In Silico Modeling Demonstrates that User Variability During Tumor Measurement Can Affect In Vivo Therapeutic Efficacy Outcomes.

User measurement bias during subcutaneous tumor measurement is a source of variation in preclinical in vivo studies. We investigated whether this user variability could impact efficacy study outcomes, in the form of the false negative result rate when comparing treated and control groups. Two tumor measurement methods were compared; calipers which rely on manual measurement, and an automatic 3D and thermal imaging device. Tumor growth curve data were used to create an in silico efficacy study with control and treated groups. Before applying user variability, treatment group tumor volumes were statistically different to the control group. Utilizing data collected from 15 different users across 9 in vivo studies, user measurement variability was computed for both methods and simulation was used to investigate its impact on the in silico study outcome. User variability produced a false negative result in 0.7% to 18.5% of simulated studies when using calipers, depending on treatment efficacy. When using an imaging device with lower user variability this was reduced to 0.0% to 2.6%, demonstrating that user variability impacts study outcomes and the ability to detect treatment effect. Reducing variability in efficacy studies can increase confidence in efficacy study outcomes without altering group sizes. By using a measurement device with lower user variability, the chance of missing a therapeutic effect can be reduced and time and resources spent pursuing false results could be saved. This improvement in data quality is of particular interest in discovery and dosing studies, where being able to detect small differences between groups is crucial.

Comparing Variability in Measurement of Subcutaneous Tumors in Mice Using 3D Thermal Imaging and Calipers.

Repeatable tumor measurements are key to accurately assessing tumor growth and treatment efficacy. A preliminary study that we conducted showed that a novel 3D and thermal imaging system (3D-TI) for measuring subcutaneous tumors in rodents significantly reduced interoperator variability across 3 in vivo efficacy studies. Here we further studied this reduction in interoperator variability across a much larger dataset. A dataset consisting of 6,532 paired 3D-TI and caliper interoperator measurements was obtained from tumor scans and measurements in 27 laboratories across 289 studies, 153 operators, over 20 mouse strains, and 100 cell lines. Interoperator variability in both measurement methods was analyzed using coefficient of variation (CV), intraclass correlation (ICC) analysis, and significance testing. The median 3D-TI CV was significantly lower than the median caliper CV. The effects of large interoperator variability at critical points in the study were also investigated. At stratified randomization, changing the operator performing caliper measurements resulted in a 59% probability that a mouse would be reassigned to a different group. The probability that this would occur when using 3D-TI was significantly lower at 29%. In studies in which a tumor was expected to regress, changing the operator during the study was associated with a tumor volume increase of approximately 500mm³ when using calipers. This change did not occur when using 3D-TI. We conclude that 3D-TI significantly reduces interoperator variability as compared with calipers and can improve reproducibility of in vivo studies across a wide range of mouse strains and cell lines.

The red edge excitation shift phenomenon can be used to unmask protein structural ensembles: implications for NEMO-ubiquitin interactions.

To understand complex molecular interactions, it is necessary to account for molecular flexibility and the available equilibrium of conformational states. Only a small number of experimental approaches can access such information. Potentially steady-state red edge excitation shift (REES) spectroscopy can act as a qualitative metric of changes to the protein free energy landscape (FEL) and the equilibrium of conformational states. First, we validate this hypothesis using a single Trp-containing protein, NF-κB essential modulator (NEMO). We provide detailed evidence from chemical denaturation studies, macromolecular crowding studies, and the first report of the pressure dependence of the REES effect. Combination of these data demonstrate that the REES effect can report on the 'ruggedness' of the FEL and we present a phenomenological model, based on realistic physical interpretations, for fitting steady-state REES data to allow quantification of this aspect of the REES effect. We test the conceptual framework we have developed by correlating findings from NEMO ligand-binding studies with the REES data in a range of NEMO-ligand binary complexes. Our findings shed light on the nature of the interaction between NEMO and poly-ubiquitin, suggesting that NEMO is differentially regulated by poly-ubiquitin chain length and that this regulation occurs via a modulation of the available equilibrium of conformational states, rather than gross structural change. This study therefore demonstrates the potential of REES as a powerful tool for tackling contemporary issues in structural biology and biophysics and elucidates novel information on the structure-function relationship of NEMO and key interaction partners.