Improving the integrity and reproducibility of research that uses antibodies: a technical, data sharing, behavioral and policy challenge

Antibodies are one of the most important reagents used in biomedical and fundamental research, used to identify, and quantify proteins, contribute to knowledge of disease mechanisms, and validate drug targets. Yet many antibodies used in research do not recognize their intended target, or recognize additional molecules, compromising the integrity of research findings and leading to waste of resources, lack of reproducibility, failure of research projects, and delays in drug development. Researchers frequently use antibodies without confirming that they perform as intended in their application of interest. Here we argue that the determinants of end-user antibody choice and use are critical, and under-addressed, behavioral drivers of this problem. This interacts with the batch-to-batch variability of these biological reagents, and the paucity of available characterization data for most antibodies, making it more difficult for researchers to choose high quality reagents and perform necessary validation experiments. The open-science company YCharOS works with major antibody manufacturers and knockout cell line producers to characterize antibodies, identifying high-performing renewable antibodies for many targets in neuroscience. This shows the progress that can be made by stakeholders working together. However, their work so far applies to only a tiny fraction of available antibodies. Where characterization data exists, end-users need help to find and use it appropriately. While progress has been made in the context of technical solutions and antibody characterization, we argue that initiatives to make best practice behaviors by researchers more feasible, easy, and rewarding are needed. Global cooperation and coordination between multiple partners and stakeholders will be crucial to address the technical, policy, behavioral, and open data sharing challenges. We offer potential solutions by describing our Only Good Antibodies initiative, a community of researchers and partner organizations working toward the necessary change. We conclude with an open invitation for stakeholders, including researchers, to join our cause.

A multiphasic approach to solve misidentification of Cutibacterium acnes as Atopobium vaginae during routine bacterial screening of platelet concentrates using the VITEK 2 system

Skin flora bacteria, such as Cutibacterium acnes , are the predominant contaminants of blood products used for transfusion. Platelet concentrates (PCs), a therapeutic product used to treat patients with platelet deficiencies, are stored at ambient temperature under agitation, providing ideal conditions for bacterial proliferation. At Canadian Blood Services, PCs are screened for microbial contamination using the automated BACT/ALERT culture system. Positive cultures are processed and contaminating organisms are identified using the VITEK 2 system. Over a period of approximately 2 years, several PC isolates were identified as Atopobium vaginae to a high level of confidence. However, since A. vaginae is associated with bacterial vaginosis and is not a common PC contaminant, a retrospective investigation revealed that in all cases C. acnes was misidentified as A. vaginae . Our investigation demonstrated that the media type used to grow PC bacterial isolates can have a significant impact on the results obtained on the VITEK 2 system. Furthermore, other identification methods such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALD-TOF MS) and PCR amplification of the 16S RNA gene were only partially successful in the identification of C. acnes . Therefore, our findings support a multiphasic approach when PC isolates are identified as A. vaginae by the VITEK 2 system for proper identification of C. acnes using macroscopic, microscopic and other biochemical analyses.

Theory of a Quantum Scanning Microscope for Cold Atoms

We propose and analyze a scanning microscope to monitor "live" the quantum dynamics of cold atoms in a cavity QED setup. The microscope measures the atomic density with subwavelength resolution via dispersive couplings to a cavity and homodyne detection within the framework of continuous measurement theory. We analyze two modes of operation. First, for a fixed focal point the microscope records the wave packet dynamics of atoms with time resolution set by the cavity lifetime. Second, a spatial scan of the microscope acts to map out the spatial density of stationary quantum states. Remarkably, in the latter case, for a good cavity limit, the microscope becomes an effective quantum nondemolition device, such that the spatial distribution of motional eigenstates can be measured backaction free in single scans, as an emergent quantum nondemolition measurement.

Weak qubit measurement with a nonlinear cavity: beyond perturbation theory

We analyze the use of a driven nonlinear cavity to make a weak continuous measurement of a dispersively coupled qubit. We calculate the backaction dephasing rate and measurement rate beyond leading-order perturbation theory using a phase-space approach which accounts for cavity noise squeezing. Surprisingly, we find that increasing the coupling strength beyond the regime describable by leading-order perturbation theory (i.e., linear response) allows one to come significantly closer to the quantum limit on the measurement efficiency. We interpret this behavior in terms of the non-Gaussian photon number fluctuations of the nonlinear cavity. Our results are relevant to recent experiments using superconducting microwave circuits to study quantum measurement.

P1-12-12: Evaluation of Ile655Val HER2 Polymorphism Associated with Cardiac Toxicity Following the Administration of Trastuzumab in Women with Non-Metastatic Breast Cancer

Background: Trastuzumab is well tolerated without major side effects except for cardiac toxicity. Although a number of clinical parameters have been associated with trastuzumab-associated cardiac toxicity (TACT), there is some indication that genetic variation of the HER2 gene may be associated with TACT in a population of metastatic breast cancer patients. However, this finding needs confirmation and we looked at a population of non-metastatic breast cancer.

Purpose: This study aimed to evaluate the association between cardiac toxicity and HER2 [Ile655Val] polymorphism in non-metastatic breast cancer patients treated with trastuzumab.

Method: The Ile655Val HER2 polymorphism was assessed in 41 women using TaqMan technology. For this study, the genotyping was performed using DNA extracted from normal breast tissue located at more than 1 cm of any other lesions. Charts review was used to collect information on TACT which was defined as a decrease in the left ventricular ejection fraction (LVEF) of ≥15% or ≥10% with a resulting LVEF < 50% or any follow-up LVEF of < 45%. The Fisher exact test was used to evaluate the association between cardiac toxicity and HER2 polymorphism.

Results: No deviation from the Hardy-Weinberg equilibrium has been observed for the allele and genotype frequencies. The distribution of HER2 polymorphism was 10 Ile/Val (24%) and 31 Ile/Ile (76%). In this population, 22% (9/41) developed a cardiac toxicity. The Val655Ile genotype was associated with cardiac toxicity (0.03). In this preliminary study, 50% (5/10) of Ile/Val carriers compared to 13% (4/31) of Ile/Ile carriers showed TACT.

Conclusion: HER2 Ile655Val polymorphism may be an efficient marker of TACT considering this tendency with this small cohort of patients. Larger sample is needed to strengthen this conclusion, since this result may influence on prescribing decision for adjuvant chemotherapy and anti-HER2 therapy in HER2 positive patients.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-12-12.

Development of an engineering autologous palatal mucosa-like tissue for potential clinical applications

The goal of this study was to optimize key processes in recreating functional and viable palatal mucosa-like tissue that would be easy to handle and would promote wound healing. Normal human gingival fibroblasts and epithelial cells and a clinically useful biomaterial, CollaTape, were used. Structural and ultrastructural analyses showed that the gingival fibroblasts and epithelial cells adhered to the biomaterial and proliferated. Following a 6-day culture, using 10(5) fibroblasts and 10(6) epithelial cells, a well-organized palatal mucosa-like tissue was engineered. The engineered epithelium displayed various layers, including a stratum corneum, and contained cytokeratin 16-positive cells located in the supra-basal layer. This palatal mucosa-like engineered tissue was designed to meet a variety of surgical needs. The biodegradable collagen membrane (CollaTape) contributed to the flexibility of the engineered tissue. This engineered innovative tissue may contribute to the reconstruction of oral soft-tissue defects secondary to trauma, congenital defects, and acquired diseases.

Detection of Legionella spp. by fluorescent in situ hybridization in dental unit waterlines

AIMS

To confirm the presence of viable Legionella spp. in dental unit waterlines (DUWL) using fluorescent in situ hybridization (FISH) and compare this method with culture approach and also to validate the utility of an enrichment to increase FISH sensitivity.

METHODS AND RESULTS

Water samples from 40 dental units were analysed. Three different techniques for detecting Legionella spp. were compared: (i) culture approach, (ii) direct FISH and (iii) FISH with a previous R2A medium enrichment (R2A/FISH). The FISH detection was confirmed by PCR. The use of the direct FISH does not improve significantly the detection of legionellae when compared with the culture. On the contrary, when R2A/FISH was performed, sensitivity was, respectively, two- and threefold higher than that with the direct FISH and culture approach. Using R2A/FISH, 63% of water samples analysed showed a contamination by legionellae.

CONCLUSIONS

Legionellae detection by direct FISH and R2A/FISH in dental unit water is possible but is more rapid and more sensitive (R2A/FISH) than the culture approach.

SIGNIFICANCE AND IMPACT OF THE STUDY

R2A/FISH showed that several pathogens present in DUWL are viable but may not be culturable. Unlike PCR, R2A/FISH is designed to detect only metabolically active cells and therefore provides more pertinent information on infectious risk.

Assessment of bacterial endospore viability with fluorescent dyes

AIM

To validate three fluorescence viability assays designed primarily for vegetative cells on pure Bacillus endospores.

METHODS AND RESULTS

Purified fresh and gamma-irradiated Bacillus endospores (Bacillus cereus, B. coagulans and two strains of B. subtilis) were used. The viability assays were: 5-cyano-2,3-diotolyl tetrazolium chloride (CTC) to test respiratory activity and early germination, DiBAC4(3) and Live/Dead BacLight to measure membrane energization and permeabilization, respectively. Gamma irradiation treatment completely eliminated spore culturability and was used as negative control. The untreated spores showed respiratory activity after 1 h of incubation and this was characteristic of almost 100% of spores after 24 h. The membrane potential assessment gave no answer about spore viability. A lower proportion of untreated spores had permeabilized membrane compared with gamma-irradiated spores using Live/Dead BacLight (P < 0.02).

CONCLUSION

It is possible to use CTC and Live/Dead BacLight to rapidly test endospore viability and evaluate the proportion of spores in a preparation that could not be recovered with plate count.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that fluorescence tests could be applied to assess viability in potentially pathogenic Bacillus spore preparations within 1 h.

Apoptosis of bronchoalveolar lavage lymphocytes in hypersensitivity pneumonitis

The aim of this study was to look at the apoptosis of alveolar lymphocytes in hypersensitivity pneumonitis (HP). HP patients and normal unexposed controls were studied. The percentage of apoptotic lymphocytes was significantly lower in HP patients than in normal patients (37.4 +/- 3.4 versus 56.5 +/- 5.5% for Annexin V and propidium iodine detection methods and 0.4 +/- 0.1 versus 1.0 +/- 0.2% for dUTP nick end-labelling technique (TUNEL)). The proportion of bronchoalveolar lavage (BAL) lymphocytes positive for Fas antigen was significantly higher in HP patients than in normal subjects (71.7 +/- 5.4 versus 50.4 +/- 9.0%). However, no significant difference was found in the proportion of BAL lymphocytes positive for Fas ligand (FasL) between the two groups. Soluble Fas (sFas) levels in the BAL fluid of the patients and normals were 80.5 +/- 8.5 pg x mL(-1) and 23.2 +/- 3.1 pg x mL(-1), respectively. A positive correlation was found between the percentage of BAL lymphocytes and the levels of sFas for the total subjects but not within the separate study groups. The intracellular quantity of the inducible anti-apoptotic gene Bcl-xL product was significantly higher in the pulmonary lymphocytes of HP patients than in lymphocytes of the control, while no difference was found for constitutive anti-apoptotic protein (Bcl-2). In conclusion, the apoptosis of pulmonary lymphocytes is lower in hypersensitivity pneumonitis than in normal subjects. This could be explained, at least in part, by an increase of soluble Fas, the anti-apoptic gene, and Bcl-xL.

Catheter-assisted totally thoracoscopic coronary artery bypass grafting: a feasibility study

BACKGROUND

The purpose of this study is to examine the feasibility of performing totally thoracoscopic internal mammary-to-coronary artery bypass grafting with the assistance of radiologically guided catheter intervention.

METHODS

Fourteen dogs were subjected to mobilization of the internal mammary artery and anastomosis of it to the left anterior descending coronary artery over an angiographic catheter inserted into the internal mammary artery under fluoroscopy. The anastomosis was completed over the catheter using sutures and the application of fibrin glue. Eight animals underwent the anastomosis after their sacrifice. The other 6 animals were put on closed chest cardiopulmonary bypass and had their anastomosis done after intraaortic balloon occlusion and cardioplegic arrest of the heart. All animals had an angiographic and pathologic examination at the completion of the anastomosis.

RESULTS

Anastomosis was completed in all dogs. Three anastomoses leaked and two were noted to be stenosed at completion of the anastomosis. One leak was sealed by application of fibrin glue. Both stenotic anastomoses were caused by suturing of the back wall when a short angiographic catheter could not be positioned across the anastomosis.

CONCLUSIONS

Minimally invasive totally thoracoscopic mammary-to-coronary artery bypass grafting with catheter assistance is feasible. Technical improvement and appropriate instrumentation are required to minimize anastomotic failure.