The influence of resolution on the predictive power of spatial heterogeneity measures as biomarkers of liver fibrosis.

Spatial heterogeneity of cells in liver biopsies can be used as biomarker for disease severity of patients. This heterogeneity can be quantified by non-parametric statistics of point pattern data, which make use of an aggregation of the point locations. The method and scale of aggregation are usually chosen ad hoc, despite values of the aforementioned statistics being heavily dependent on them. Moreover, in the context of measuring heterogeneity, increasing spatial resolution will not endlessly provide more accuracy. The question then becomes how changes in resolution influence heterogeneity indicators, and subsequently how they influence their predictive abilities. In this paper, cell level data of liver biopsy tissue taken from chronic Hepatitis B patients is used to analyze this issue. Firstly, Morisita-Horn indices, Shannon indices and Getis-Ord statistics were evaluated as heterogeneity indicators of different types of cells, using multiple resolutions. Secondly, the effect of resolution on the predictive performance of the indices in an ordinal regression model was investigated, as well as their importance in the model. A simulation study was subsequently performed to validate the aforementioned methods. In general, for specific heterogeneity indicators, a downward trend in predictive performance could be observed. While for local measures of heterogeneity a smaller grid-size is outperforming, global measures have a better performance with medium-sized grids. In addition, the use of both local and global measures of heterogeneity is recommended to improve the predictive performance.

Automated Spot Counting in Microbiology.

Biological samples are routinely analyzed for microbe concentration. The samples are diluted, loaded onto established host cell cultures, and incubated. If infectious agents are present in the samples, they form circular spots that do not contain the host cells. Each spot is assumed to be originated from a single microbial unit such as a bacterial colony forming unit or viral plaque forming unit. The undiluted sample concentration is estimated by counting the spots and back-calculating. Counting the number of spots by trained technicians is currently the gold standard but it is laborious, subjective, and hard to scale. This paper presents a new automated algorithm for spot counting, Localized and Sequential Thresholding (LoST). Validation studies showed that LoST performance was comparable with manual counting and outperformed several existing tools on images with overlapping spots. The LoST algorithm employs sequential thresholding through a two-stage segmentation and borrows information across all images from the same dilution series to fine-tune the count and identify right censoring. The algorithm increases the efficiency of the spot counting and the quality of the downstream analysis, especially when coupled with an appropriate statistical serial dilution model to enhance the undiluted sample concentration estimation procedure.

Measures of spatial heterogeneity in the liver tissue micro-environment as predictive factors for fibrosis score.

The organization and interaction between hepatocytes and other hepatic non-parenchymal cells plays a pivotal role in maintaining normal liver function and structure. Although spatial heterogeneity within the tumor micro-environment has been proven to be a fundamental feature in cancer progression, the role of liver tissue topology and micro-environmental factors in the context of liver damage in chronic infection has not been widely studied yet. We obtained images from 110 core needle biopsies from a cohort of chronic hepatitis B patients with different fibrosis stages according to METAVIR score. The tissue sections were immunofluorescently stained and imaged to determine the locations of CD45 positive immune cells and HBsAg-negative and HBsAg-positive hepatocytes within the tissue. We applied several descriptive techniques adopted from ecology, including Getis-Ord, the Shannon Index and the Morisita-Horn Index, to quantify the extent to which immune cells and different types of liver cells co-localize in the tissue biopsies. Additionally, we modeled the spatial distribution of the different cell types using a joint log-Gaussian Cox process and proposed several features to quantify spatial heterogeneity. We then related these measures to the patient fibrosis stage by using a linear discriminant analysis approach. Our analysis revealed that the co-localization of HBsAg-negative hepatocytes with immune cells and the co-localization of HBsAg-positive hepatocytes with immune cells are equally important factors for explaining the METAVIR score in chronic hepatitis B patients. Moreover, we found that if we allow for an error of 1 on the METAVIR score, we are able to reach an accuracy of around 80%. With this study we demonstrate how methods adopted from ecology and applied to the liver tissue micro-environment can be used to quantify heterogeneity and how these approaches can be valuable in biomarker analyses for liver topology.

AI/ML Models to Predict the Severity of Drug-Induced Liver Injury for Small Molecules.

Drug-induced liver injury (DILI), believed to be a multifactorial toxicity, has been a leading cause of attrition of small molecules during discovery, clinical development, and postmarketing. Identification of DILI risk early reduces the costs and cycle times associated with drug development. In recent years, several groups have reported predictive models that use physicochemical properties or in vitro and in vivo assay endpoints; however, these approaches have not accounted for liver-expressed proteins and drug molecules. To address this gap, we have developed an integrated artificial intelligence/machine learning (AI/ML) model to predict DILI severity for small molecules using a combination of physicochemical properties and off-target interactions predicted in silico. We compiled a data set of 603 diverse compounds from public databases. Among them, 164 were categorized as Most DILI (M-DILI), 245 as Less DILI (L-DILI), and 194 as No DILI (N-DILI) by the FDA. Six machine learning methods were used to create a consensus model for predicting the DILI potential. These methods include k-nearest neighbor (k-NN), support vector machine (SVM), random forest (RF), Naïve Bayes (NB), artificial neural network (ANN), logistic regression (LR), weighted average ensemble learning (WA) and penalized logistic regression (PLR). Among the analyzed ML methods, SVM, RF, LR, WA, and PLR identified M-DILI and N-DILI compounds, achieving a receiver operating characteristic area under the curve of 0.88, sensitivity of 0.73, and specificity of 0.9. Approximately 43 off-targets, along with physicochemical properties (fsp3, log S, basicity, reactive functional groups, and predicted metabolites), were identified as significant factors in distinguishing between M-DILI and N-DILI compounds. The key off-targets that we identified include: PTGS1, PTGS2, SLC22A12, PPARγ, RXRA, CYP2C9, AKR1C3, MGLL, RET, AR, and ABCC4. The present AI/ML computational approach therefore demonstrates that the integration of physicochemical properties and predicted on- and off-target biological interactions can significantly improve DILI predictivity compared to chemical properties alone.

A novel statistical test for treatment differences in clinical trials using a response-adaptive forward-looking Gittins Index Rule.

The most common objective for response-adaptive clinical trials is to seek to ensure that patients within a trial have a high chance of receiving the best treatment available by altering the chance of allocation on the basis of accumulating data. Approaches that yield good patient benefit properties suffer from low power from a frequentist perspective when testing for a treatment difference at the end of the study due to the high imbalance in treatment allocations. In this work we develop an alternative pairwise test for treatment difference on the basis of allocation probabilities of the covariate-adjusted response-adaptive randomization with forward-looking Gittins Index (CARA-FLGI) Rule for binary responses. The performance of the novel test is evaluated in simulations for two-armed studies and then its applications to multiarmed studies are illustrated. The proposed test has markedly improved power over the traditional Fisher exact test when this class of nonmyopic response adaptation is used. We also find that the test's power is close to the power of a Fisher exact test under equal randomization.

The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions.

The accurate prediction of binding affinity between protein and small molecules with free energy methods, particularly the difference in binding affinities via relative binding free energy calculations, has undergone a dramatic increase in use and impact over recent years. The improvements in methodology, hardware, and implementation can deliver results with less than 1 kcal/mol mean unsigned error between calculation and experiment. This is a remarkable achievement and beckons some reflection on the significance of calculation approaching the accuracy of experiment. In this article, we describe a statistical analysis of the implications of variance (standard deviation) of both experimental and calculated binding affinities with respect to the unknown true binding affinity. We reveal that plausible ratios of standard deviation in experiment and calculation can lead to unexpected outcomes for assessing the performance of predictions. The work extends beyond the case of binding free energies to other affinity or property prediction methods.

Bayesian pooling versus sequential integration of small preclinical trials: a comparison within linear and nonlinear modeling frameworks.

Bayesian sequential integration is an appealing approach in drug development, as it allows to recursively update posterior distributions as soon as new data become available, thus considerably reducing the computation time. However, preclinical trials are often characterized by small sample sizes, which may affect the estimation process during the first integration steps, particularly when complex PK-PD models are used. In this case, sequential integration would not be practicable, and trials should be pooled together. This work is aimed at comparing simple Bayesian pooling with sequential integration through a simulation study. The two techniques are compared under several scenarios using linear as well as nonlinear models. The results of our simulation study encourage the use of Bayesian sequential integration with linear models. However, in the case of nonlinear models several caveats arise. This paper outlines some important recommendations and precautions in that respect.

Testing of acetaminophen in support of the international multilaboratory in vivo rat Pig-a assay validation trial.

Acetaminophen, a nonmutagenic compound as previously concluded from bacteria, in vitro mammalian cell, and in vivo transgenic rat assays, presented a good profile as a nonmutagenic reference compound for use in the international multilaboratory Pig-a assay validation. Acetaminophen was administered at 250, 500, 1,000, and 2,000 mg·kg-1 ·day-1 to male Sprague Dawley rats once daily in 3 studies (3 days, 2 weeks, and 1 month with a 1-month recovery group). The 3-Day and 1-Month Studies included assessments of the micronucleus endpoint in peripheral blood erythrocytes and the comet endpoint in liver cells and peripheral blood cells in addition to the Pig-a assay; appropriate positive controls were included for each assay. Within these studies, potential toxicity of acetaminophen was evaluated and confirmed by inclusion of liver damage biomarkers and histopathology. Blood was sampled pre-treatment and at multiple time points up to Day 57. Pig-a mutant frequencies were determined in total red blood cells (RBCs) and reticulocytes (RETs) as CD59-negative RBC and CD59-negative RET frequencies, respectively. No increases in DNA damage as indicated through Pig-a, micronucleus, or comet endpoints were seen in treated rats. All positive controls responded as appropriate. Data from this series of studies demonstrate that acetaminophen is not mutagenic in the rat Pig-a model. These data are consistent with multiple studies in other nonclinical models, which have shown that acetaminophen is not mutagenic. At 1,000 mg·kg-1 ·day-1 , Cmax values of acetaminophen on Day 28 were 153,600 ng/ml and 131,500 ng/ml after single and repeat dosing, respectively, which were multiples over that of clinical therapeutic exposures (2.6-6.1 fold for single doses of 4,000 mg and 1,000 mg, respectively, and 11.5 fold for multiple dose of 4,000 mg) (FDA 2002). Data generated were of high quality and valid for contribution to the international multilaboratory validation of the in vivo Rat Pig-a Mutation Assay.

Marginalized models for right-truncated and interval-censored time-to-event data.

Analysis of clustered data is often performed using random effects regression models. In such conditional models, a cluster-specific random effect is often introduced into the linear predictor function. Parameter interpretation of the covariate effects is then conditioned on the random effects, leading to a subject-specific interpretation of the regression parameters. Recently, Marginalized Multilevel Models (MMM) and the Bridge distribution models have been proposed as a unified approach, which allows one to capture the within-cluster correlations by specifying random effects while still allowing for marginal parameter interpretation. In this paper, we investigate these two approaches, and the conditional Generalized Linear Mixed Model (GLMM), in the context of right-truncated, interval-censored time-to-event data, further characterized by clustering and additional overdispersion. While these models have been applied in literature to model the mean, here we extend their application to modeling the hazard function for the survival endpoints. The models are applied to analyze data from the HET-CAMVT experiment which was designed to assess the potential of a compound to cause injection site reaction. Results show that the MMM and Bridge distribution approaches are useful when interest is in the marginal interpretation of the covariate effects.

Bayesian sequential integration within a preclinical pharmacokinetic and pharmacodynamic modeling framework: Lessons learned.

The present manuscript aims to discuss the implications of sequential knowledge integration of small preclinical trials in a Bayesian pharmacokinetic and pharmacodynamic (PK-PD) framework. While, at first sight, a Bayesian PK-PD framework seems to be a natural framework to allow for sequential knowledge integration, the scope of this paper is to highlight some often-overlooked challenges while at the same time providing some guidances in the many and overwhelming choices that need to be made. Challenges as well as opportunities will be discussed that are related to the impact of (1) the prior specification, (2) the choice of random effects, (3) the type of sequential integration method. In addition, it will be shown how the success of a sequential integration strategy is highly dependent on a carefully chosen experimental design when small trials are analyzed.

A Bayesian K-PD model for synergy: A case study.

Coadministration of 2 or more compounds can alter both the pharmacokinetics and pharmacodynamics of individual compounds. While experiments on pharmacodynamic drug-drug interactions are usually performed in an in vitro setting, this experiment focuses on an in vivo setting. The change over time of a safety biomarker is modeled using an indirect response model, in which the virtual pharmacokinetic profile of one compound drives the effect of the other. Several experiments at different dose level combinations were performed sequentially. While a traditional frequentist analysis consists of estimating the model parameters based on all the data simultaneously, in this work, we consider a Bayesian inference framework allowing to incorporate the results from a historical dose-response experiment.

Detecting influential observations in a model-based cluster analysis.

Finite mixture models have been used to model population heterogeneity and to relax distributional assumptions. These models are also convenient tools for clustering and classification of complex data such as, for example, repeated-measurements data. The performance of model-based clustering algorithms is sensitive to influential and outlying observations. Methods for identifying outliers in a finite mixture model have been described in the literature. Approaches to identify influential observations are less common. In this paper, we apply local-influence diagnostics to a finite mixture model with known number of components. The methodology is illustrated on real-life data.

Comparing sampling methods for pharmacokinetic studies using model averaged derived parameters.

Pharmacokinetic studies aim to study how a compound is absorbed, distributed, metabolised, and excreted. The concentration of the compound in the blood or plasma is measured at different time points after administration and pharmacokinetic parameters such as the area under the curve (AUC) or maximum concentration (Cmax ) are derived from the resulting concentration time profile. In this paper, we want to compare different methods for collecting concentration measurements (traditional sampling versus microsampling) on the basis of these derived parameters. We adjust and evaluate an existing method for testing superiority of multiple derived parameters that accounts for model uncertainty. We subsequently extend the approach to allow testing for equivalence. We motivate the methods through an illustrative example and evaluate the performance using simulations. The extensions show promising results for application to the desired setting.

Models for zero-inflated, correlated count data with extra heterogeneity: when is it too complex?

Statistical analysis of count data typically starts with a Poisson regression. However, in many real-life applications, it is observed that the variation in the counts is larger than the mean, and one needs to deal with the problem of overdispersion in the counts. Several factors may contribute to overdispersion: (1) unobserved heterogeneity due to missing covariates, (2) correlation between observations (such as in longitudinal studies), and (3) the occurrence of many zeros (more than expected from the Poisson distribution). In this paper, we discuss a model that allows one to explicitly take each of these factors into consideration. The aim of this paper is twofold: (1) investigate whether we can identify the cause of overdispersion via model selection, and (2) investigate the impact of a misspecification of the model on the power of a covariate. The paper is motivated by a study of the occurrence of drug-induced arrhythmia in beagle dogs based on electrocardiogram recordings, with the objective to evaluate the effect of potential drugs on the heartbeat irregularities. Copyright © 2016 John Wiley & Sons, Ltd.

A clustering algorithm for multivariate longitudinal data.

Latent growth modeling approaches, such as growth mixture models, are used to identify meaningful groups or classes of individuals in a larger heterogeneous population. But when applied to multivariate repeated measures computational problems are likely, due to the high dimension of the joint distribution of the random effects in these mixed-effects models. This article proposes a cluster algorithm for multivariate repeated data, using pseudo-likelihood and ideas based on k-means clustering, to reveal homogenous subgroups. The algorithm was demonstrated on an electro-encephalogram dataset set quantifying the effect of psychoactive compounds on the brain activity in rats.

Evaluation of p-phenylenediamine, o-phenylphenol sodium salt, and 2,4-diaminotoluene in the rat comet assay as part of the Japanese Center for the Validation of Alternative Methods (JaCVAM)-initiated international validation study of in vivo rat alkaline comet assay.

As part of the Japanese Center for the Validation of Alternative Methods (JaCVAM)-initiated international validation study of in vivo rat alkaline comet assay (comet assay), p-phenylenediamine dihydrochloride (PPD), o-phenylphenol sodium salt (OPP), and 2,4-diaminotoluene (2,4-DAT), were analyzed in this laboratory as coded test chemicals. Male Sprague-Dawley rats (7-9 weeks of age) were given three oral doses of the test compounds, 24 and 21 h apart and liver and stomach were sampled 3h after the final dose administration. Under the conditions of the test, no increases in DNA damage were observed in liver and stomach with PPD and OPP up to 100 and 1000 mg/kg/day, respectively. 2,4-DAT, a known genotoxic carcinogen, induced a weak but reproducible, dose-related and statistically significant increase in DNA damage in liver cells while no increases were observed in stomach cells.

Flexible modelling of simultaneously interval censored and truncated time-to-event data.

This paper deals with the analysis of data from a HET-CAM(VT) experiment. From a statistical perspective, such data yield many challenges. First of all, the data are typically time-to-event like data, which are at the same time interval censored and right truncated. In addition, one has to cope with overdispersion as well as clustering. Traditional analysis approaches ignore overdispersion and clustering and summarize the data into a continuous score that can be analysed using simple linear models. In this paper, a novel combined frailty model is developed that simultaneously captures all of the aforementioned statistical challenges posed by the data.

Carcinogenicity in rats of the SGLT2 inhibitor canagliflozin.

The carcinogenicity potential of canagliflozin, an inhibitor of SGLT2, was evaluated in a 2-year rat study (10, 30, and 100 mg/kg). Rats showed an increase in pheochromocytomas, renal tubular tumors, and testicular Leydig cell tumors. Systemic exposure multiples at the highest dose relative to the maximum clinical dose were 12- to 21-fold. Pheochromocytomas and renal tubular tumors were noted in both sexes at 100 mg/kg. Leydig cell tumors were observed in males in all dose groups and were associated with increased luteinizing hormone levels. Hyperplasia was increased in the adrenal medulla at 100 mg/kg, but only a limited increase in simple tubular hyperplasia was observed in the kidney of males at 100 mg/kg. Hyperostosis occurred and was accompanied by substantial effects on calcium metabolism, including increased urinary calcium excretion and decreased levels of calcium regulating hormones (1,25-dihydroxyvitamin D and parathyroid hormone). A separate study with radiolabeled calcium confirmed that increased urinary calcium excretion was mediated via increased calcium absorption from the gastrointestinal tract. It was hypothesized that, at high doses, canagliflozin might have inhibited glucose absorption in the intestine via SGLT1 inhibition that resulted in glucose malabsorption, which increased calcium absorption by stimulating colonic glucose fermentation and reducing intestinal pH. Pheochromocytomas and adrenal medullary hyperplasia were attributed to altered calcium homeostasis, which have a known relationship in the rat. In conclusion, Leydig cell tumors were associated with increased luteinizing hormone levels and pheochromocytomas were most likely related to glucose malabsorption and altered calcium homeostasis. Renal tubular tumors may also have been linked to glucose malabsorption.

The concordance between nonclinical and phase I clinical cardiovascular assessment from a cross-company data sharing initiative.

It is widely accepted that more needs to be done to bring new, safe, and efficacious drugs to the market. Cardiovascular toxicity detected both in early drug discovery as well as in the clinic, is a major contributor to the high failure rate of new molecules. The growth of translational safety offers a promising approach to improve the probability of success for new molecules. Here we describe a cross-company initiative to determine the concordance between the conscious telemetered dog and phase I outcome for 3 cardiovascular parameters. The data indicate that, in the context of the methods applied in this analysis, the ability to detect compounds that affect the corrected QT interval (QTc) was good within the 10-30x exposure range but the predictive or detective value for heart rate and diastolic blood pressure was poor. These findings may highlight opportunities to refine both the animal and the clinical study designs, as well as refocusing the assessment of value of dog cardiovascular assessments beyond phase 1. This investigation has also highlighted key considerations for cross-company data sharing and presents a unique learning opportunity to improve future translational projects.

In vivo longitudinal micro-CT study of bent long limb bones in rat offspring.

Micro-computed X-ray tomography (micro-CT) has been reported as a reliable method to assess ex vivo rat and rabbit fetal skeletons in embryo-fetal developmental toxicity studies. Since micro-CT is a non-invasive imaging modality it has the potential for longitudinal, in vivo investigation of postnatal skeletal development. This is the first paper using micro-CT to assess the reversibility of drug-induced bent long bones in a longitudinal study from birth to early adulthood in rat offspring. Analysis of the scans obtained on postnatal Day 0, 7, 21 and 80 showed complete recovery or repair of the bent long limb bones (including the scapula) within the first 3 weeks. When assessing risk the ability to demonstrate recovery is highly advantageous when interpreting such transient skeletal change. In summary, in vivo micro-CT of small laboratory animals can aid in non-clinical safety assessment, particularly for specific mechanistic purposes or to address a particular concern in developmental biology.