Resistance models to EGFR inhibition and chemotherapy in non-small cell lung cancer via analysis of tumour size dynamics

Understanding tumour growth variability in breast cancer xenograft models identifies PARP inhibition resistance biomarkers

Understanding the mechanisms of resistance to PARP inhibitors (PARPi) is a clinical priority, especially in breast cancer. We developed a novel mathematical framework accounting for intrinsic resistance to olaparib, identified by fitting the model to tumour growth metrics from breast cancer patient-derived xenograft (PDX) data. Pre-treatment transcriptomic profiles were used with the calculated resistance to identify baseline biomarkers of resistance, including potential combination targets. The model provided both a classification of responses, as well as a continuous description of resistance, allowing for more robust biomarker associations and capturing the observed variability. Thirty-six resistance gene markers were identified, including multiple homologous recombination repair (HRR) pathway genes. High WEE1 expression was also linked to resistance, highlighting an opportunity for combining PARP and WEE1 inhibitors. This framework facilitates a fully automated way of capturing intrinsic resistance, and accounts for the pharmacological response variability captured within PDX studies and hence provides a precision medicine approach.

Quantitative modeling of tumor dynamics and development of drug resistance in non-small cell lung cancer patients treated with erlotinib

Insight into the development of treatment resistance can support the optimization of anticancer treatments. This study aims to characterize the tumor dynamics and development of drug resistance in patients with non-small cell lung cancer treated with erlotinib, and investigate the relationship between baseline circulating tumor DNA (ctDNA) data and tumor dynamics. Data obtained for the analysis included (1) intensively sampled erlotinib concentrations from 29 patients from two previous pharmacokinetic (PK) studies, and (2) tumor sizes, ctDNA measurements, and sparsely sampled erlotinib concentrations from 18 patients from the START-TKI study. A two-compartment population PK model was first developed which well-described the PK data. The PK model was subsequently applied to investigate the exposure-tumor dynamics relationship. To characterize the tumor dynamics, models accounting for intra-tumor heterogeneity and acquired resistance with or without primary resistance were investigated. Eventually, the model assumed acquired resistance only resulted in an adequate fit. Additionally, models with or without exposure-dependent treatment effect were explored, and no significant exposure-response relationship for erlotinib was identified within the observed exposure range. Subsequently, the correlation of baseline ctDNA data on EGFR and TP53 variants with tumor dynamics' parameters was explored. The analysis indicated that higher baseline plasma EGFR mutation levels correlated with increased tumor growth rates, and the inclusion of ctDNA measurements improved model fit. This result suggests that quantitative ctDNA measurements at baseline have the potential to be a predictor of anticancer treatment response. The developed model can potentially be applied to design optimal treatment regimens that better overcome resistance.

Explaining in-vitro to in-vivo efficacy correlations in oncology pre-clinical development via a semi-mechanistic mathematical model

In-vitro to in-vivo correlations (IVIVC), relating in-vitro parameters like IC50 to in-vivo drug exposure in plasma and tumour growth, are widely used in oncology for experimental design and dose decisions. However, they lack a deeper understanding of the underlying mechanisms. Our paper therefore focuses on linking empirical IVIVC relations for small-molecule kinase inhibitors with a semi-mechanistic tumour-growth model. We develop an approach incorporating parameters like the compound's peak-trough ratio (PTR), Hill coefficient of in-vitro dose-response curves, and xenograft-specific properties. This leads to formulas for determining efficacious doses for tumor stasis under linear pharmacokinetics equivalent to traditional empirical IVIVC relations, but enabling more systematic analysis. Our findings reveal that in-vivo xenograft-specific parameters, specifically the growth rate (g) and decay rate (d), along with the average exposure, are generally more significant determinants of tumor stasis and effective dose than the compound's peak-trough ratio. However, as the Hill coefficient increases, the dependency of tumor stasis on the PTR becomes more pronounced, indicating that the compound is more influenced by its maximum or trough values rather than the average exposure. Furthermore, we discuss the translation of our method to predict population dose ranges in clinical studies and propose a resistance mechanism that solely relies on specific in-vivo xenograft parameters instead of IC50 exposure coverage. In summary, our study aims to provide a more mechanistic understanding of IVIVC relations, emphasizing the importance of xenograft-specific parameters and PTR on tumor stasis.

Treatment of evolving cancers will require dynamic decision support

Cancer research has traditionally focused on developing new agents, but an underexplored question is that of the dose and frequency of existing drugs. Based on the modus operandi established in the early days of chemotherapies, most drugs are administered according to predetermined schedules that seek to deliver the maximum tolerated dose and are only adjusted for toxicity. However, we believe that the complex, evolving nature of cancer requires a more dynamic and personalized approach. Chronicling the milestones of the field, we show that the impact of schedule choice crucially depends on processes driving treatment response and failure. As such, cancer heterogeneity and evolution dictate that a one-size-fits-all solution is unlikely-instead, each patient should be mapped to the strategy that best matches their current disease characteristics and treatment objectives (i.e. their 'tumorscape'). To achieve this level of personalization, we need mathematical modeling. In this perspective, we propose a five-step 'Adaptive Dosing Adjusted for Personalized Tumorscapes (ADAPT)' paradigm to integrate data and understanding across scales and derive dynamic and personalized schedules. We conclude with promising examples of model-guided schedule personalization and a call to action to address key outstanding challenges surrounding data collection, model development, and integration.

How translational modeling in oncology needs to get the mechanism just right

Translational model‐based approaches have played a role in increasing success in the development of novel anticancer treatments. However, despite this, significant translational uncertainty remains from animal models to patients. Optimization of dose and scheduling (regimen) of drugs to maximize the therapeutic utility (maximize efficacy while avoiding limiting toxicities) is still predominately driven by clinical investigations. Here, we argue that utilizing pragmatic mechanism‐based translational modeling of nonclinical data can further inform this optimization. Consequently, a prototype model is demonstrated that addresses the required fundamental mechanisms.

Which factors matter the most? Revisiting and dissecting antibody therapeutic doses

Factors such as antibody clearance and target affinity can influence antibodies' effective doses for specific indications. However, these factors vary considerably across antibody classes, precluding direct and quantitative comparisons. Here, we apply a dimensionless metric, the therapeutic exposure affinity ratio (TEAR), which normalizes the therapeutic doses by antibody bioavailability, systemic clearance and target-binding property to enable direct and quantitative comparisons of therapeutic doses. Using TEAR, we revisited and dissected the doses of up to 60 approved antibodies. We failed to detect a significant influence of target baselines, turnovers or anatomical locations on antibody therapeutic doses, challenging the traditional perceptions. We highlight the importance of antibodies' modes of action for therapeutic doses and dose selections; antibodies that work through neutralizing soluble targets show higher TEARs than those working through other mechanisms. Overall, our analysis provides insights into the factors that influence antibody doses, and the factors that are crucial for antibodies' pharmacological effects.

A meta-analysis of tumour response and relapse kinetics based on 34,881 patients: A question of cancer type, treatment and line of treatment

PURPOSE

Cancer disease burden is commonly assessed radiologically in solid tumours in support of response assessment via the RECIST criteria. These longitudinal data are amenable to mathematical modelling and these models characterise the initial tumour size, initial tumour shrinkage in responding patients and rate of regrowth as patient's disease progresses. Knowing how these parameters vary between patient populations and treatments would inform translational modelling approaches from non-clinical data as well as clinical trial design.

EXPERIMENTAL DESIGN

Here a meta-analysis of reported model parameter values is reported. Appropriate literature was identified via a PubMed search and the application of text-based clustering approaches. The resulting parameter estimates are examined graphically and with ANOVA.

RESULTS

Parameter values from a total of 80 treatment arms were identified based on 80 trial arms containing a total of 34,881 patients. Parameter estimates are generally consistent. It is found that a significant proportion of the variation in rates of tumour shrinkage and regrowth are explained by differing cancer and treatment: cancer type accounts for 66% of the variation in shrinkage rate and 71% of the variation in reported regrowth rates. Mean average parameter values by cancer and treatment are also reported.

CONCLUSIONS

Mathematical modelling of longitudinal data is most often reported on a per clinical trial basis. However, the results reported here suggest that a more integrative approach would benefit the development of new treatments as well as the further optimisation of those currently used.

Clone Wars: Quantitatively Understanding Cancer Drug Resistance

A key aim of early clinical development for new cancer treatments is to detect the potential for efficacy early and to identify a safe therapeutic dose to take forward to phase II. Because of this need, researchers have sought to build mathematical models linking initial radiologic tumor response, often assessed after 6 to 8 weeks of treatment, with overall survival. However, there has been mixed success of this approach in the literature. We argue that evolutionary selection pressure should be considered to interpret these early efficacy signals and so optimize cancer therapy.

Opportunities for Quantitative Translational Modeling in Oncology

A 2-day meeting was held by members of the UK Quantitative Systems Pharmacology Network () in November 2018 on the topic of Translational Challenges in Oncology. Participants from a wide range of backgrounds were invited to discuss current and emerging modeling applications in nonclinical and clinical drug development, and to identify areas for improvement. This resulting perspective explores opportunities for impactful quantitative pharmacology approaches. Four key themes arose from the presentations and discussions that were held, leading to the following recommendations: Evaluate the predictivity and reproducibility of animal cancer models through precompetitive collaboration. Apply mechanism of action (MoA) based mechanistic models derived from nonclinical data to clinical trial data. Apply MoA reflective models across trial data sets to more robustly quantify the natural history of disease and response to differing interventions. Quantify more robustly the dose and concentration dependence of adverse events through mathematical modelling techniques and modified trial design.

Artificial Intelligence and Mechanistic Modeling for Clinical Decision Making in Oncology

The amount of "big" data generated in clinical oncology, whether from molecular, imaging, pharmacological, or biological origin, brings novel challenges. To mine efficiently this source of information, mathematical models able to produce predictive algorithms and simulations are required, with applications for diagnosis, prognosis, drug development, or prediction of the response to therapy. Such mathematical and computational constructs can be subdivided into two broad classes: biologically agnostic, statistical models using artificial intelligence techniques, and physiologically based, mechanistic models. In this review, recent advances in the applications of such methods in clinical oncology are outlined. These include machine learning applied to big data (omics, imaging, or electronic health records), pharmacometrics and quantitative systems pharmacology, as well as tumor kinetics and metastasis modeling. Focus is set on studies with high potential of clinical translation, and particular attention is given to cancer immunotherapy. Perspectives are given in terms of combinations of the two approaches: "mechanistic learning."

Modeling Tumor Growth and Treatment Resistance Dynamics Characterizes Different Response to Gefitinib or Chemotherapy in Non-Small Cell Lung Cancer

Differences in the effect of gefitinib and chemotherapy on tumor burden in non-small cell lung cancer remain to be fully understood. Using a Bayesian hierarchical model of tumor size dynamics, we estimated the rates of tumor growth and treatment resistance for patients in the Iressa Pan-Asia Study study (NCT00322452). The following relationships characterize greater efficacy of gefitinib in epidermal growth factor receptor (EGFR) positive tumors: Maximum drug effect is, in decreasing order, gefitinib in EGFR-positive, chemotherapy in EGFR-positive, chemotherapy in EGFR-negative, and gefitinib in EGFR-negative tumors; the rate of resistance emergence is, in increasing order: gefitinib in EGFR positive, chemotherapy in EGFR positive, while each is plausibly similar to the rate in EGFR negative tumors, which are estimated with less certainty. The rate of growth is smaller in EGFR-positive than in EGFR-negative fully resistant tumors, regardless of treatment. The model can be used to compare treatment effects and resistance dynamics among different drugs.

Progress and Opportunities to Advance Clinical Cancer Therapeutics Using Tumor Dynamic Models

There is a need for new approaches and endpoints in oncology drug development, particularly with the advent of immunotherapies and the multiple drug combinations under investigation. Tumor dynamics modeling, a key component to oncology "model-informed drug development," has shown a growing number of applications and a broader adoption by drug developers and regulatory agencies in the past years to support drug development and approval in a variety of ways. Tumor dynamics modeling is also being investigated in personalized cancer therapy approaches. These models and applications are reviewed and discussed, as well as the limitations and issues open for further investigations. A close collaboration between stakeholders like clinical investigators, statisticians, and pharmacometricians is warranted to advance clinical cancer therapeutics.