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Systems Biology and Emerging Technologies |
1 Optimata Ltd., Ramat-Gan, Israel; 2 CTRC Institute for Drug Development, San Antonio, Texas; 3 New Hope Pharmaceuticals, Inc., Bethesda, Maryland; 4 John Hopkins University School of Medicine, Baltimore, Maryland; and 5 Institute for Medical Biomathematics, Bene-Ataroth, Israel
Requests for reprints: Zvia Agur, Institute for Medical Biomathematics, P. O. Box 282, 10 HaTe'ena Street, Bene-Ataroth 60991, Israel. Phone: 972-3-9733075; Fax: 972-3-9733410; E-mail: agur{at}imbm.org.
| Abstract |
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| Introduction |
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Prediction of personalized therapy, or theranostics, is the process of selecting the best treatment for a given patient by accounting for patient-specific factors, such as gender, age, and genetic characteristics. A possible theranostic solution is to assess the relative efficacy of various treatments in laboratory animals, which bear the patient's cancer (3). However, xenograft models suffer from three major impediments: slow, costly, and labor-intensive cellular acquisition from tumor biopsies and xenograft growth; animal physiology not reflecting the human pharmacokinetics (PK); and xenograft methods not accounting for patient safety.
Underlying these impediments is the complexity of the involved dynamics due to which one cannot estimate, by intuition alone, the relationships between measurable molecular biomarkers and the behavior of the organism as a whole. In contrast, mathematical models formally and systematically describe the major biological processes that relate the measured biomarkers to the phenotype in question. By integrating these mathematical models into comprehensive computer algorithms, one can compute what will be the effect on the phenotype of changes, even small changes, in biomarker levels. In theranostics, laboratory experiments in xenografted animals could be used in conjunction with mathematical models for the pathologic and physiologic growth dynamics and for drug PK and pharmacodynamics (PD).
Mathematical models for tumor progression (4–6), cancer therapy (7–10), and related genetic (11, 12), hematologic (13, 14), and immunologic processes (15, 16) have been developed. Using these models, the efficacy of various drug monotherapy and combination schedules was predicted (7, 8, 14, 15, 17, 18). These computer-implemented models allow clinicians to analyze the effects of drug regimens on disease progression, as well as provide the power to check various biomarkers for their suitability to represent different aspects of the disease in question. New methods for treatment optimization have also been developed, which grade the therapeutic potential of specific regimens according to clinical criteria, such as efficacy/toxicity ratio (17, 19). The biological process models, in conjunction with the optimization methods, introduce into clinical oncology a quantitative prediction-based decision-making facility.
Several preclinical and clinical trials have been carried out for testing the prediction accuracy of mathematical model for tumor progression (20–24). In the present work, we applied a validated model for vascular tumor progression (see below) to create a novel theranostic method for a large class of anticancer drugs. The method was validated in xenografts derived from a MCS patient's lung metastasis and then used for predicting an improved therapy for the patient himself.
By controlling its variable values, the validated model was adapted to describe the metastatic tumor growth of a specific MCS patient as well as of its xenografted biopsy. We used these two new models to analyze the reasons underlying the relative advantage of one treatment option over another.
| Materials and Methods |
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Study Design
The workflow of this study is described schematically in Supplementary Fig. S1.
Tumor fragments were taken from lung metastases of the MCS patient and implanted in mice. This xenograft model was established and amplified until sufficient tumor was available to implant a control and several treatment groups. In this model, cells are only propagated directly as smaller pieces from a previous xenograft and never propagated as a cell line. Mice were divided into groups, each treated by different drug regimen, in addition to a control group of untreated animals. In parallel to the laboratory work, a general mathematical model for vascular tumor growth dynamics was adapted to describe the growth of untreated xenografts of the MCS patient's lung metastases. In silico experiments, similar to those performed in vivo, were conducted to predict growth of MCS xenografts and their response to various drug therapies. This was done by simulating the adapted tumor growth model in conjunction with the relevant PK/PD models and the particular dosing regimens. Where available, patient-specific chemosensitivity information was used to fine-tune the PD models. Otherwise, only publicly available data were used for the mathematical PK and PD models of the drugs in the xenograft experiments. Following the initial assessment of model prediction accuracy (25), the variables of several drug models were reevaluated and the accuracy was assessed again.
Subsequently, the mathematical model was adjusted to describe the patient's metastatic growth dynamics. This was done using gene expression analysis of key proteins in mice and human and various treatment regimens were tested for efficacy in the MCS patient.
Experimental Setup
Immunohistochemistry. Tissue from the primary sarcoma was removed after surgery and fixed in 10% buffered formalin and embedded in paraffin. Tissue sections of 5 µm were deparaffinized in xylene and rehydrated in increasing concentrations of ethanol. Endogenous peroxidase activity was quenched with 0.01% H2O2, sections were boiled in 0.01 mol/L citric acid (pH 6.0), and nonspecific binding was blocked with 10% normal rabbit serum. After washing, rat anti-mouse CD34 monoclonal primary antibody (PharMingen) specific to vascular endothelium was applied at 25 µg/mL and incubated overnight at 4°C. After washing in PBS, biotinylated rabbit anti-mouse antibody, diluted 1:100, was applied followed by incubation at room temperature for 30 min. After washing again in PBS, avidin-biotin complex (Vector Laboratories), diluted 1:25, was applied and incubated at room temperature for 30 min and washed again in PBS. Tissue sections were developed with diaminobenzidine and peroxide and counterstained with hematoxylin. Microvessel density (MVD) was assessed by counting the microvessels at x200 in a field that had the highest vascularization by scanning at x40 (12) and then converted to MVD/mm2. Stained slides were examined blind and were also scored from one to four with increasing vascularity.
Animal model. For establishment and propagation, tumor fragments obtained from the MCS patient were s.c. implanted using an 11-gauge cancer trocar on the right flank of male CD-1 nude mice, as we assumed that mouse flank provides a good mirror of primary sarcoma growth in the soft tissue microenvironment of the patient from which it originated. Mice were weighed twice weekly and tumor measurements were taken with a Vernier caliper twice weekly, beginning 7 d after implantation. Tumors were considered established once growth reached log stage as determined by tumor measurements. Once established tumors reached a predetermined volume (1–3 cm3), they were excised and sectioned into 15 to 30 mm3 fragments, which were implanted s.c. as above; implantation was unilateral on the right flank. Once tumors grew to 50 to 150 mm3 in size, animals were pair matched by tumor size into treatment and control groups. The animals were ear tagged and followed individually throughout each experiment.
Data collection and analysis. Tumor volume was calculated by conversion of two-dimensional caliper measurements as follows (19):
![]() | (A) |
![]() | (B) |
In vitro proliferation assays. Patient-specific tumor cells were obtained from xenografts, generated by inoculation of lung metastases into immunocompromised mice, which were collected when they had grown beyond 150 mm3 in size. The tumors were minced into small pieces (<1 mm), digested for 2 h with collagenase-DNase, mechanically dissociated, and passed through sterile nylon mesh to produce single-cell suspensions. Viable tumor cells were enriched by elutriation and Ficoll-diatrizoate density centrifugations (26). Tumor cell suspensions were plated in microtiter wells (50,000 per well) and incubated in the presence or absence of the indicated drugs or combinations for 4 d in 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT; ref. 27) or 7 d in the differential staining cytotoxicity (DiSC; ref. 28) assays.
Mathematically Modeling Vascular Tumor Growth
A mathematical model of angiogenesis-dependent tumor dynamics and its underlying assumptions is described in detail elsewhere (4, 5, 24). The reader is referred to Fig. 1
in ref. 24 for a schematic representation of the model. The model describes three main interactive growth dynamics: of tumor cells, of blood vessel formation (angiogenesis), and of new vessel maturation.
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Personalizing the MCS Patient Model
The growth of six untreated xenografts was monitored for estimating the variables of the MCS patient tumor model when xenografted in mice. Only three of them actually grew in size. Results of histopathologic assays of the patient's lung metastasis (e.g., tumor density, mitotic index, necrotic index, and vessel density) were used to define valid variable ranges in the evaluation process. Twelve model variables common to all the xenografts were evaluated. In addition, two variables, which represent the vascular bed at implantation site, were evaluated for each xenograft individually. Two additional xenograft growth curves were monitored for validating model predictability.
Mathematically Modeling PK/PD
We adopted linear compartmental PK models for all the drugs in this study (see refs. 40, 41 for general reviews on compartmental PK modeling). Each effect of the drug is mathematically defined as a function of drug concentration in a predefined model compartment. In general, the concentration-effect relationship is defined using a sigmoid function (42):
![]() | (C) |
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The model of drug effect depends on its actual mechanism of action. For example, the effect of a cytotoxic drug, such as docetaxel, is modeled as a fraction of cells that are killed during the current time step (Eqs. C and D). Thus, in the context of docetaxel, Emax and Emin (Eqs. C and D) are taken as 1 and 0, respectively. The overall effect on treated tumor shrinkage compared with the untreated tumor is calculated by Eq. B.
The variable identification of the MCS model and the various PK and PD models was performed using a cross-entropy method, described in ref. 43, as well as experimental records of xenograft dynamic and publicly available PK data. The sources for PK and PD data can be found in Supplementary Tables S1 and S2, respectively.
Personalizing PK/PD Models Using Xenograft Experiments
Six drugs and their combinations were tested in mice bearing xenografts from the patient's cancer tissue to determine the best possible treatment: bevacizumab, docetaxel, doxorubicin, gemcitabine, irinotecan (CPT-11), and sorafenib. Results of in vitro proliferation assays of the patient's tumor cells were used to establish patient-specific concentration-effect curves for the chemotherapeutics (docetaxel, gemcitabine, CPT-11, doxorubicin, and docetaxel/gemcitabine combination). Two different concentrations of each drug were tested, enabling to construct linear dose-response functions (Eq. D). Response was measured using DiSC and MTT methods and concentration-effect equations were constructed separately for each method and then averaged. For docetaxel and gemcitabine/docetaxel, only DiSC results were used for parameterization. These data were modeled as the fraction of cells killed during the current time step.
Modeling PD of targeted drugs (bevacizumab and sorafenib) was based on relevant data of treated lung cancer xenografts and was implemented as a sigmoid dependence (Eq. C). In our mathematical model, we included bevacizumab single-action mechanism as a VEGF inhibitor and that of sorafenib triple-action mechanism (i.e., direct inhibition of tumor maturation, inhibition of pericyte activity, and decreasing the cell proliferation rate). The estimated individualized PD was combined with the corresponding PK to yield a complete PK/PD model. No PK individualization was performed in this work.
To model drug combinations, the independent effects of each drug in the combination were added. An additive effect was assumed due to lack of quantitative information on potential PK/PD interactions. An exception is the case of docetaxel/gemcitabine combination, where data from the patient-specific in vitro proliferation assays were available. Theoretically, the combined effects of docetaxel and gemcitabine may be synergistic or antagonistic depending on the type of tumor cells and on the order of drug administration (44, 45). PK interactions are partially responsible for the dependence of the combined effect on drug sequencing (45). As the chemosensitivity tests are PK independent, and due to the shortage of quantitative data, we assumed that no PD interactions exist between the modeled drugs.
Simulating MCS Xenograft Dynamics and Response to Drug Treatment
The full PK/PD models of numerous therapy schedules were simulated in conjunction with the MCS xenograft model. Mouse body weight was taken as 30 g. Efficacy was measured in terms of TGI (Eq. B). As stated above, necrotic tumor cells do not disappear from the system immediately, but are eliminated with a finite rate, and therefore contribute to tumor volume. Thus, the control and treated tumor sizes in Eq. B may refer to the total number of cells, or to living cells alone, resulting in TGI values that consider the tumor volume as a whole (TGIT) or only the living fraction (TGIL).
Xenograft simulations were carried out for a period of 22 d, similar to the period for TGI calculations in the experimental setup.
Validating the Model Predictions
Growth of MCS xenografts treated under various therapies was monitored for 22 d after treatment initiation. Model prediction accuracy was calculated as follows. For the control group, the growth of the tumor during the experiment, G, is given by
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Prediction accuracy, A, for the control group was calculated using the observed, Gobs, and calculated, Gcalc, G values as follows.
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Prediction accuracy for the treatment groups was calculated using the observed and predicted TGI values, TGIobs and TGIcalc, respectively.
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Refining the Models
Following the initial assessment of prediction accuracy, the PK and PD models of each drug were independently revisited by detailing the action mechanisms of the involved biological drug models and by additional refinement of PK/PD variables. Only publicly available data were used in this process. Unlike the original models, the reviewing process was performed only after receiving the experimental xenograft sensitivity. However, these were blinded in the refinement process. Thus, the results below may be regarded as prospective ones. Results of the initial assessment are also reported (25).
Simulating Tumor Dynamics and Response to Drug Treatment in the MSC Patient
The personalized disease model of the MCS xenografts served as the basis for the human model. Gene expression analyses of key proteins (e.g., VEGF; ref. 46) in the patient's metastases and in the xenografted tumor (denoted as Met/F1 ratio) were used to scale relevant xenograft variables. For example, gene expression analysis shows that the Met/F1 ratio of Ang-2 is 0.7. Therefore, values of corresponding variables in the xenograft model were multiplied by this coefficient to yield a new value in the human model. Published data on the involved drugs were used to model their PK in human. We assumed that administering equivalent doses to a mouse and a human would result in effects of similar maximum magnitude but with different time profiles. Therefore, the same PD functions used in mice modeling were used in human models [i.e., patient-specific concentration-effect curves for cytotoxic drugs (CPT-11, docetaxel, doxorubicin, and gemcitabine) and literature-based functions for bevacizumab and sorafenib]. Note that for simplicity we describe here only our predictions about drug efficacy. Predictions about drug toxicity will be discussed elsewhere.
The full PK/PD models were simulated in conjunction with the MCS human model under various therapy regimens. A treatment period of 90 d was simulated, but simulations were carried out for a total period of 120 d to allow confirmation of response 4 wk after the end of treatment.
| Results and Discussion |
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The predicted efficacy ranking of the different treatment regimens was correct, except for the swapping of rank 3 and 4 (regimens 3 and 1). Note the small difference in the experimental TGI values of these two regimens—59.4% for regimen 1 and 56.4% for regimen 3. This may suggest that the difference between these two schedules is not significant.
The most accurate prediction was achieved in the bevacizumab/CPT-11 combination (regimen 1). The model-predicted and measured TGIT values were 57.2% and 59.4%, respectively (accuracy of 96.2%). The two most efficacious regimens, in terms of TGI, were regimen 2 (bevacizumab/gemcitabine/docetaxel) with measured TGIT being 109.3% and regimen 5 (bevacizumab/sorafenib) with measured TGIT being 87.22%. Our prediction for regimen 2 (TGIT = 76.6% predicted versus 109.3% measured) was the less accurate of all the predictions (accuracy of 70.1%). Nevertheless, it was correctly identified as the most potent schedule. Note that excluding this lowest accuracy value results in mean accuracy of 90.5%.
Antagonism between gemcitabine and docetaxel was experimentally observed in vitro using the patient's tumor cells (Table 1). This result is corroborated by our model simulations, which suggest that removing gemcitabine from regimen 2 (bevacizumab/gemcitabine/docetaxel) yields a slightly larger TGIT: 78.6% versus 76.6%. However, whereas the in vitro result is probably related to the drug sequencing effects on cell kinetics, we believe that the in silico predicted antagonism better reflects the in vivo setting, where the added, relatively large, cytotoxic effect of the two drugs may generate intensive angiogenesis, eventually leading to excessive tumor recovery.
Proposing an improved treatment for the MCS patient. Drug efficacy experiments in the personalized xenograft model alone are of limited use as a theranostic tool (see above). Having validated our mathematical model, we could use it, jointly with the results of the empirical xenograft experiments, for analyzing putative treatment alternatives for the patient so as to maximize the TGI (Eq. B).
Many clinical trials have been reported comparing q7d with q21d docetaxel regimens for various indications. Nevertheless, no definitive conclusion about the superiority of either dosing interval can be made. In addition, several toxic effects have been associated with weekly regimens (47). Because our preliminary simulations pinpoint the bevacizumab/docetaxel combination as superior to most other therapies in suppressing the growth of the MCS patient's xenografts (25), we wished to test whether the patient would benefit from weekly docetaxel administrations. To this end, a series of bevacizumab/docetaxel regimens was simulated (regimens 6–21; Table 3 ). In all the studied regimens, delivery of triweekly i.v. doses of 15 mg/kg bevacizumab combined with four alternative docetaxel doses (45, 60, 75, and 90 mg/m2) in four different dosing intervals (q7d, q14d, q21d, and q28d) was simulated. The associated treatment efficacy, in terms of time to progression and final tumor sizes, was predicted; time to progression is defined as the time needed for 20% increase in tumor size. Results are summarized in Table 3 and in Fig. 2A , where the predicted tumor growth curves of the 16 simulated treatments are shown. Our simulations suggested that once-weekly regimens (Fig. 2A, filled circles) would be superior to other simulated regimens for the MCS patient, both in terms of final tumor size and time to progression. The improvement in tumor dynamics that is predicted for once-weekly regimens is caused by the interdosing interval and not by increasing the total drug dose: dividing the total docetaxel dose from regimen 16 to once-weekly dosing interval [i.e., doses of 25 mg/m2 (regimen 22)] results only in a minute decrease in the predicted efficiency compared with regimen 7 (75 mg/m2 q7d). Both these weekly regimens are predicted to be more efficacious than the triweekly regimen 16 (Fig. 2). This result supports theory, suggesting that interdosing intervals per se significantly affect drug efficacy (7, 8).
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This work does not address drug-induced hematopoietic toxicity (48), which is the major dose-limiting factor in radiotherapy and chemotherapy of cancer (49). However, in another work, the superiority of calculated 10-day interdosing docetaxel intervals for alleviating neutropenia was theoretically shown, supporting the superiority of the weekly docetaxel regimens.6 A clinical decision was made to proceed with docetaxel therapy in addition to antiangiogenesis treatment with bevacizumab. For fear of aggravating the severe pancytopenia with larger q21d doses of docetaxel, a weekly schedule, as predicted here, was administered to the patient. The patient had a dramatic response to therapy with a marked decrease in serum alkaline phosphatase from bone and an immediate substantial recovery of all three blood elements (hemoglobin, WBCs, and platelet count). Soft tissue disease in the lungs and liver remained stable and the patient enjoyed a 6-month period of good quality of life, ending only after pulmonary progression of his disease to which he finally succumbed. Thus, a combined experimental and modeling approach for treatment personalization benefited this MCS patient.
Taken together, our results suggest that a methodology combining xenografted biopsies and mathematical modeling has promising prospects in personalized oncology. As our model had predicted, the patient showed a markedly improved clinical course after weekly docetaxel and bevacizumab combination. Our prediction, about the superiority of once-weekly docetaxel in patients with intensive angiogenesis, may explain observed variability in the relative efficacy of q7d versus q21d docetaxel regimens in cancer patients (47). This prediction should be validated in the preclinical and clinical setting. On further validation, it may aid physicians in identifying improved treatment schedules for individual patients.
| Disclosure of Potential Conflicts of Interest |
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| Acknowledgments |
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| Footnotes |
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D. Sidransky and Z. Agur are co–senior authors.
6 Z. Agur et al., unpublished results. ![]()
Received 5/12/08. Revised 7/28/08. Accepted 8/22/08.
| References |
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This article has been cited by other articles:
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Correction: Weekly Docetaxel Cancer Res., December 1, 2008; 68(23): 10005 - 10005. [Full Text] [PDF] |
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