An ECHO of Cartilage: In Silico Prediction of Combinatorial Treatments to Switch Between Transient and Permanent Cartilage Phenotypes With Ex Vivo Validation.

A fundamental question in cartilage biology is: what determines the switch between permanent cartilage found in the articular joints and transient hypertrophic cartilage that functions as a template for bone? This switch is observed both in a subset of OA patients that develop osteophytes, as well as in cell-based tissue engineering strategies for joint repair. A thorough understanding of the mechanisms regulating cell fate provides opportunities for treatment of cartilage disease and tissue engineering strategies. The objective of this study was to understand the mechanisms that regulate the switch between permanent and transient cartilage using a computational model of chondrocytes, ECHO. To investigate large signaling networks that regulate cell fate decisions, we developed the software tool ANIMO, Analysis of Networks with interactive Modeling. In ANIMO, we generated an activity network integrating 7 signal transduction pathways resulting in a network containing over 50 proteins with 200 interactions. We called this model ECHO, for executable chondrocyte. Previously, we showed that ECHO could be used to characterize mechanisms of cell fate decisions. ECHO was first developed based on a Boolean model of growth plate. Here, we show how the growth plate Boolean model was translated to ANIMO and how we adapted the topology and parameters to generate an articular cartilage model. In ANIMO, many combinations of overactivation/knockout were tested that result in a switch between permanent cartilage (SOX9+) and transient, hypertrophic cartilage (RUNX2+). We used model checking to prioritize combination treatments for wet-lab validation. Three combinatorial treatments were chosen and tested on metatarsals from 1-day old rat pups that were treated for 6 days. We found that a combination of IGF1 with inhibition of ERK1/2 had a positive effect on cartilage formation and growth, whereas activation of DLX5 combined with inhibition of PKA had a negative effect on cartilage formation and growth and resulted in increased cartilage hypertrophy. We show that our model describes cartilage formation, and that model checking can aid in choosing and prioritizing combinatorial treatments that interfere with normal cartilage development. Here we show that combinatorial treatments induce changes in the zonal distribution of cartilage, indication possible switches in cell fate. This indicates that simulations in ECHO aid in describing pathologies in which switches between cell fates are observed, such as OA.

Modeling Diagnostic Strategies to Manage Toxic Adverse Events following Cancer Immunotherapy.

BACKGROUND: Although immunotherapy (IMT) provides significant survival benefits in selected patients, approximately 10% of patients experience (serious) immune-related adverse events (irAEs). The early detection of adverse events will prevent irAEs from progressing to severe stages, and routine testing for irAEs has become common practice. Because a positive test outcome might indicate a clinically manifesting irAE that requires treatment to (temporarily) discontinue, the occurrence of false-positive test outcomes is expected to negatively affect treatment outcomes. This study explores how the UPPAAL modeling environment can be used to assess the impact of test accuracy (i.e., test sensitivity and specificity), on the probability of patients entering palliative care within 11 IMT cycles. METHODS: A timed automata-based model was constructed using real-world data and expert consultation. Model calibration was performed using data from 248 non-small-cell lung cancer patients treated with nivolumab. A scenario analysis was performed to evaluate the effect of changes in test accuracy on the probability of patients transitioning to palliative care. RESULTS: The constructed model was used to estimate the cumulative probabilities for the patients' transition to palliative care, which were found to match real-world clinical observations after model calibration. The scenario analysis showed that the specificity of laboratory tests for routine monitoring has a strong effect on the probability of patients transitioning to palliative care, whereas the effect of test sensitivity was limited. CONCLUSION: We have obtained interesting insights by simulating a care pathway and disease progression using UPPAAL. The scenario analysis indicates that an increase in test specificity results in decreased discontinuation of treatment due to suspicion of irAEs, through a reduction of false-positive test outcomes.

A methodology for evaluating tooth wear monitoring using timed automata modelling.

OBJECTIVES: Tooth wear is a multifactorial condition leading to the loss of dental hard tissues. A counselling/monitoring protocol is of importance in order to keep that loss as limited as possible. Since many factors are involved and a time span of decades is included, research to disentangle all these processes in patients is difficult. Instead, a modelling technique was used that is able to deal with time, costs and probabilistic and stochastic information. The aim was to shed light on the question: does a yearly or a once-in-five-years counselling/monitoring protocol yield better outcome measures? METHODS: A so-called timed automata model was adopted, analysed with the tool UPPAAL. To our knowledge, this is the first time that formal modelling is applied in dentistry. In this article, a UPPAAL model for the evaluation of tooth wear is described. RESULTS: Using the UPPAAL model, it was calculated that with a yearly counselling/monitoring protocol the severity of tooth wear at age 74, the total costs per person and the number of restorative treatments were less, and the number of so-called "good years" was higher. CONCLUSIONS: With the use of the UPPAAL model, it may be concluded that a yearly counselling/monitoring protocol can yield better outcome measures. CLINICAL SIGNIFICANCE: Regarding dentistry in general and tooth wear in particular, with the use of a timed automata model in UPPAAL, actual research questions can be answered, factors of influence in a multifactorial condition like tooth wear can be clarified, and future research topics can be determined.

ECHO, the executable CHOndrocyte: A computational model to study articular chondrocytes in health and disease.

Computational modeling can be used to investigate complex signaling networks in biology. However, most modeling tools are not suitable for molecular cell biologists with little background in mathematics. We have built a visual-based modeling tool for the investigation of dynamic networks. Here, we describe the development of computational models of cartilage development and osteoarthritis, in which a panel of relevant signaling pathways are integrated. In silico experiments give insight in the role of each of the pathway components and reveal which perturbations may deregulate the basal healthy state of cells and tissues. We used a previously developed computational modeling tool Analysis of Networks with Interactive Modeling (ANIMO) to generate an activity network integrating 7 signal transduction pathways resulting in a network containing over 50 nodes and 200 interactions. We performed in silico experiments to characterize molecular mechanisms of cell fate decisions. The model was used to mimic biological scenarios during cell differentiation using RNA-sequencing data of a variety of stem cell sources as input. In a case-study, we wet-lab-tested the model-derived hypothesis that expression of DKK1 (Dickkopf-1) and FRZB (Frizzled related protein, WNT antagonists) and GREM1 (gremlin 1, BMP antagonist) prevents IL1ß (Interleukin 1 beta)-induced MMP (matrix metalloproteinase) expression, thereby preventing cartilage degeneration, at least in the short term. We found that a combination of DKK1, FRZB and GREM1 may play a role in modulating the effects of IL1ß induced inflammation in human primary chondrocytes.

Comparison of Timed Automata with Discrete Event Simulation for Modeling of Biomarker-Based Treatment Decisions: An Illustration for Metastatic Castration-Resistant Prostate Cancer.

BACKGROUND: With the advent of personalized medicine, the field of health economic modeling is being challenged and the use of patient-level dynamic modeling techniques might be required. OBJECTIVES: To illustrate the usability of two such techniques, timed automata (TA) and discrete event simulation (DES), for modeling personalized treatment decisions. METHODS: An early health technology assessment on the use of circulating tumor cells, compared with prostate-specific antigen and bone scintigraphy, to inform treatment decisions in metastatic castration-resistant prostate cancer was performed. Both modeling techniques were assessed quantitatively, in terms of intermediate outcomes (e.g., overtreatment) and health economic outcomes (e.g., net monetary benefit). Qualitatively, among others, model structure, agent interactions, data management (i.e., importing and exporting data), and model transparency were assessed. RESULTS: Both models yielded realistic and similar intermediate and health economic outcomes. Overtreatment was reduced by 6.99 and 7.02 weeks by applying circulating tumor cell as a response marker at a net monetary benefit of -€1033 and -€1104 for the TA model and the DES model, respectively. Software-specific differences were observed regarding data management features and the support for statistical distributions, which were considered better for the DES software. Regarding method-specific differences, interactions were modeled more straightforward using TA, benefiting from its compositional model structure. CONCLUSIONS: Both techniques prove suitable for modeling personalized treatment decisions, although DES would be preferred given the current software-specific limitations of TA. When these limitations are resolved, TA would be an interesting modeling alternative if interactions are key or its compositional structure is useful to manage multi-agent complex problems.

Modelling with ANIMO: between fuzzy logic and differential equations.

BACKGROUND: Computational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computational support and allow insight into the complex networks of signaling events occurring in living cells. ANIMO makes use of timed automata as an underlying model, thereby enabling analysis techniques from computer science like model checking. Biology experts are able to use ANIMO via a user interface specifically tailored for biological applications. In this paper we compare the use of ANIMO with some established formalisms on two case studies. RESULTS: ANIMO is a powerful and user-friendly tool that can compete with existing continuous and discrete paradigms. We show this by presenting ANIMO models for two case studies: Drosophila melanogaster circadian clock, and signal transduction events downstream of TNF α and EGF in HT-29 human colon carcinoma cells. The models were originally developed with ODEs and fuzzy logic, respectively. CONCLUSIONS: Two biological case studies that have been modeled with respectively ODE and fuzzy logic models can be conveniently modeled using ANIMO. The ANIMO models require less parameters than ODEs and are more precise than fuzzy logic. For this reason we position the modelling paradigm of ANIMO between ODEs and fuzzy logic.

Modeling biological pathway dynamics with timed automata.

Living cells are constantly subjected to a plethora of environmental stimuli that require integration into an appropriate cellular response. This integration takes place through signal transduction events that form tightly interconnected networks. The understanding of these networks requires capturing their dynamics through computational support and models. ANIMO (analysis of Networks with Interactive Modeling) is a tool that enables the construction and exploration of executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analyzed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signaling pathways, contributing to the integration of isolated signaling events into complex network models. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic behavior of the network of interest. A user-friendly interface hides the use of Timed Automata from the user, while keeping the expressive power intact. Abstraction to single-parameter kinetics speeds up construction of models that remain faithful enough to provide meaningful insight. The resulting dynamic behavior of the network components is displayed graphically, allowing for an intuitive and interactive modeling experience.