Facile generation of biepitopic antibodies with intrinsic agonism for activating tumor necrosis factor receptors

Agonist antibodies are being pursued for therapeutic applications ranging from neurodegenerative diseases to cancer. For the tumor necrosis factor (TNF) receptor superfamily, higher-order clustering of three or more receptors is key to their activation, which can be achieved using antibodies that recognize two unique epitopes. However, the generation of biepitopic (i.e., biparatopic) antibodies typically requires animal immunization and is laborious and unpredictable. Here, we report a simple method for identifying biepitopic antibodies that potently activate TNF receptors without the need for additional animal immunization. Our approach uses existing, receptor-specific IgGs, which lack intrinsic agonist activity, to block their corresponding epitopes, then selects single-chain antibodies that bind accessible epitopes. The selected antibodies are fused to the light chains of IgGs to generate human tetravalent antibodies. We highlight the broad utility of this approach by converting several clinical-stage antibodies against OX40 and CD137 (4-1BB) into biepitopic antibodies with potent agonist activity.

In vivo Auto-tuning of Antibody-Drug Conjugate Delivery for Effective Immunotherapy using High-Avidity, Low-Affinity Antibodies

Antibody-drug conjugates (ADCs) have experienced a surge in clinical approvals in the past five years. Despite this success, a major limitation to ADC efficacy in solid tumors is poor tumor penetration, which leaves many cancer cells untargeted. Increasing antibody doses or co-administering ADC with an unconjugated antibody can improve tumor penetration and increase efficacy when target receptor expression is high. However, it can also reduce efficacy in low-expression tumors where ADC delivery is limited by cellular uptake. This creates an intrinsic problem because many patients express different levels of target between tumors and even within the same tumor. Here, we generated High-Avidity, Low-Affinity (HALA) antibodies that can automatically tune the cellular ADC delivery to match the local expression level. Using HER2 ADCs as a model, HALA antibodies were identified with the desired HER2 expression-dependent competitive binding with ADCs in vitro. Multi-scale distribution of trastuzumab emtansine and trastuzumab deruxtecan co-administered with the HALA antibody were analyzed in vivo, revealing that the HALA antibody increased ADC tumor penetration in high-expression systems with minimal reduction in ADC uptake in low-expression tumors. This translated to greater ADC efficacy in immunodeficient mouse models across a range of HER2 expression levels. Furthermore, Fc-enhanced HALA antibodies showed improved Fc-effector function at both high and low expression levels and elicited a strong response in an immunocompetent mouse model. These results demonstrate that HALA antibodies can expand treatment ranges beyond high expression targets and leverage strong immune responses.

Optimal computed tomography-based biomarkers for prediction of incisional hernia formation

PURPOSE

Unstructured data are an untapped source for surgical prediction. Modern image analysis and machine learning (ML) can harness unstructured data in medical imaging. Incisional hernia (IH) is a pervasive surgical disease, well-suited for prediction using image analysis. Our objective was to identify optimal biomarkers (OBMs) from preoperative abdominopelvic computed tomography (CT) imaging which are most predictive of IH development.

METHODS

Two hundred and twelve rigorously matched colorectal surgery patients at our institution were included. Preoperative abdominopelvic CT scans were segmented to derive linear, volumetric, intensity-based, and textural features. These features were analyzed to find a small subset of OBMs, which are maximally predictive of IH. Three ML classifiers (Ensemble Boosting, Random Forest, SVM) trained on these OBMs were used for prediction of IH.

RESULTS

Altogether, 279 features were extracted from each CT scan. The most predictive OBMs found were: (1) abdominopelvic visceral adipose tissue (VAT) volume, normalized for height; (2) abdominopelvic skeletal muscle tissue volume, normalized for height; and (3) pelvic VAT volume to pelvic outer aspect of body wall skeletal musculature (OAM) volume ratio. Among ML prediction models, Ensemble Boosting produced the best performance with an AUC of 0.85, accuracy of 0.83, sensitivity of 0.86, and specificity of 0.81.

CONCLUSION

These OBMs suggest increased intra-abdominopelvic volume/pressure as the salient pathophysiologic driver and likely mechanism for IH formation. ML models using these OBMs are highly predictive for IH development. The next generation of surgical prediction will maximize the utility of unstructured data using advanced image analysis and ML.

Facile generation of biepitopic antibodies with intrinsic agonism for activating receptors in the tumor necrosis factor superfamily

Agonist antibodies that activate cellular receptors are being pursued for therapeutic applications ranging from neurodegenerative diseases to cancer. For the tumor necrosis factor (TNF) receptor superfamily, higher-order clustering of three or more receptors is key to their potent activation. This can be achieved using antibodies that recognize two unique epitopes on the same receptor and mediate receptor superclustering. However, identifying compatible pairs of antibodies to generate biepitopic antibodies (also known as biparatopic antibodies) for activating TNF receptors typically requires animal immunization and is a laborious and unpredictable process. Here, we report a simple method for systematically identifying biepitopic antibodies that potently activate TNF receptors without the need for additional animal immunization. Our approach uses off-the-shelf, receptor-specific IgG antibodies, which lack intrinsic (Fc-gamma receptor-independent) agonist activity, to first block their corresponding epitopes. Next, we perform selections for single-chain antibodies from human nonimmune libraries that bind accessible epitopes on the same ectodomains using yeast surface display and fluorescence-activated cell sorting. The selected single-chain antibodies are finally fused to the light chains of IgGs to generate human tetravalent antibodies that engage two different receptor epitopes and mediate potent receptor activation. We highlight the broad utility of this approach by converting several existing clinical-stage antibodies against TNF receptors, including ivuxolimab and pogalizumab against OX40 and utomilumab against CD137, into biepitopic antibodies with highly potent agonist activity. We expect that this widely accessible methodology can be used to systematically generate biepitopic antibodies for activating other receptors in the TNF receptor superfamily and many other receptors whose activation is dependent on strong receptor clustering.

Flow cytometric isolation of drug-like conformational antibodies specific for amyloid fibrils

Antibodies that recognize specific protein conformational states are broadly important for research, diagnostic and therapeutic applications, yet they are difficult to generate in a predictable and systematic manner using either immunization or in vitro antibody display methods. This problem is particularly severe for conformational antibodies that recognize insoluble antigens such as amyloid fibrils associated with many neurodegenerative disorders. Here we report a quantitative fluorescence-activated cell sorting (FACS) method for directly selecting high-quality conformational antibodies against different types of insoluble (amyloid fibril) antigens using a single, off-the-shelf human library. Our approach uses quantum dots functionalized with antibodies to capture insoluble antigens, and the resulting quantum dot conjugates are used in a similar manner as conventional soluble antigens for multi-parameter FACS selections. Notably, we find that this approach is robust for isolating high-quality conformational antibodies against tau and α-synuclein fibrils from the same human library with combinations of high affinity, high conformational specificity and, in some cases, low off-target binding that rival or exceed those of clinical-stage antibodies specific for tau (zagotenemab) and α-synuclein (cinpanemab). This approach is expected to enable conformational antibody selection and engineering against diverse types of protein aggregates and other insoluble antigens (e.g., membrane proteins) that are compatible with presentation on the surface of antibody-functionalized quantum dots.

Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space

Therapeutic antibody development requires selection and engineering of molecules with high affinity and other drug-like biophysical properties. Co-optimization of multiple antibody properties remains a difficult and time-consuming process that impedes drug development. Here we evaluate the use of machine learning to simplify antibody co-optimization for a clinical-stage antibody (emibetuzumab) that displays high levels of both on-target (antigen) and off-target (non-specific) binding. We mutate sites in the antibody complementarity-determining regions, sort the antibody libraries for high and low levels of affinity and non-specific binding, and deep sequence the enriched libraries. Interestingly, machine learning models trained on datasets with binary labels enable predictions of continuous metrics that are strongly correlated with antibody affinity and non-specific binding. These models illustrate strong tradeoffs between these two properties, as increases in affinity along the co-optimal (Pareto) frontier require progressive reductions in specificity. Notably, models trained with deep learning features enable prediction of novel antibody mutations that co-optimize affinity and specificity beyond what is possible for the original antibody library. These findings demonstrate the power of machine learning models to greatly expand the exploration of novel antibody sequence space and accelerate the development of highly potent, drug-like antibodies.

Facile isolation of high-affinity nanobodies from synthetic libraries using CDR-swapping mutagenesis

The generation of high-affinity nanobodies for diverse biomedical applications typically requires immunization or affinity maturation. Here, we report a simple protocol using complementarity-determining region (CDR)-swapping mutagenesis to isolate high-affinity nanobodies from common framework libraries. This approach involves shuffling the CDRs of low-affinity variants during the sorting of yeast-displayed libraries to directly isolate high-affinity nanobodies without the need for lead isolation and optimization. We expect this approach, which we demonstrate for SARS-CoV-2 neutralizing nanobodies, will simplify the generation of high-affinity nanobodies.

For complete details on the use and execution of this profile, please refer to Zupancic et al. (2021).

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Protocol enables direct isolation of high-affinity nanobodies from synthetic libraries

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Individual CDRs are amplified and recombined to obtain nanobodies with shuffled CDRs

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Libraries of CDR-shuffled nanobodies are rapidly sorted to obtain high-affinity clones

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Monovalent and bivalent nanobody affinities are determined using flow cytometry

Rapid and Quantitative In Vitro Evaluation of SARS-CoV-2 Neutralizing Antibodies and Nanobodies

Neutralizing monoclonal antibodies and nanobodies have shown promising results as potential therapeutic agents for COVID-19. Identifying such antibodies and nanobodies requires evaluating the neutralization activity of a large number of lead molecules via biological assays, such as the virus neutralization test (VNT). These assays are typically time-consuming and demanding on-lab facilities. Here, we present a rapid and quantitative assay that evaluates the neutralizing efficacy of an antibody or nanobody within 1.5 h, does not require BSL-2 facilities, and consumes only 8 μL of a low concentration (ng/mL) sample for each assay run. We tested the human angiotensin-converting enzyme 2 (ACE2) binding inhibition efficacy of seven antibodies and eight nanobodies and verified that the IC₅₀ values of our assay are comparable with those from SARS-CoV-2 pseudovirus neutralization tests. We also found that our assay could evaluate the neutralizing efficacy against three widespread SARS-CoV-2 variants. We observed increased affinity of these variants for ACE2, including the β and γ variants. Finally, we demonstrated that our assay enables the rapid identification of an immune-evasive mutation of the SARS-CoV-2 spike protein, utilizing a set of nanobodies with known binding epitopes.

Reduction of therapeutic antibody self-association using yeast-display selections and machine learning

Self-association governs the viscosity and solubility of therapeutic antibodies in high-concentration formulations used for subcutaneous delivery, yet it is difficult to reliably identify candidates with low self-association during antibody discovery and early-stage optimization. Here, we report a high-throughput protein engineering method for rapidly identifying antibody candidates with both low self-association and high affinity. We find that conjugating quantum dots to IgGs that strongly self-associate (pH 7.4, PBS), such as lenzilumab and bococizumab, results in immunoconjugates that are highly sensitive for detecting other high self-association antibodies. Moreover, these conjugates can be used to rapidly enrich yeast-displayed bococizumab sub-libraries for variants with low levels of immunoconjugate binding. Deep sequencing and machine learning analysis of the enriched bococizumab libraries, along with similar library analysis for antibody affinity, enabled identification of extremely rare variants with co-optimized levels of low self-association and high affinity. This analysis revealed that co-optimizing bococizumab is difficult because most high-affinity variants possess positively charged variable domains and most low self-association variants possess negatively charged variable domains. Moreover, negatively charged mutations in the heavy chain CDR2 of bococizumab, adjacent to its paratope, were effective at reducing self-association without reducing affinity. Interestingly, most of the bococizumab variants with reduced self-association also displayed improved folding stability and reduced nonspecific binding, revealing that this approach may be particularly useful for identifying antibody candidates with attractive combinations of drug-like properties.Abbreviations: AC-SINS: affinity-capture self-interaction nanoparticle spectroscopy; CDR: complementarity-determining region; CS-SINS: charge-stabilized self-interaction nanoparticle spectroscopy; FACS: fluorescence-activated cell sorting; Fab: fragment antigen binding; Fv: fragment variable; IgG: immunoglobulin; QD: quantum dot; PBS: phosphate-buffered saline; V_H: variable heavy; V_L: variable light.

Isolating Anti-amyloid Antibodies from Yeast-Displayed Libraries

Conformational antibodies specific for amyloid-forming peptides and proteins are important for a range of biomedical applications, including detecting, inhibiting, and potentially treating protein aggregation disorders ranging from Alzheimer's to Parkinson's diseases. Generation of anti-amyloid antibodies is greatly complicated by the complex, heterogeneous and insoluble nature of amyloid antigens. Here we describe systematic methods for isolating and affinity maturing anti-amyloid antibodies using yeast surface display. Magnetic-activated cell sorting is used to sort single-chain antibody libraries positively for binding to amyloid antigens and negatively against the corresponding disaggregated antigens to remove antibodies that bind in a conformation-independent manner. Isolated lead antibody clones with conformational specificity are affinity matured via targeted CDR mutagenesis and magnetic-activated cell sorting.

Discovery and characterization of high-affinity, potent SARS-CoV-2 neutralizing antibodies via single B cell screening

Monoclonal antibodies that target SARS-CoV-2 with high affinity are valuable for a wide range of biomedical applications involving novel coronavirus disease (COVID-19) diagnosis, treatment, and prophylactic intervention. Strategies for the rapid and reliable isolation of these antibodies, especially potent neutralizing antibodies, are critical toward improved COVID-19 response and informed future response to emergent infectious diseases. In this study, single B cell screening was used to interrogate antibody repertoires of immunized mice and isolate antigen-specific IgG1⁺ memory B cells. Using these methods, high-affinity, potent neutralizing antibodies were identified that target the receptor-binding domain of SARS-CoV-2. Further engineering of the identified molecules to increase valency resulted in enhanced neutralizing activity. Mechanistic investigation revealed that these antibodies compete with ACE2 for binding to the receptor-binding domain of SARS-CoV-2. These antibodies may warrant further development for urgent COVID-19 applications. Overall, these results highlight the potential of single B cell screening for the rapid and reliable identification of high-affinity, potent neutralizing antibodies for infectious disease applications.

A hybridoma-derived monoclonal antibody with high homology to the aberrant myeloma light chain

The identification of antibody variable regions in the heavy (V_H) and light (V_L) chains from hybridomas is necessary for the production of recombinant, sequence-defined monoclonal antibodies (mAbs) and antibody derivatives. This process has received renewed attention in light of recent reports of hybridomas having unintended specificities due to the production of non-antigen specific heavy and/or light chains for the intended antigen. Here we report a surprising finding and potential pitfall in variable domain sequencing of an anti-human CD63 hybridoma. We amplified multiple V_L genes from the hybridoma cDNA, including the well-known aberrant Sp2/0 myeloma V_K and a unique, full-length V_L. After finding that the unique V_L failed to yield a functional antibody, we discovered an additional full-length sequence with surprising similarity (~95% sequence identify) to the non-translated myeloma kappa chain but with a correction of its key frameshift mutation. Expression of the recombinant mAb confirmed that this highly homologous sequence is the antigen-specific light chain. Our results highlight the complexity of PCR-based cloning of antibody genes and strategies useful for identification of correct sequences.

Engineered Multivalent Nanobodies Potently and Broadly Neutralize SARS-CoV-2 Variants

The COVID-19 pandemic continues to be a severe threat to human health, especially due to current and emerging SARS-CoV-2 variants with potential to escape humoral immunity developed after vaccination or infection. The development of broadly neutralizing antibodies that engage evolutionarily conserved epitopes on coronavirus spike proteins represents a promising strategy to improve therapy and prophylaxis against SARS-CoV-2 and variants thereof. Herein, a facile multivalent engineering approach is employed to achieve large synergistic improvements in the neutralizing activity of a SARS-CoV-2 cross-reactive nanobody (VHH-72) initially generated against SARS-CoV. This synergy is epitope specific and is not observed for a second high-affinity nanobody against a non-conserved epitope in the receptor-binding domain. Importantly, a hexavalent VHH-72 nanobody retains binding to spike proteins from multiple highly transmissible SARS-CoV-2 variants (B.1.1.7 and B.1.351) and potently neutralizes them. Multivalent VHH-72 nanobodies also display drug-like biophysical properties, including high stability, high solubility, and low levels of non-specific binding. The unique neutralizing and biophysical properties of VHH-72 multivalent nanobodies make them attractive as therapeutics against SARS-CoV-2 variants.

Directed evolution of potent neutralizing nanobodies against SARS-CoV-2 using CDR-swapping mutagenesis

There is widespread interest in facile methods for generating potent neutralizing antibodies, nanobodies, and other affinity proteins against SARS-CoV-2 and related viruses to address current and future pandemics. While isolating antibodies from animals and humans are proven approaches, these methods are limited to the affinities, specificities, and functional activities of antibodies generated by the immune system. Here we report a surprisingly simple directed evolution method for generating nanobodies with high affinities and neutralization activities against SARS-CoV-2. We demonstrate that complementarity-determining region swapping between low-affinity lead nanobodies, which we discovered unintentionally but find is simple to implement systematically, results in matured nanobodies with unusually large increases in affinity. Importantly, the matured nanobodies potently neutralize both SARS-CoV-2 pseudovirus and live virus, and possess drug-like biophysical properties. We expect that our methods will improve in vitro nanobody discovery and accelerate the generation of potent neutralizing nanobodies against diverse coronaviruses.

Rational affinity maturation of anti-amyloid antibodies with high conformational and sequence specificity

The aggregation of amyloidogenic polypeptides is strongly linked to several neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Conformational antibodies that selectively recognize protein aggregates are leading therapeutic agents for selectively neutralizing toxic aggregates, diagnostic and imaging agents for detecting disease, and biomedical reagents for elucidating disease mechanisms. Despite their importance, it is challenging to generate high-quality conformational antibodies in a systematic and site-specific manner due to the properties of protein aggregates (hydrophobic, multivalent, and heterogeneous) and limitations of immunization (uncontrolled antigen presentation and immunodominant epitopes). Toward addressing these challenges, we have developed a systematic directed evolution procedure for affinity maturing antibodies against Alzheimer's Aβ fibrils and selecting variants with strict conformational and sequence specificity. We first designed a library based on a lead conformational antibody by sampling combinations of amino acids in the antigen-binding site predicted to mediate high antibody specificity. Next, we displayed this library on the surface of yeast, sorted it against Aβ42 aggregates, and identified promising clones using deep sequencing. The resulting antibodies displayed similar or higher affinities than clinical-stage Aβ antibodies (aducanumab and crenezumab). Moreover, the affinity-matured antibodies retained high conformational specificity for Aβ aggregates, as observed for aducanumab and unlike crenezumab. Notably, the affinity-maturated antibodies displayed extremely low levels of nonspecific interactions, as observed for crenezumab and unlike aducanumab. We expect that our systematic methods for generating antibodies with unique combinations of desirable properties will improve the generation of high-quality conformational antibodies specific for diverse types of aggregated conformers.

Highly sensitive detection of antibody nonspecific interactions using flow cytometry

The rapidly evolving nature of antibody drug development has resulted in technologies that generate vast numbers (hundreds to thousands) of lead antibody candidates during early discovery. These candidates must be rapidly pared down to identify the most drug-like candidates for in-depth analysis of their safety and efficacy, which can only be performed on a limited number of antibodies due to time and resource requirements. One key biophysical property of successful antibody therapeutics is high specificity, defined as low levels of nonspecific binding or polyspecificity. Although there has been some progress in developing assays for detecting antibody polyspecificity, most of these assays are limited by poor sensitivity or assay formats that require proprietary antibody surface display methods, and some of these assays use complex and poorly defined polyspecificity reagents. Here we report the PolySpecificity Particle (PSP) assay, a sensitive flow cytometry assay for evaluating antibody nonspecific interactions that overcomes previous limitations and can be used for evaluating diverse types of IgGs, multispecific antibodies and Fc-fusion proteins. Our approach uses micron-sized magnetic beads coated with Protein A to capture antibodies at extremely dilute concentrations (<0.02 mg/mL). Flow cytometry analysis of polyspecificity reagent binding to these conjugates results in sensitive detection of differences in nonspecific interactions for clinical-stage antibodies. Our PSP assay strongly discriminates between antibodies with different levels of polyspecificity using previously reported polyspecificity reagents that are either well-defined proteins or highly complex protein mixtures. Moreover, we also find that a unique reagent, namely ovalbumin, results in the best assay sensitivity and specificity. Importantly, our assay is much more sensitive than standard assays such as ELISAs. We expect that our simple, sensitive, and high-throughput PSP assay will accelerate the development of safe and effective antibody therapeutics.

Directed evolution of conformation-specific antibodies for sensitive detection of polypeptide aggregates in therapeutic drug formulations

Biologics such as peptides and proteins possess a number of attractive attributes that make them particularly valuable as therapeutics, including their high activity, high specificity, and low toxicity. However, one of the key challenges associated with this class of drugs is their propensity to aggregate. Given the safety and immunogenicity concerns related to polypeptide aggregates, it is particularly important to sensitively detect aggregates in therapeutic drug formulations as part of the quality control process. Here, we report the development of conformation-specific antibodies that recognize polypeptide aggregates composed of a GLP-1 receptor agonist (liraglutide) and their integration into a sensitive immunoassay for detecting liraglutide amyloid fibrils. We sorted single-chain antibody libraries against liraglutide fibrils using yeast surface display and magnetic-activated cell sorting, and identified several antibodies with high conformational specificity. Interestingly, these antibodies cross-react with amyloid fibrils formed by several other polypeptides, revealing that they recognize molecular features common to different types of fibrils. Moreover, we find that our immunoassay using these antibodies is >50-fold more sensitive than the conventional method for detecting liraglutide aggregation (Thioflavin T fluorescence). We expect that our systematic approach for generating a sensitive, aggregate-specific immunoassay can be readily extended to other biologics to improve the quality and safety of formulated drug products.

Physicochemical Rules for Identifying Monoclonal Antibodies with Drug-like Specificity

The ability of antibodies to recognize their target antigens with high specificity is fundamental to their natural function. Nevertheless, therapeutic antibodies display variable and difficult-to-predict levels of nonspecific and self-interactions that can lead to various drug development challenges, including antibody aggregation, abnormally high viscosity, and rapid antibody clearance. Here we report a method for predicting the overall specificity of antibodies in terms of their relative risk for displaying high levels of nonspecific or self-interactions at physiological conditions. We find that individual and combined sets of chemical rules that limit the maximum and minimum numbers of certain solvent-exposed amino acids in antibody variable regions are strong predictors of specificity for large panels of preclinical and clinical-stage antibodies. We also demonstrate how the chemical rules can be used to identify sites that mediate nonspecific interactions in suboptimal antibodies and guide the design of targeted sublibraries that yield variants with high antibody specificity. These findings can be readily used to improve the selection and engineering of antibodies with drug-like specificity.

Nature-inspired design and evolution of anti-amyloid antibodies

Antibodies that recognize amyloidogenic aggregates with high conformational and sequence specificity are important for detecting and potentially treating a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. However, these types of antibodies are challenging to generate because of the large size, hydrophobicity, and heterogeneity of protein aggregates. To address this challenge, we developed a method for generating antibodies specific for amyloid aggregates. First, we grafted amyloidogenic peptide segments from the target polypeptide [Alzheimer's amyloid-β (Aβ) peptide] into the complementarity-determining regions (CDRs) of a stable antibody scaffold. Next, we diversified the grafted and neighboring CDR sites using focused mutagenesis to sample each WT or grafted residue, as well as one to five of the most commonly occurring amino acids at each site in human antibodies. Finally, we displayed these antibody libraries on the surface of yeast cells and selected antibodies that strongly recognize Aβ-amyloid fibrils and only weakly recognize soluble Aβ. We found that this approach enables the generation of monovalent and bivalent antibodies with nanomolar affinity for Aβ fibrils. These antibodies display high conformational and sequence specificity as well as low levels of nonspecific binding and recognize a conformational epitope at the extreme N terminus of human Aβ. We expect that this systematic approach will be useful for generating antibodies with conformational and sequence specificity against a wide range of peptide and protein aggregates associated with neurodegenerative disorders.

Understanding and overcoming trade-offs between antibody affinity, specificity, stability and solubility

The widespread use of monoclonal antibodies for therapeutic applications has led to intense interest in optimizing several of their natural properties (affinity, specificity, stability, solubility and effector functions) as well as introducing non-natural activities (bispecificity and cytotoxicity mediated by conjugated drugs). A common challenge during antibody optimization is that improvements in one property (e.g., affinity) can lead to deficits in other properties (e.g., stability). Here we review recent advances in understanding trade-offs between different antibody properties, including affinity, specificity, stability and solubility. We also review new approaches for co-optimizing multiple antibody properties and discuss how these methods can be used to rapidly and systematically generate antibodies for a wide range of applications.

The Contribution of Common Surgically Implanted Hardware to Functional MR Imaging Artifacts

BACKGROUND AND PURPOSE

Blood oxygenation level-dependent MR imaging is increasingly used clinically to noninvasively assess cerebrovascular reactivity and/or language and motor function. However, many patients have metallic implants, which will induce susceptibility artifacts, rendering the functional information uninformative. Here, we calculate and interpret blood oxygenation level-dependent MR imaging artifact impact arising from surgically implanted hardware.

MATERIALS AND METHODS

A retrospective analysis of all blood oxygenation level-dependent MRIs (n = 343; B0 = 3T; TE = 35 ms; gradient echo EPI) acquired clinically (year range = 2006-2014) at our hospital was performed. Blood oxygenation level-dependent MRIs were most commonly prescribed for patients with cerebrovascular disease (n = 80) or patients undergoing language or motor localization (n = 263). Artifact volume (cubic centimeters) and its impact on clinical interpretation were determined by a board-certified neuroradiologist.

RESULTS

Mean artifact volume associated with intracranial hardware was 4.3 ± 3.2 cm(3) (range = 1.1-9.4 cm(3)). The mean artifact volume from extracranial hardware in patients with cerebrovascular disease was 28.4 ± 14.0 cm(3) (range = 6.1-61.7 cm(3)), and in patients with noncerebrovascular disease undergoing visual or motor functional mapping, it was 39.9 (3)± 27.0 cm(3) (range = 6.9-77.1 cm(3)). The mean artifact volume for ventriculoperitoneal shunts was 95.7 ± 39.3 cm(3) (range = 64.0-139.6 cm(3)). Artifacts had no-to-mild effects on clinical interpretability in all patients with intracranial implants. Extracranial hardware artifacts had no-to-moderate impact on clinical interpretability, with the exception of 1 patient with 12 KLS-Martin maxDrive screws with severe artifacts precluding clinical interpretation. All examined ventriculoperitoneal shunts resulted in moderate-to-severe artifacts, limiting clinical interpretation.

CONCLUSIONS

Blood oxygenation level-dependent MR imaging yields interpretable functional maps in most patients beyond a small (30-40 cm(3)) artifact surrounding the hardware. Exceptions were ventriculoperitoneal shunts, particularly those with programmable valves and siphon gauges, and large numbers of KLS-Martin maxDrive screws.

A phase I study of antisense oligonucleotide GTI-2040 given by continuous intravenous infusion in patients with advanced solid tumors

BACKGROUND

This study of GTI-2040, a 20-mer phosphorothioate oligonucleotide complementary to the messenger ribonucleic acid (mRNA) of the R2 subunit of ribonucleotide reductase (RNR), was conducted to determine the dose-limiting toxicity (DLT) and maximum-tolerated dose (MTD) of the agent in patients with advanced solid tumors or lymphoma. Plasma pharmacokinetics of GTI-2040 and suppression of RNR expression in peripheral blood mononuclear cells were also studied.

PATIENTS AND METHODS

GTI-2040 was administered as a continuous intravenous infusion for 21 days every 4 weeks. Dose escalation was performed using an accelerated, dose-doubling schedule until any drug related toxicity > or = grade 2 was observed; subsequent dose escalation followed a more conservative dose escalation scheme with three patients/cohort.

RESULTS

A total of 49 cycles of therapy were administered to 36 patients at GTI-2040 doses ranging from 18.5 mg/m(2)/day to 222 mg/m(2)/day. GTI-2040 was generally well tolerated. At the highest dose level examined, two patients experienced dose limiting reversible hepatic toxicity. Constitutional toxicities consisting of fatigue and anorexia were the most common toxicities.

CONCLUSIONS

The recommended dose of GTI-2040 given on this infusion schedule is 185 mg/m(2)/day. GTI-2040 appears to have a manageable toxicity profile and is generally well tolerated as a single agent.

Post operative sensorineural hearing loss after middle ear surgery

Mild Sensorineural hearing loss subsequent to middle ear surgery has till today been an important complication to middle ear surgery inspite of advances in surgical techniques, operative instruments, monitoring devices and better treatment options. Lack of proper knowledge about this problem is because of under reporting of exact magnitude of hearing loss on account of difficulty in measuring hearing threshold of patients in immediate postoperative period as it may lead to post operative infection and discomfort to the patient.In our study of 80 cases carried out at ENT department, Baroda Medical College and S.S.G Hospital, Baroda, we have utilized weber's lateralisation principle and measured bone conduction thresholds of patients undergoing middle ear surgery for evaluation of postoperative Sensorineural loss as a result of middle ear surgery. Probable causes of post operative hearing loss in a patient undergoing middle ear surgery are, noise due to drills, continuous suction irrigation, vibrations, inner ear injury, manipulation of ossicles and a few unknown reasons.

Role of parecoxib in pre-emptive analgesia: comparison of the efficacy and safety of pre- and postoperative parecoxib in patients undergoing general surgery

Management of acute postoperative pain remains sub-optimal despite the availability of multiple analgesics and improved pain management strategies (with nearly 80 % of patients reporting moderate to extreme pain following surgery). To evaluate the role of parecoxib as a pre-emptive analgesic in patients undergoing general surgery, the present study was undertaken. Eighty patients of either sex, aged 18 to 70 years, requiring elective ambulatory general surgery like hernioplasty, appendicectomy, cholecystectomy, etc, were enrolled in this prospective, randomised, assessor-blind, parallel-group, comparative trial. Eligible patients were randomised to receive a single dose of 40 mg of parecoxib IM/IV either 30-45 minutes prior to induction of anesthesia (pre-emptive analgesia) or in the postoperative period when one reported pain or when the effects of anesthesia were worn off (whichever was earlier). The primary measures of efficacy were pain intensity scores measured on a visual analog scale (VAS) and pain relief before and after therapy. Adverse event monitoring, physical examination and changes in laboratory tests, chest x-ray and ECG were used to evaluate safety. A comparison of the pain intensity scores between the two groups revealed that patients treated with parecoxib preoperatively did not complain of pain in the entire postoperative period up to 12 hours. Mild pain (1.05+/-1.36) was reported by patients in this group only at the 24 hours assessment. On the other hand, patients treated with parecoxib in the postoperative period, experienced severe pain at baseline, which declined gradually up to 12 hours. The difference in the pain intensity scores between the two groups was statistically significant at all the time intervals from 0 hour to 24 hours. All the 40 patients (100%) in the pre-operatively treated group reported total pain relief at 12 hours compared to only 22 patients (55%) in the postoperative period. At 24 hours total pain relief was reported by 70% of the patients in the pre-operatively treated group, compared to only 20% (8) patients in the postoperatively treated group. The difference between the two groups was statistically significant in favour of the pre-operatively treated group (p<0.05). Present results suggested that pre-operative administration of parecoxib was more effective than a postoperative use in providing pain relief in postoperative period in patients undergoing elective general surgical procedures. Both the regimens were well tolerated. Based on the above data, it appears that pre-operative dose of parecoxib 40 mg IV/IM is a useful optionfor pre-emptive analgesia in general surgical practice.

The quality of care in Barrett's esophagus: endoscopist and pathologist practices

BACKGROUND

The diagnosis of Barrett's esophagus (BE) has important psychological and economic implications. Although accepted standards for endoscopic biopsy methods and pathological interpretation for BE exist, adherence to these standards as a measure of the quality of care in BE has not been evaluated. Our aim was to assess the quality of care in BE by evaluating the process of care and adherence to accepted standards of practice.

METHODS

Explicit process-of-care criteria were developed using a systematic literature review and expert opinion in four domains of care: the quality of biopsy methods, the adequacy in identifying endoscopic landmarks, endoscopist-pathologist communication, and pathological interpretation and reporting. We reviewed all endoscopy and pathology reports of BE patients at two institutions from 1994-1997. An academic medical center (N = 237) with staff endoscopists and an academically affiliated community hospital (N = 100) with private-practice endoscopists were analyzed.

RESULTS

Physicians showed the highest adherence to accepted standards of care in the "adequacy of identifying landmarks" and "endoscopist-pathologist communication" domains, with a > or =70% adherence rate in most criteria. Conversely, physicians demonstrated the poorest adherence with the "quality of biopsy methods" and "pathologist interpretation and reporting" domains, with adherence rates frequently <60%. Significantly, biopsies were taken in the presence of visible esophagitis 35% of the time. Performance on several of the quality indicators varied significantly by the practice setting.

CONCLUSIONS

We have identified several opportunities for quality improvement efforts. In every domain, there is room for improvement, particularly in the quality of biopsy methods. As initiatives to screen the large population of gastroesophageal reflux disease patients for BE may be imminent, the time is now to define the critical process-of-care measures to minimize the risk of overdiagnosis and inadequate endoscopic surveillance.

Nasopharyngeal angiofibroma (a report of 19 cases)

Nasopharyngeal Angiofibroma is a relatively rare benign, but locally aggresive tumor of the nasopharynx afflicting the adolescent males. The management of these tumors has been a subject of much interest and controversy in the past Here we present a series of 19 patients of nasopharyngeal angiofibroma (with CT Scan as the main stay of diagnosis) managed over the last 5 years at ENT and Head & Neck Surgery Department of S.S.G. Hospital, Vadodara, with infraoperative internal maxillary artery ligation via the trans maxillary approach permitting accurate removal of tumor with no major post operative complications, minimal blood loss, good cosmetic result and no recurrence till date. If further experience with this approach to management in a larger series of patients has the same results, surgery should be the gold standard in treatment of Nasopharyngeal angiofibroma.

Moebius syndrome (moebius sequence)

Moebius Syndrome is one of the rare disorder amongst the oromandibular limb hypogenesis. It is of a unknown atiology with sporadic occurrence in which there is congenital bilateral facial palsy,-bilateral involvement of abducent nerve along with other cranial nerves like III, V, IX, X, Xllth and the patient having masklike expressionless face. We are reporting a case of Moebius Sequence who presented to us in the department of ENT and Head and Neck Surgery, Baroda.

Diagnostic role of ultrasonography in neck swellings

Diagnostic Role of Ultrasonography in Neck Swellings The study of ultrasonographic features of various neck swellings in fifty patients was done. There were 22 thyroid and thyroid related swelling, 8 salivary gland lesions, 9 lymph nodes and 14 swellings of miscellaneous origin. Various ultrasonographic features like echogenicity, echotextures were noted. There were no specific echogenicity in benign and malignant thyroid neoplasms. Various ultrasonographic features of benign and malignant salivary neoplasms and lymph nodes are described. Specific sonographic features of various miscellaneous neck swellings are also described.

Early response to therapy and outcome in childhood acute lymphoblastic leukemia: a review

BACKGROUND

Early response to therapy is defined as the initial response prior to Day 28 of treatment, the conventional time of marrow evaluation. The number of reports linking early response to therapy with the ultimate outcome of childhood acute lymphoblastic leukemia is substantial and growing. When this study began, these experiences had yet to be comprehensively reviewed.

METHODS

A comprehensive search of the published literature yielded contributory reports of 14 trials conducted in the United States and Europe. In addition, unpublished data from one Children's Cancer Group trial were made available. Outcome measures were standardized by conversion to ratios of the incidence of adverse events among poorer and better responders.

RESULTS

Early response to therapy was an independent prognostic factor in each of the 15 trials, which together included more than 10,000 patients. The incidence of slower early response ranged from 2-33%, with various measures and criteria used in different trials. Patients with a slower early response were 1.5-6.1 times (median, 2.7) more likely to have an adverse event than patients with a more rapid early response, however defined. Early response maintained prognostic significance after the exclusion of induction failure and within risk strata defined by age, white blood cell count, and/or immunophenotype. Its significance was also maintained in multivariate analyses where performed.

CONCLUSIONS

Early response to therapy, whether determined by evaluation of bone marrow or peripheral blood, is a consistent, independent prognostic factor in childhood acute lymphoblastic leukemia. Slower early response may serve as a useful surrogate for outcome, a more complex end point, in investigations of the cellular and molecular determinants of resistance to therapy. It may also allow early identification of a patient subpopulation for whom current therapy is less effective and alternative strategies may be justified.

Tryptophan depletion as a mechanism of gamma interferon-mediated chlamydial persistence

Previous studies have shown that the immune-regulated cytokine gamma interferon (IFN-gamma) activates host cells to restrict intracellular growth of the bacterial pathogen Chlamydia trachomatis by induction of the tryptophan-catabolizing enzyme indoleamine 2,3-dioxygenase (IDO). Recently, subinhibitory levels of IFN-gamma were used to generate an in vitro persistent chlamydial infection characterized by large aberrant, noninfectious reticulate bodies from which infectious progeny could be recovered following the removal of IFN-gamma. Studies were done to determine if the mechanism functioning to induce chlamydiae to enter a persistent state in the presence of low levels of IFN-gamma was similar to that reported to inhibit chlamydial growth. Host cells treated with levels of IFN-gamma required to induce persistence were assessed for IDO activity by high-performance liquid chromatography analysis of tryptophan and its catabolic products. Substantial tryptophan catabolism was detected in acid-soluble cellular pools, indicating that the intracellular availability of this essential amino acid was limited under these conditions. In addition, a mutant cell line responsive to IFN-gamma but deficient in IDO activity was shown to support C. trachomatis growth, but aberrant organisms were not induced in response to IFN-gamma treatment. Analyses of infected cells cultured in medium with incremental levels of exogenous tryptophan indicated that persistent growth was induced by reducing the amount of this essential amino acid. These studies confirmed that nutrient deprivation by IDO-mediated tryptophan catabolism was the mechanism by which IFN-gamma mediates persistent growth of C. trachomatis.

Frontoethmoidal meningoencephalocystocele

A rare variety of frontoethmoidal meningoencephalocystocele is reported. Transillumination of the mass and cross-fluctuation to the anterior frontanelle are diagnostic. Herniation of the anterior horn of the lateral ventricle is probably being reported for the first time.