in the molecular design of ADC owing to drug resistance, cancer heterogeneity along the adverse effects of treatment. The review critically analyses ADC function mechanisms, unraveling the intricate interplay between antibodies, linkers, and payloads in facilitating targeted drug delivery to cancer cells. The article also highlights notable advancements in antibody engineering, which aid in creating highly selective and potent ADCs. Additionally, the review details significant progress in clinical ADC development with an in-depth examination of pivotal trials and approved formulations. Antibody Drug Conjugates (ADCs) are a ground-breaking approach to targeted drug delivery, especially in cancer treatment. They offer unparalleled precision and specificity in directing drugs to cancer cells while minimizing off-target effects. This review provides a comprehensive examination of the current state of ADC development, covering their design, mechanisms of action, and clinical applications. The article emphasizes the need for greater precision in drug delivery and explains why ADCs are necessary.

Nanobody assemblies with fully flexible topology enabled by genetically encoded tetrazine amino acids

Assembling nanobodies (Nbs) into polyvalent multimers is a powerful strategy for improving the effectiveness of Nb-based therapeutics and biotechnological tools. However, generally effective approaches to Nb assembly are currently restricted to the amino or carboxyl termini, greatly limiting the diversity of Nb multimer topologies that can be produced. Here, we show that reactive tetrazine groups-site-specifically inserted by genetic code expansion at Nb surface sites-are compatible with Nb folding and function, enabling Nb assembly at any desired point. Using two anti-SARS-CoV-2 Nbs with viral neutralization ability, we created Nb homo- and heterodimers with improved properties compared with conventionally linked Nb homodimers, which, in the case of our tetrazine-conjugated trimer, translated into enhanced viral neutralization. Thus, this tetrazine-based approach is a generally applicable strategy that greatly increases the accessible range of Nb assembly topologies, and thereby adds the optimization of topology as an effective avenue to generate Nb assemblies with improved efficacy.

Identifying the Immunological Gene Signatures of Immune Cell Subtypes

The immune system is a complicated defensive system that comprises multiple functional cells and molecules acting against endogenous and exogenous pathogenic factors. Identifying immune cell subtypes and recognizing their unique immunological functions are difficult because of the complicated cellular components and immunological functions of the immune system. With the development of transcriptomics and high-throughput sequencing, the gene expression profiling of immune cells can provide a new strategy to explore the immune cell subtyping. On the basis of the new profiling data of mouse immune cell gene expression from the Immunological Genome Project (ImmGen), a novel computational pipeline was applied to identify different immune cell subtypes, including αβ T cells, B cells, γδ T cells, and innate lymphocytes. First, the profiling data was analyzed by a powerful feature selection method, Monte-Carlo Feature Selection, resulting in a feature list and some informative features. For the list, the two-stage incremental feature selection method, incorporating random forest as the classification algorithm, was applied to extract essential gene signatures and build an efficient classifier. On the other hand, a rule learning scheme was applied on the informative features to construct quantitative expression rules. A group of gene signatures was found as qualitatively related to the biological processes of four immune cell subtypes. The quantitative expression rules can efficiently cluster immune cells. This work provides a novel computational tool for immune cell quantitative subtyping and biomarker recognition.

Trends in therapeutic antibody affinity maturation: From in-vitro towards next-generation sequencing approaches

Current advances in antibody engineering driving the strongest growth area in biotherapeutic agents development. Affinity improvement that is mainly important for biological activity and clinical efficacy of therapeutic antibodies, has still remained a challenging task. In the human body, during a course of immune response affinity maturation increase antibody activity by several rounds of somatic hypermutation and clonal selection in the germinal center. The final outputs are antibodies representing higher affinity and specificity against a particular antigen. In the realm of biotechnology, exploring of mutations which improve antibody affinity while preserving its specificity and stability is an extremely time-consuming and laborious process. Recent advances in computational algorithms and DNA sequencing technologies help researchers to redesign antibody structure to achieve desired properties such as improved binding affinity. In this review, we briefly described the principle of affinity maturation and different corresponding in vitro techniques. Also, we recapitulated the most recent advancements in the field of antibody affinity maturation including computational approaches and next-generation sequencing (NGS).

Novel recombinant immunotoxin of EGFR specific nanobody fused with cucurmosin, construction and antitumor efficiency in vitro

Epidermal growth factor receptor (EGFR) overexpression is related to the increased aggressiveness, metastases, and poor prognosis in various cancers. In this study, we successfully constructed a new EGFR nanobody-based immunotoxin rE/CUS containing cucurmosin (CUS), The immunotoxin was expressed by prokaryotic system and we obtained a yield of 5 mg protein per liter expression medium. The percentage of it's binding ability totumor cell lines A549, HepG2, SW116, which highly expressed EGFR was 55.6%, 79.6% and 97.1%, respectively, but SW620 was only 4.45%. rE/CUS has the ability to bind A549, HepG2, SW116 cells specifically, and the antigen binding capability was not affected because of extra part of CUS component. The rE/CUS significantly inhibited the cell viability against EGFR over expression tumor cell lines in a dose-and time-dependent manner. Moreover, rE/CUS also induced apoptosis of HepG2 and A549 mightily. Our results demonstrate that rE/CUS is a potential therapeutic strategy for treating EGFR-positive solid tumors.

Chimeric Small Antibody Fragments as Strategy to Deliver Therapeutic Payloads

Antibody-drug conjugates (ADCs) represent an innovative class of biopharmaceuticals, which aim at achieving a site-specific delivery of cytotoxic agents to the target cell. The use of ADCs represents a promising strategy to overcome the disadvantages of conventional pharmacotherapy of cancer or neurological diseases, based on cytotoxic or immunomodulatory agents. ADCs consist of monoclonal antibodies attached to biologically active drugs by means of cleavable chemical linkers. Advances in technologies for the coupling of antibodies to cytotoxic drugs promise to deliver greater control of drug pharmacokinetic properties and to significantly improve pharmacodelivery applications, minimizing exposure of healthy tissue. The clinical success of brentuximab vedotin and trastuzumab emtansine has led to an extensive expansion of the clinical ADC pipeline. Although the concept of an ADC seems simple, designing a successful ADC is complex and requires careful selection of the receptor antigen, antibody, linker, and payload. In this review, we explore insights in the antibody and antigen requirements needed for optimal payload delivery and support the development of novel and improved ADCs for the treatment of cancer and neurological diseases.

In vitro and in vivo anti-tumor activities of anti-EGFR single-chain variable fragment fused with recombinant gelonin toxin

PURPOSE

Epidermal growth factor receptor (EGFR) plays an important role in the growth and metastasis of many solid tumors. Strategies that target EGFR hold promising therapeutic potential for the treatment for non-small cell lung cancer (NSCLC), as EGFR is normally overexpressed in these tumors. This study was designed to determine whether an anti-EGFR immunotoxin has anti-tumor activity against NSCLC, and if so, to further investigate the possible mechanisms of cytotoxicity.

METHODS

A fusion protein of anti-EGFR single-chain variable fragment (anti-EGFR scFv) and the plant toxin gelonin (rGel) was constructed, expressed in bacteria, and purified to homogeneity. Cytotoxicity of anti-EGFR scFv/rGel (E/rG) immunotoxin was assessed on A549, HCC827, and H1975 cells (EGFR-overexpressing NSCLC-derived cell lines) and A549 xenografts in nude mice.

RESULTS

Cytotoxicity experiments using E/rG on A549, HCC827, and H1975 cells demonstrated that E/rG can specifically inhibit proliferation of these cells, whereas it did not affect the proliferation of Raji cells that do not express EGFR. Treatment for A549 xenografts in nude mice with E/rG resulted in significant suppression of tumor growth compared to controls. Immunofluorescence in frozen tissue sections confirmed that E/rG could specifically bind to tumor tissues in nude mice bearing A549 tumor xenografts, while rGel alone showed no binding activity. Furthermore, E/rG inhibited the growth of A549 cells by cytotoxic effects that blocked tumor proliferation, and the immunotoxin-induced cell death may be mediated by autophagy.

CONCLUSIONS

These results showed that E/rG might have significant potential as a novel clinical therapeutic agent against human NSCLC.

Bridging the gap: facilities and technologies for development of early stage therapeutic mAb candidates

Therapeutic monoclonal antibodies (mAbs) currently dominate the biologics marketplace. Development of a new therapeutic mAb candidate is a complex, multistep process and early stages of development typically begin in an academic research environment. Recently, a number of facilities and initiatives have been launched to aid researchers along this difficult path and facilitate progression of the next mAb blockbuster. Complementing this, there has been a renewed interest from the pharmaceutical industry to reconnect with academia in order to boost dwindling pipelines and encourage innovation. In this review, we examine the steps required to take a therapeutic mAb from discovery through early stage preclinical development and toward becoming a feasible clinical candidate. Discussion of the technologies used for mAb discovery, production in mammalian cells and innovations in single-use bioprocessing is included. We also examine regulatory requirements for product quality and characterization that should be considered at the earliest stages of mAb development. We provide details on the facilities available to help researchers and small-biotech build value into early stage product development, and include examples from within our own facility of how technologies are utilized and an analysis of our client base.

Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies

Background

All polypeptide backbones have the potential to form amyloid fibrils, which are associated with a number of degenerative disorders. However, the likelihood that amyloidosis would actually occur under physiological conditions depends largely on the amino acid composition of a protein. We explore using a naive Bayesian classifier and a weighted decision tree for predicting the amyloidogenicity of immunoglobulin sequences.

Results

The average accuracy based on leave-one-out (LOO) cross validation of a Bayesian classifier generated from 143 amyloidogenic sequences is 60.84%. This is consistent with the average accuracy of 61.15% for a holdout test set comprised of 103 AM and 28 non-amyloidogenic sequences. The LOO cross validation accuracy increases to 81.08% when the training set is augmented by the holdout test set. In comparison, the average classification accuracy for the holdout test set obtained using a decision tree is 78.64%. Non-amyloidogenic sequences are predicted with average LOO cross validation accuracies between 74.05% and 77.24% using the Bayesian classifier, depending on the training set size. The accuracy for the holdout test set was 89%. For the decision tree, the non-amyloidogenic prediction accuracy is 75.00%.

Conclusions

This exploratory study indicates that both classification methods may be promising in providing straightforward predictions on the amyloidogenicity of a sequence. Nevertheless, the number of available sequences that satisfy the premises of this study are limited, and are consequently smaller than the ideal training set size. Increasing the size of the training set clearly increases the accuracy, and the expansion of the training set to include not only more derivatives, but more alignments, would make the method more sound. The accuracy of the classifiers may also be improved when additional factors, such as structural and physico-chemical data, are considered. The development of this type of classifier has significant applications in evaluating engineered antibodies, and may be adapted for evaluating engineered proteins in general.

Application of the Fc fusion format to generate tag-free bi-specific diabodies

We previously reported the use of a humanized bi-specific diabody that targets epidermal growth factor receptor and CD3 (hEx3-Db) for cancer immunotherapy. Bacterial expression can be used to express small recombinant antibodies on a large scale; however, their overexpression often results in the formation of insoluble aggregates, and in most cases artificial affinity peptide tags need to be fused to the antibodies for purification by affinity chromatography. Here, we propose a novel method for preparing refined, functional, tag-free bi-specific diabodies from IgG-like bi-specific antibodies (BsAbs) in a mammalian expression system. We created an IgG-like BsAb in which bi-specific diabodies were fused to the human Fc region via a designed human rhinovirus 3C (HRV3C) protease recognition site. The BsAb was purified by protein A affinity chromatography, and the refined tag-free hEx3-Db was efficiently produced from the Fc fusion format by protease digestion. The tag-free hEx3-Db from the Fc fusion format showed a greater inhibition of cancer growth than affinity-tagged hEx3-Db prepared directly from Chinese hamster ovary cells. We also applied our novel method to another small recombinant antibody fragment, hEx3 single-chain diabody (hEx3-scDb), and demonstrated the versatility and advantages of our proposed method compared with papain digestion of hEx3-scDb. This approach may be used for industrial-scale production of functional tag-free small therapeutic antibodies.

The construction and expression of a novel chimeric anti-DR5 antibody

Human tumor necrosis factor related apoptosis inducing ligand (TRAIL) could selectively induce apoptosis in a variety of transformed cells and is currently being developed as a cancer therapeutic drug. Unfortunately it has been reported that some forms of TRAIL could cause damage to normal liver cells. In order to avoid this side effect, many groups are now developing agonistic monoclonal antibody (MAb) against DR5. Previously, we developed a MAb (mDRA6) against DR5 with apoptosis inducing ability. The application of mouse origin antibody is limited in clinical use because it can induce human anti-mouse antibody (HAMA) responses that can cause allergic reaction and damage in the human body. Therefore, the variable region genes of this MAb were cloned and ligated into chimeric antibody expression vector (pCMV-VH and pCMV-VL), generating chimeric anti-human DR5 MAb (cmDRA6) expression vectors. The two plasmids were introduced into 293T cells with Lipofectamine 2000. The cell culture supernatant was collected and the expression level of cmDRA6 was detected with standard ELISA method. The chimeric mDRA6 could bind to its target antigen as demonstrated by the results of both ELISA and Western blot. This study of mDRA6 has laid the solid foundation for further application research in the future.

Advances in Radioimmunotherapy in the Age of Molecular Engineering and Pretargeting

Now that radioimmunotherapy is an approved method for the treatment of certain types of non-Hodgkin's lymphoma, investigators are turning to new approaches to further improve radionuclide targeting in hopes of expanding the use of this technology. A number of innovative recombinant proteins have been developed with more favorable pharmacokinetic and targeting properties than standard whole IgG, which conceivably could improve the therapeutic index for cancer treatment. Pretargeting methods also are coming of age, with preclinical and early clinical studies in a variety of cancers illustrating how this alternative approach can enhance the therapeutic window several-fold of what has been possible with directly radiolabeled IgG. This review will discuss some of these promising new developments.

Specificity tuning of antibody fragments to neutralize two human chemokines with a single agent

Chemokines are important mediators of the immune response that are responsible for the trafficking of immune cells between lymphoid organs and migration towards sites of inflammation.Using phage display selection and a functional screening approach, we have isolated a panel of single-chain fragment variable (scFv) capable of neutralizing the activity of the human chemokine CXCL10 (hCXCL10). One of the isolated scFv was weakly cross-reactive against another human chemokine CXCL9,but was unable to block its biological activity. We diversified the complementarity determining region 3 (CDR3) of the light chain variable domain (VL) of this scFv and combined phage display with high throughput antibody array screening to identify variants capable of neutralizing both chemokines. Using this approach it is therefore possible to engineer pan-specific antibodies that could prove very useful to antagonize redundant signaling pathways such as the chemokine signaling network.

Generation and validation of affinity reagents on a proteome-wide level

There is a need for protein-specific affinity reagents to explore the gene products encoded by the genome. Recently, systematic efforts to generate validated affinity reagents on a whole human proteome level have been initiated. There are several issues for such efforts, including choice of antigen, type of affinity reagent, and the subsequent validation of the generated protein-specific binders. The advantages and disadvantages with the different approaches are discussed and the problems related to quality assessment of antibodies to be used in multi-platform applications are addressed. This review also describes the efforts to create a virtual resource of validated antibodies using a community-based portal and summarizes the status and visions for the publicly available human protein atlas (http://www.proteinatlas.org) showing the human protein profiles in a large number of normal and cancer tissues as well as a large set of human cell lines.

Homology modelling and bivalent single-chain Fv construction of anti-HepG2 single-chain immunoglobulin Fv fragments from a phage display library

We prepared single-chain immunoglobulin Fv fragments (scFv) SLH10 specific for the HepG2 cell line after biopanning from a large human-naive phage display library (Griffin. 1 Library). The three-dimensional (3D) structure of SLH10 was modelled by the Insight II molecule simulation software.The structure was refined using the molecular dynamics method.The structures with the least steric clashes and lowest energy were determined finally. The optimized structures of heavy (VH) and light (VL) variable chains of SLH10 scFv were obtained.Then SLH10 bivalent single-chain Fv (BsFv) was constructed that would be suitable for high-affinity targeting.SLH10 BsFv was generated by linking scFvs together and identified by sequencing. Its expression products were confirmed by western blot analysis.The relative molecular masses of scFv and BsFv were approximately 30 kDa and 60 kDa,respectively. Flow cytometry revealed that SLH10 BsFv bound the selected cell lines with greater signal intensity than the parental scFv. The improved antigen binding of SLH10 BsFv may be useful for immunodiagnostics or targeted gene therapy for liver cancer.

Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains

Diversity in antibody structure is crucial to the ability of the adaptive immune system to recognize the tremendously diverse set of potential antigens. The diversity in structure is most apparent in the six hypervariable loops of the complementarity-determining regions. However, given that these loops occur at the interface of the heavy- and light-chain variable domains and form the antigen-binding site, the relative orientation of the heavy- and light-chain variable domains can create another source of structural diversity leading to changes in antigen binding. Here, we first reexamine the diversity of V(L):V(H) orientations in existing antibody crystal structures using 153 nonredundant sequences, demonstrating that the variation in V(L):V(H) orientation is greater than that expected from effects of crystal packing, antigen binding, or the presence of antibody constant regions and increases, on average, as sequence similarity decreases for residues in the interface between the domains. We developed a tool for predicting the relative orientations of the heavy- and light-chain variable domains using side-chain rotamer sampling in the interface and molecular-mechanics-based energy calculations. When using variable domain backbones from the crystal structures, the predicted orientation is very close (<1 A RMSD) to the crystallographically observed orientation in most cases, confirming that the V(L):V(H) orientation is determined by the antibody sequence and suggesting an approach to predicting the relative orientation of the variable domains when building homology models of antibodies. When applied to antibody homology models generated from templates with 55-75% sequence identity, we predict the V(L):V(H) orientation of 20 antibodies with an average/median RMSD of 2.1/1.6 A to the crystal structures.

Multisensory enhancement in the optic tectum of the barn owl: spike count and spike timing

Temporal and spatial correlations between auditory and visual stimuli facilitate the perception of unitary events and improve behavioral responses. However, it is not clear how combined visual and auditory information is processed in single neurons. Here we studied responses of multisensory neurons in the barn owl's optic tectum (the avian homologue of the superior colliculus) to visual, auditory, and bimodal stimuli. We specifically focused on responses to sequences of repeated stimuli. We first report that bimodal stimulation tends to elicit more spikes than in the responses to its unimodal components (a phenomenon known as multisensory enhancement). However, this tendency was found to be history-dependent; multisensory enhancement was mostly apparent in the first stimulus of the sequence and to a much lesser extent in the subsequent stimuli. Next, a vector-strength analysis was applied to quantify the phase locking of the responses to the stimuli. We report that in a substantial number of multisensory neurons responses to sequences of bimodal stimuli elicited spike trains that were better phase locked to the stimulus than spike trains elicited by stimulating with the unimodal counterparts (visual or auditory). We conclude that multisensory enhancement can be manifested in better phase locking to the stimulus as well as in more spikes.

Rapid screening platform for stabilization of scFvs in Escherichia coli

The poor biophysical properties of antibody fragments such as scFvs and diabodies can preclude their use as therapeutic agents. The non-ideal biophysical properties and insufficient thermal stability of antibody fragments often leads to poor expression, poor solubility, and a predisposition of the proteins to aggregate. We have developed a general platform for engineering stability into antibody fragments. By promoting Escherichia coli cultures to secrete scFvs directly into growth media, automated screening methods can be applied to empirically evaluate multiple stability design strategies including rational, sequence-based, and structure-based designs. Once stabilized, these antibody fragments demonstrate improved expression and durability during purification, handling, and storage. Stabilized antibody fragments can also be used as building blocks for multivalent or bispecific antibody-like molecules.

Understanding structural/functional properties of immunoconjugates for cancer therapy by computational approaches

Monoclonal antibodies coupled to highly toxic molecules (immunoconjugates) are currently being developed for cancer therapy. We have used an in silico procedure for evaluating some physicochemical properties of two tumor-targeting anti-HER2 immunoconjugates: (a) the single-chain antibody scFv(FRP5) linked to a bacterial toxin, that has been recently progressed to phase I clinical trial in human cancer; (b) the putative molecule formed by the intrinsically stable scFv(800E6), which has been proposed as toxin carrier to cancer cells in human therapy, joined to the same toxin of (a). Structural models of the immunoconjugates have been built by homology modeling and assessed by molecular dynamics simulations. The trajectories have been analyzed to extract some biochemical properties and to assess the potential effects of the toxin on the structure and dynamics of the anti-HER2 antibodies. The results of the computational approach indicate that the antibodies maintain their correct folding even in presence of the toxin, whereas a certain stiffness in correspondence of some structural regions is observed. Furthermore, the toxin does not seem to affect the antibody solubility, whereas it enhances the structural stability. The proposed computational approach represent a promising tool for analyzing some physicochemical properties of immunoconjugates and for predicting the effects of the linked toxin on structure, dynamics, and functionality of the antibodies.

Structure and dynamics of the anti-AMCV scFv(F8): effects of selected mutations on the antigen combining site

The recombinant antibody fragment scFv(F8), which recognizes the coat protein of the plant virus AMCV, is characterized by peculiar high in vitro stability and functional folding even in reducing environments, making it fit for designing stable antibodies with desired properties. Mutagenesis and functional analysis evidenced two residues, at positions 47 and 58 of the V(H) chain, playing a crucial role in the antigen binding recognition. Here, we used a computational procedure to assess the effects of these mutations on the stability, structure and dynamics of the antigen-binding site. Structural models of the wild type scFv(F8) and of its H47 and H58 mutants were built by homology modelling and assessed by multiple 15.5ns of molecular dynamics simulations. Computational results indicate that the 47H substitution strongly affects the CDR-H(2) conformation, destabilizes the V(H)/V(L) interface and confers high conformational flexibility to the antigen-binding site, leading the mutant to functional loss. The mutation at position H58 strenghtens the binding site, bestowing a high antigen specificity on the mutant. The essential dynamics and the analysis of the protein-solvent interface further corroborate the correspondence between the extent of the structurally-determined flexibility of the binding site with the different functional behaviours proved by the wild-type and its mutants. These results may have useful implications for structure-based design of antibody combining site.

Antibody-cytokine fusion proteins: applications in cancer therapy

BACKGROUND

Antibody-cytokine fusion proteins consist of cytokines fused to an antibody to improve antibody-targeted cancer immunotherapy. These molecules have the capacity to enhance the tumoricidal activity of the antibodies and/or activate a secondary antitumor immune response.

OBJECTIVE

To review the strategies used to develop antibody-cytokine fusion proteins and their in vitro and in vivo properties, including preclinical and clinical studies focusing on IL-2, IL-12 and GM-CSF.

METHODS

Articles were found by searching databases such as PubMed and Clinical Trials of the US National Institutes of Health.

RESULTS/CONCLUSION

Multiple antibody-cytokine fusion proteins have demonstrated significant antitumor activity as direct therapeutics or as adjuvants of cancer vaccines in preclinical studies, paving the way for their clinical evaluation.

The way forward, enhanced characterization of therapeutic antibody glycosylation: comparison of three level mass spectrometry-based strategies

Glycosylation which plays a crucial role in the pharmacological properties of therapeutic monoclonal antibodies (MAbs) is influenced by several factors like production systems, selected clonal population and manufacturing processes. Efficient analytical methods are therefore required in order to characterize glycosylation at different stages of MAbs discovery and production. Three mass spectrometry (MS)-based strategies were compared to analyze N-glycosylation of MAbs either expressed in murine myeloma (NS0) or Chinese Hamster Ovary (CHO) cell lines, the two current main production systems used for therapeutic MAbs. First a top-down approach was used on intact and reduced MAbs by liquid chromatography coupled to an electrospray ionization-time of flight mass spectrometer (LC-ESI-TOF), which provided fast and accurate profiles of MAbs glycosylation patterns for routine controls. Secondly, after digestion of the antibody with the peptide N-glycosidase F (PNGase F) enzyme, released N-linked glycans were directly analyzed by electrospray ionization-tandem mass spectrometry (ESI-MS/MS) without any prior derivatization, which gave precise details on the structure of the most abundant glycoforms. Finally, a bottom-up approach on tryptic glycopeptides using a nanoLC-Chip-MS/MS ion trap (IT) system equipped with a graphitized carbon column was investigated. Data were compared to those obtained with a more classical C18 reversed phase column showing that this last method is well suited to detect low abundant glycoforms and to provide in one shot information regarding both the oligosaccharide structure and the amino acid sequence of its peptide moiety.

Phase I to III Trials of Anti–B Cell Therapy in Non–Hodgkin's Lymphoma

Led by the anti-CD20 antibody rituximab, therapeutic monoclonal antibodies have dramatically altered the treatment of patients with non-Hodgkin's lymphoma. As the understanding of the biology of this novel therapy improves, so does the potential for further progress. There are currently four monoclonal antibodies approved by the Food and Drug Administration for the treatment of B-cell malignancies and dozens more are in various stages of development. The indications for the currently available antibodies, both labeled and unlabeled, are being expanded to include first-line treatment, maintenance strategies, and combinations with chemotherapy. Newer agents are being engineered to target novel antigens, and to interact more specifically with the host immune system. These promising therapeutics face a significant challenge in evaluation and integration in the post-rituximab world.

The rational design of biological complexity: A deceptive metaphor

Biologists often claim that they follow a rational design strategy when their research is based on molecular knowledge of biological systems. This claim implies that their knowledge of the innumerable causal connections present in biological systems is sufficient to allow them to deduce and predict the outcome of their experimental interventions. The design metaphor is shown to originate in human intentionality and in the anthropomorphic fallacy of interpreting objects, events, and the behavior of all living organisms in terms of goals and purposes. Instead of presenting rational design as an effective research strategy, it would be preferable to acknowledge that advances in biomedicine are nearly always derived from empirical observations based on trial and error experimentation. The claim that rational design is an effective research strategy was tested in the case of current attempts to develop synthetic vaccines, in particular against human immunodeficiency virus. It was concluded that in this field of biomedicine, trial and error experimentation is more likely to succeed than a rational design approach. Current developments in systems biology may give us eventually a better understanding of the immune system and this may enable us in the future to develop improved vaccines.

Biologic therapies in rheumatology: lessons learned, future directions

During the past decade biologic therapies such as monoclonal antibodies and fusion proteins have revolutionized the management of rheumatic disease. By targeting key cytokines and immune cells biologics have provided more specific therapeutic interventions with less immunosuppression. Clinical use, however, has revealed that their theoretical simplicity hides a more complex reality. Efficacy, toxicity and even pharmacodynamic effects can deviate from those predicted, as poignantly illustrated by the catastrophic effects witnessed during the first-into-human administration of TGN1412. This review summarizes lessons gleaned from practical experience and discusses how these can inform future discovery and development of new biologic therapies for rheumatology.

The use of immunoliposome for nutrient target regulation (a review)

Although research on the role of genetically engineered antibodies and liposomes in the immunology or the nutrition field is extensive, there is no case for immunoliposome to nutrient target regulation. It is known that liposomes are spherical particles that encapsulate a fraction of the solvent, in which they freely diffuse (float) into their interior. Therefore, identification of immunoliposomes in hypothalamic site or intestinal epithelial cells that are differentially regulated by liposomes encapsulating nutrients or drugs will be an important step toward understanding the role of immunoliposomes in nutrition regulation progression and ingredient stability. Consequently, a useful model (immunoliposomal nutrient delivery system, ILNDS) of nutrient target regulation via immunoliposomes is designed to regulate the endocrine system effectively. This review focuses on antibody libraries' construction, display and selection, a brief introduction of immunoliposome, and how to use ILNDS for nutrient target regulation.

Immunotherapy for non-Hodgkin's lymphoma: monoclonal antibodies and vaccines

Advances in the development of monoclonal antibodies have led to new agents rapidly incorporated into standard lymphoma therapy. The characteristics of the target antigen and the properties of the antibody including interaction with the host immune system have been found to correlate with outcome. Antibodies targeting the CD20 antigen on B cells have been most widely used, led by the chimeric antibody rituximab, now used in nearly all types of B-cell non-Hodgkin's lymphoma (NHL). New antibodies targeting CD20 with augmented complement or Fc receptor binding are now being evaluated and will eventually have to be compared with rituximab. Challenges to these new antibodies include the nearly universal use of rituximab early in NHL therapy, and its increasing use as maintenance therapy. It is not clear what the activity of these antibodies will be in rituximab-refractory patients. New antibodies targeting antigens such as CD40 and CD80 are also being tested alone and in combination with rituximab. Vaccine trials using patient-specific immunization with immunoglobulin idiotype (Ig-Id present on the surface of most B-cell NHL) isolated by molecular rescue or by cell hybridization techniques are also nearing completion. These approaches attempt to actively induce specific humoral or cellular immune responses to the Ig-Id by attaching the protein to a carrier protein and the use of an immunologic adjuvant such as granulocyte macrophage colony-stimulating factor. Prior rituximab appears to delay humoral responses to the idiotype but may still allow cellular responses. The incorporation of all these approaches into optimal NHL therapy remains a challenge.

Characterization by liquid chromatography combined with mass spectrometry of monoclonal anti-IGF-1 receptor antibodies produced in CHO and NS0 cells

7H2HM is a new humanized recombinant monoclonal antibody (MAb) directed against insulin-like growth factor-1 receptor and produced in CHO cells. Homogeneity of intact antibody, reduced light and heavy chains, Fab and Fc fragments were investigated by analytical methods based on mass (SDS-PAGE, SEC), charge (IEF, C-IEX) and hydrophobicity differences (RP-HPLC, HIC) and compared side-by-side with A2CHM, produced in NS0 cells. Primary structures and disulfide bridge pairing were analyzed by microsequencing (Edman degradation), mass spectrometry (MALDI-TOF, ES-TOF) and peptide mapping after enzymatic digestion (Trypsin, endoprotease Lys-C, papain). The light chains demonstrated the expected sequences. The heavy chains yielded post-translational modifications previously reported for other recombinant humanized or human IgG1 such as N-terminal pyroglutamic acid, C-terminal lysine clipping and N-glycosylation for asparagine 297. More surprisingly, two-thirds of the 7H2HM heavy chains were shown to contain an additional 24-amino-acid sequence, corresponding to the translation of an intron located between the variable and the constant domains. Taken together these data suggest that 7H2HM is a mixture of three families of antibodies corresponding (i) to the expected structure (17%; 14,9297 Da; 1330 amino acids), (ii) a variant with a translated intron in one heavy chains (33%; 15,2878 Da; 1354 amino acids) and (iii) a variant with translated introns in two heavy chains (50%; 15,4459 Da; 1378 amino acids), respectively. RP-HPLC is not a commonly used chromatographic method to assess purity of monoclonal antibodies but unlike to SEC and SDS-PAGE, was able to show and to quantify the family of structures present in 7H2HM, which were also identified by peptide mapping, mass spectrometry and microsequencing.

A functional antibody lacking N-linked glycans is efficiently folded, assembled and secreted by tobacco mesophyll protoplasts

A potential drawback in the use of plants as an expression platform for pharmaceutical proteins such as antibodies is that plant-specific N-glycosylation can result in proteins with altered function and potential antigenicity. In many cases, the N-glycans are essential for the correct folding, assembly and transport of the recombinant proteins. We tested whether progressive removal of glycosylation sites had a detrimental effect on the synthesis, assembly and secretion of a plant-made immunoglobulin G, Guy's 13. Our results indicate that the plant secretory pathway can cope well with aglycosylated antibody chains. The immunoglobulin without N-linked glycans is correctly assembled and secreted by tobacco protoplasts. Capture enzyme-linked immunosorbent assay also shows that antigen-binding properties are unaffected. Our results therefore suggest one possible alternative to the engineering of a humanized glycosylation machinery in plants.

Upping the ante on antibodies

The current generation of antibodies has done more than make a few companies rich. It has laid the groundwork for ambitious companies to move to maturity.

Conversion of CTLA-4 from inhibitor to activator of T cells with a bispecific tandem single-chain Fv ligand

Abs or their recombinant fragments against surface receptors of the Ig superfamily can induce or block the receptors' native function depending on whether they induce or prevent the assembly of signalosomes on their cytoplasmic tails. In this study, we introduce a novel paradigm based on the observation that a bispecific tandem single-chain variable region fragment ligand of CTLA-4 by itself converts this inhibitory receptor into an activating receptor for primary human T lymphocytes. This reversal of function results from increased recruitment of the serine/threonine phosphatase 2A to the cytoplasmic tail of CTLA-4, consistent with a role of this phosphatase in the regulation of CTLA-4 function, and assembly of a distinct signalosome that activates an lck-dependent signaling cascade and induces IL-2 production. Our data demonstrate that the cytoplasmic domain of CTLA-4 has an inherent plasticity for signaling that can be exploited therapeutically with recombinant ligands for this receptor.