Predicting response to pembrolizumab in metastatic melanoma by a new personalization algorithm.

BACKGROUND: At present, immune checkpoint inhibitors, such as pembrolizumab, are widely used in the therapy of advanced non-resectable melanoma, as they induce more durable responses than other available treatments. However, the overall response rate does not exceed 50% and, considering the high costs and low life expectancy of nonresponding patients, there is a need to select potential responders before therapy. Our aim was to develop a new personalization algorithm which could be beneficial in the clinical setting for predicting time to disease progression under pembrolizumab treatment. METHODS: We developed a simple mathematical model for the interactions of an advanced melanoma tumor with both the immune system and the immunotherapy drug, pembrolizumab. We implemented the model in an algorithm which, in conjunction with clinical pretreatment data, enables prediction of the personal patient response to the drug. To develop the algorithm, we retrospectively collected clinical data of 54 patients with advanced melanoma, who had been treated by pembrolizumab, and correlated personal pretreatment measurements to the mathematical model parameters. Using the algorithm together with the longitudinal tumor burden of each patient, we identified the personal mathematical models, and simulated them to predict the patient's time to progression. We validated the prediction capacity of the algorithm by the Leave-One-Out cross-validation methodology. RESULTS: Among the analyzed clinical parameters, the baseline tumor load, the Breslow tumor thickness, and the status of nodular melanoma were significantly correlated with the activation rate of CD8+ T cells and the net tumor growth rate. Using the measurements of these correlates to personalize the mathematical model, we predicted the time to progression of individual patients (Cohen's κ = 0.489). Comparison of the predicted and the clinical time to progression in patients progressing during the follow-up period showed moderate accuracy (R2 = 0.505). CONCLUSIONS: Our results show for the first time that a relatively simple mathematical mechanistic model, implemented in a personalization algorithm, can be personalized by clinical data, evaluated before immunotherapy onset. The algorithm, currently yielding moderately accurate predictions of individual patients' response to pembrolizumab, can be improved by training on a larger number of patients. Algorithm validation by an independent clinical dataset will enable its use as a tool for treatment personalization.

Predicting time to castration resistance in hormone sensitive prostate cancer by a personalization algorithm based on a mechanistic model integrating patient data.

BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer death of men worldwide. In hormone-sensitive prostate cancer (HSPC), androgen deprivation therapy (ADT) is widely used, but an eventual failure on ADT heralds the passage to the castration-resistant prostate cancer (CRPC) stage. Because predicting time to failure on ADT would allow improved planning of personal treatment strategy, we aimed to develop a predictive personalization algorithm for ADT efficacy in HSPC patients. METHODS: A mathematical mechanistic model for HSPC progression and treatment was developed based on the underlying disease dynamics (represented by prostate-specific antigen; PSA) as affected by ADT. Following fine-tuning by a dataset of ADT-treated HSPC patients, the model was embedded in an algorithm, which predicts the patient's time to biochemical failure (BF) based on clinical metrics obtained before or early in-treatment. RESULTS: The mechanistic model, including a tumor growth law with a dynamic power and an elaborate ADT-resistance mechanism, successfully retrieved individual time-courses of PSA (R(2) = 0.783). Using the personal Gleason score (GS) and PSA at diagnosis, as well as PSA dynamics from 6 months after ADT onset, and given the full ADT regimen, the personalization algorithm accurately predicted the individual time to BF of ADT in 90% of patients in the retrospective cohort (R(2) = 0.98). CONCLUSIONS: The algorithm we have developed, predicting biochemical failure based on routine clinical tests, could be especially useful for patients destined for short-lived ADT responses and quick progression to CRPC. Prospective studies must validate the utility of the algorithm for clinical decision-making.

Complex pattern of interleukin-11-induced inflammation revealed by mathematically modeling the dynamics of C-reactive protein.

Inflammation underlies many diseases and is an undesired effect of several therapy modalities. Biomathematical modeling can help unravel the complex inflammatory processes and the mechanisms triggering their emergence. We developed a model for induction of C-reactive protein (CRP), a clinically reliable marker of inflammation, by interleukin (IL)-11, an approved cytokine for treatment of chemotherapy-induced thrombocytopenia. Due to paucity of information on the mechanisms underlying inflammation-induced CRP dynamics, our model was developed by systematically evaluating several models for their ability to retrieve variable CRP profiles observed in IL-11-treated breast cancer patients. The preliminary semi-mechanistic models were designed by non-linear mixed-effects modeling, and were evaluated by various performance criteria, which test goodness-of-fit, parsimony and uniqueness. The best-performing model, a robust population model with minimal inter-individual variability, uncovers new aspects of inflammation dynamics. It shows that CRP clearance is a nonlinear self-controlled process, indicating an adaptive anti-inflammatory reaction in humans. The model also reveals a dual IL-11 effect on CRP elevation, whereby the drug has not only a potent immediate influence on CRP incline, but also a long-term influence inducing elevated CRP levels for several months. Consistent with this, model simulations suggest that periodic IL-11 therapy may result in prolonged low-grade (chronic) inflammation post treatment. Future application of the model can therefore help design improved IL-11 regimens with minimized long-term CRP toxicity. Our study illuminates the dynamics of inflammation and its control, and provides a prototype for progressive modeling of complex biological processes in the medical realm and beyond.

The resonance phenomenon in population persistence: can the same theory guide both national security policies and personalized medicine?

The theory of resonance in population persistence proposes that the survival of a population that is exposed to externally inflicted loss processes (disturbances) during part of its life cycle is dependent on the relation between the average period of the disturbances and the average generation time of the population. This suggests that the size of a population can be controlled by manipulating the period between external disturbances. This theory, first formalized in a study of intertidal Red Sea mollusks exposed to periodic storms, has been found to apply to such seemingly disparate phenomena as the spread of a pathogen among susceptible individuals and the response of malignant cancer cells to chemotherapy. The current article provides a brief review of the evolution of the resonance theory into a tool that can be applied to designing vaccination policies - specifically, in preparedness for bio-terrorism attacks - and in personalized medicine. A personalized protocol based on the resonance theory was applied to a cancer patient, stabilizing his tumor progression, relieving his hematopoietic toxicity, and extending his survival.

A new validated mathematical model of the Wnt signalling pathway predicts effective combinational therapy by sFRP and Dkk.

The Wnt signalling pathway controls cell proliferation and differentiation, and its deregulation is implicated in different diseases including cancer. Learning how to manipulate this pathway could substantially contribute to the development of therapies. We developed a mathematical model describing the initial sequence of events in the Wnt pathway, from ligand binding to ß-catenin accumulation, and the effects of inhibitors, such as sFRPs (secreted Frizzled-related proteins) and Dkk (Dickkopf). Model parameters were retrieved from experimental data reported previously. The model was retrospectively validated by accurately predicting the effects of Wnt3a and sFRP1 on ß-catenin levels in two independent published experiments (R(2) between 0.63 and 0.91). Prospective validation was obtained by testing the model's accuracy in predicting the effect of Dkk1 on Wnt-induced ß-catenin accumulation (R(2)≈0.94). Model simulations under different combinations of sFRP1 and Dkk1 predicted a clear synergistic effect of these two inhibitors on ß-catenin accumulation, which may point towards a new treatment avenue. Our model allows precise calculation of the effect of inhibitors applied alone or in combination, and provides a flexible framework for identifying potential targets for intervention in the Wnt signalling pathway.

Strategies for cancer stem cell elimination: insights from mathematical modeling.

The cancer stem cell (CSC) hypothesis states that only a small fraction of a malignant cell population is responsible for tumor growth and relapse. Understanding the relationships between CSC dynamics and cancer progression may contribute to improvements in cancer treatment. Analysis of a simple discrete mathematical model has suggested that homeostasis in developing tissues is governed by a "quorum sensing" control mechanism, in which stem cells differentiate or proliferate according to feedback they receive from neighboring cell populations. Further analysis of the same model has indicated that excessive stem cell proliferation leading to malignant transformation mainly results from altered sensitivity to such micro-environmental signals. Our aim in this work is to expand the analysis to the dynamics of established populations of cancer cells and to examine possible therapeutic avenues for eliminating CSCs. The proposed model considers two populations of cells: CSCs, which can divide indefinitely, and differentiated cancer cells, which do not divide and have a limited lifespan. We assume that total cell density has negative feedback on CSC proliferation and that high CSC density activates CSC differentiation. We show that neither stimulation of CSC differentiation nor inhibition of CSC proliferation alone is sufficient for complete CSC elimination and cancer cure, since each of these two therapies affects a different subpopulation of CSCs. However, a combination of these two strategies can substantially reduce the population sizes and densities of all types of cancer cells. Therefore, we propose that in clinical trials, CSC differentiation therapy should only be examined in combination with chemotherapy. Our conclusions are corroborated by clinical experience with differentiating agents in acute promyelocytic leukemia and neuroblastoma.

An integrated disease/pharmacokinetic/pharmacodynamic model suggests improved interleukin-21 regimens validated prospectively for mouse solid cancers.

Interleukin (IL)-21 is an attractive antitumor agent with potent immunomodulatory functions. Yet thus far, the cytokine has yielded only partial responses in solid cancer patients, and conditions for beneficial IL-21 immunotherapy remain elusive. The current work aims to identify clinically-relevant IL-21 regimens with enhanced efficacy, based on mathematical modeling of long-term antitumor responses. For this purpose, pharmacokinetic (PK) and pharmacodynamic (PD) data were acquired from a preclinical study applying systemic IL-21 therapy in murine solid cancers. We developed an integrated disease/PK/PD model for the IL-21 anticancer response, and calibrated it using selected "training" data. The accuracy of the model was verified retrospectively under diverse IL-21 treatment settings, by comparing its predictions to independent "validation" data in melanoma and renal cell carcinoma-challenged mice (R(2)>0.90). Simulations of the verified model surfaced important therapeutic insights: (1) Fractionating the standard daily regimen (50 µg/dose) into a twice daily schedule (25 µg/dose) is advantageous, yielding a significantly lower tumor mass (45% decrease); (2) A low-dose (12 µg/day) regimen exerts a response similar to that obtained under the 50 µg/day treatment, suggestive of an equally efficacious dose with potentially reduced toxicity. Subsequent experiments in melanoma-bearing mice corroborated both of these predictions with high precision (R(2)>0.89), thus validating the model also prospectively in vivo. Thus, the confirmed PK/PD model rationalizes IL-21 therapy, and pinpoints improved clinically-feasible treatment schedules. Our analysis demonstrates the value of employing mathematical modeling and in silico-guided design of solid tumor immunotherapy in the clinic.

Analyzing transformation of myelodysplastic syndrome to secondary acute myeloid leukemia using a large patient database.

One-third of patients with myelodysplastic syndrome (MDS) progress to secondary acute myeloid leukemia (sAML), with its concomitant poor prognosis. Recently, multiple mutations have been identified in association with MDS-to-sAMLtransition, but it is still unclear whether all these mutations are necessary for transformation. If multiple independent mutations are required for the transformation, sAML risk should increase with time from MDS diagnosis. In contrast, if a single critical biological event determines sAML transformation; its risk should be constant in time elapsing from MDS diagnosis. To elucidate this question, we studied a database of 1079 patients with MDS. We classified patients according to the International Prognostic Scoring System (IPSS), using either the French-American-British (FAB) or the World Health Organization (WHO) criteria, and statistically analyzed the resulting transformation risk curves of each group. The risk of transformation after MDS diagnosis remained constant in time within three out of four risk groups, and in all four risk groups, when patients were classified according to FAB or to the WHO-determined criteria, respectively. Further subdivision by blast percentage or cytogenetics had no influence on this result. Our analysis suggests that a single random biological event leads to transformation to sAML, thus calling for the exclusion of time since MDS diagnosis from the clinical decision-making process.

Developing and validating a machine learning prognostic model for alerting to imminent deterioration of hospitalized patients with COVID-19.

Our study was aimed at developing and validating a new approach, embodied in a machine learning-based model, for sequentially monitoring hospitalized COVID-19 patients and directing professional attention to patients whose deterioration is imminent. Model development employed real-world patient data (598 prediction events for 210 patients), internal validation (315 prediction events for 97 patients), and external validation (1373 prediction events for 307 patients). Results show significant divergence in longitudinal values of eight routinely collected blood parameters appearing several days before deterioration. Our model uses these signals to predict the personal likelihood of transition from non-severe to severe status within well-specified short time windows. Internal validation of the model's prediction accuracy showed ROC AUC of 0.8 and 0.79 for prediction scopes of 48 or 96 h, respectively; external validation showed ROC AUC of 0.7 and 0.73 for the same prediction scopes. Results indicate the feasibility of predicting the forthcoming deterioration of non-severe COVID-19 patients by eight routinely collected blood parameters, including neutrophil, lymphocyte, monocyte, and platelets counts, neutrophil-to-lymphocyte ratio, CRP, LDH, and D-dimer. A prospective clinical study and an impact assessment will allow implementation of this model in the clinic to improve care, streamline resources and ease hospital burden by timely focusing the medical attention on potentially deteriorating patients.