Computational Trials: Unraveling Motility Phenotypes, Progression Patterns, and Treatment Options for Glioblastoma Multiforme

Inference of glioblastoma migration and proliferation rates using single time-point images

Cancer cell migration is a driving mechanism of invasion in solid malignant tumors. Anti-migratory treatments provide an alternative approach for managing disease progression. However, we currently lack scalable screening methods for identifying novel anti-migratory drugs. To this end, we develop a method that can estimate cell motility from single end-point images in vitro by estimating differences in the spatial distribution of cells and inferring proliferation and diffusion parameters using agent-based modeling and approximate Bayesian computation. To test the power of our method, we use it to investigate drug responses in a collection of 41 patient-derived glioblastoma cell cultures, identifying migration-associated pathways and drugs with potent anti-migratory effects. We validate our method and result in both in silico and in vitro using time-lapse imaging. Our proposed method applies to standard drug screen experiments, with no change needed, and emerges as a scalable approach to screen for anti-migratory drugs.

LINC01152 upregulates MAML2 expression to modulate the progression of glioblastoma multiforme via Notch signaling pathway

Glioblastoma multiforme (GBM) brings serious physical and psychological pain to GBM patients, whose survival rate remains not optimistic. Long noncoding RNAs (lncRNAs) have been reported to participate in the progression of many cancers, including GBM. However, the mechanism and function of long intergenic non-protein coding RNA 1152 (LINC01152) in GBM are still unclear. In our study, we aimed to explore the function and mechanism of LINC01152 in GBM. Then qRT-PCR analysis was implemented to search the expression of RNAs in GBM tissues and cells. Functional assays such as EdU assay, colony formation assay, TUNEL assay and flow cytometry analysis were conducted to estimate GBM cell proliferation and apoptosis. RNA pull down assay, luciferase reporter assay, RIP and ChIP assays were implemented to search the binding between molecules. As a result, we discovered that LINC01152 was upregulated in GBM tissues and cells. LINC01152 and mastermind like transcriptional coactivator 2 (MAML2) could both play the oncogenic part in GBM. Moreover, LINC01152 positively regulated MAML2 in GBM by sponging miR-466 and recruiting SRSF1. In turn, RBPJ/MAML2 transcription complex was found to activate the transcription of LINC01152 in GBM cells. In conclusion, LINC01152 could upregulate the expression of MAML2 to promote tumorigenesis in GBM via Notch signaling pathway.

Radiological evaluation of ex novo high grade glioma: velocity of diametric expansion and acceleration time study

Background

One of the greatest neuro-oncological concern remains the lack of knowledge about the etiopathogenesis and physiopathology of gliomas. Several studies reported a strict correlation between radiological features and biological behaviour of gliomas; in this way the velocity of diametric expansion (VDE) correlate with lower grade glioma aggressiveness. However, there are no the same strong evidences for high grade gliomas (HGG) because of the lack of several preoperative MRI.

Patients and methods

We describe a series of 4 patients affected by HGG followed from 2014 to January 2019. Two patients are male and two female; two had a pathological diagnosis of glioblastoma (GBM), one of anaplastic astrocytoma (AA) and one had a neuroradiological diagnosis of GBM. The VDE and the acceleration time (AT) was calculated for fluid attenuated inversion recovery (FLAIR) volume and for the enhancing nodule (EN). Every patients underwent sequential MRI study along a mean period of 413 days.

Results

Mean VDE evaluated on FLAIR volume was 39.91 mm/year. Mean percentage ratio between peak values and mean value of acceleration was 282.7%. Median appearance time of EN after first MRI scan was 432 days. Mean VDE was 45.02 mm/year. Mean percentage ratio between peak values and mean value of acceleration was 257.52%.

Conclusions

To our knowledge, this is the first report on VDE and acceleration growth in HGG confirming their strong aggressiveness. In a case in which we need to repeat an MRI, time between consecutive scans should be reduced to a maximum of 15–20 days and surgery should be executed as soon as possible.

Optimization of Dose Fractionation for Radiotherapy of a Solid Tumor with Account of Oxygen Effect and Proliferative Heterogeneity

A spatially-distributed continuous mathematical model of solid tumor growth and treatment by fractionated radiotherapy is presented. The model explicitly accounts for three time and space-dependent factors that influence the efficiency of radiotherapy fractionation schemes—tumor cell repopulation, reoxygenation and redistribution of proliferative states. A special algorithm is developed, aimed at finding the fractionation schemes that provide increased tumor cure probability under the constraints of maximum normal tissue damage and maximum fractional dose. The optimization procedure is performed for varied radiosensitivity of tumor cells under the values of model parameters, corresponding to different degrees of tumor malignancy. The resulting optimized schemes consist of two stages. The first stages are aimed to increase the radiosensitivity of the tumor cells, remaining after their end, sparing the caused normal tissue damage. This allows to increase the doses during the second stages and thus take advantage of the obtained increased radiosensitivity. Such method leads to significant expansions in the curative ranges of the values of tumor radiosensitivity parameters. Overall, the results of this study represent the theoretical proof of concept that non-uniform radiotherapy fractionation schemes may be considerably more effective that uniform ones, due to the time and space-dependent effects.

A Coupled Mass Transport and Deformation Theory of Multi-constituent Tumor Growth

We develop a general class of thermodynamically consistent, continuum models based on mixture theory with phase effects that describe the behavior of a mass of multiple interacting constituents. The constituents consist of solid species undergoing large elastic deformations and compressible viscous fluids. The fundamental building blocks framing the mixture theories consist of the mass balance law of diffusing species and microscopic (cellular scale) and macroscopic (tissue scale) force balances, as well as energy balance and the entropy production inequality derived from the first and second laws of thermodynamics. A general phase-field framework is developed by closing the system through postulating constitutive equations (i.e., specific forms of free energy and rate of dissipation potentials) to depict the growth of tumors in a microenvironment. A notable feature of this theory is that it contains a unified continuum mechanics framework for addressing the interactions of multiple species evolving in both space and time and involved in biological growth of soft tissues (e.g., tumor cells and nutrients). The formulation also accounts for the regulating roles of the mechanical deformation on the growth of tumors, through a physically and mathematically consistent coupled diffusion and deformation framework. A new algorithm for numerical approximation of the proposed model using mixed finite elements is presented. The results of numerical experiments indicate that the proposed theory captures critical features of avascular tumor growth in the various microenvironment of living tissue, in agreement with the experimental studies in the literature.

Towards personalized computational oncology: from spatial models of tumour spheroids, to organoids, to tissues

A main goal of mathematical and computational oncology is to develop quantitative tools to determine the most effective therapies for each individual patient. This involves predicting the right drug to be administered at the right time and at the right dose. Such an approach is known as precision medicine. Mathematical modelling can play an invaluable role in the development of such therapeutic strategies, since it allows for relatively fast, efficient and inexpensive simulations of a large number of treatment schedules in order to find the most effective. This review is a survey of mathematical models that explicitly take into account the spatial architecture of three-dimensional tumours and address tumour development, progression and response to treatments. In particular, we discuss models of epithelial acini, multicellular spheroids, normal and tumour spheroids and organoids, and multi-component tissues. Our intent is to showcase how these in silico models can be applied to patient-specific data to assess which therapeutic strategies will be the most efficient. We also present the concept of virtual clinical trials that integrate standard-of-care patient data, medical imaging, organ-on-chip experiments and computational models to determine personalized medical treatment strategies.

Diagnosing growth in low-grade gliomas with and without longitudinal volume measurements: A retrospective observational study

BACKGROUND

Low-grade gliomas cause significant neurological morbidity by brain invasion. There is no universally accepted objective technique available for detection of enlargement of low-grade gliomas in the clinical setting; subjective evaluation by clinicians using visual comparison of longitudinal radiological studies is the gold standard. The aim of this study is to determine whether a computer-assisted diagnosis (CAD) method helps physicians detect earlier growth of low-grade gliomas.

METHODS AND FINDINGS

We reviewed 165 patients diagnosed with grade 2 gliomas, seen at the University of Alabama at Birmingham clinics from 1 July 2017 to 14 May 2018. MRI scans were collected during the spring and summer of 2018. Fifty-six gliomas met the inclusion criteria, including 19 oligodendrogliomas, 26 astrocytomas, and 11 mixed gliomas in 30 males and 26 females with a mean age of 48 years and a range of follow-up of 150.2 months (difference between highest and lowest values). None received radiation therapy. We also studied 7 patients with an imaging abnormality without pathological diagnosis, who were clinically stable at the time of retrospective review (14 May 2018). This study compared growth detection by 7 physicians aided by the CAD method with retrospective clinical reports. The tumors of 63 patients (56 + 7) in 627 MRI scans were digitized, including 34 grade 2 gliomas with radiological progression and 22 radiologically stable grade 2 gliomas. The CAD method consisted of tumor segmentation, computing volumes, and pointing to growth by the online abrupt change-of-point method, which considers only past measurements. Independent scientists have evaluated the segmentation method. In 29 of the 34 patients with progression, the median time to growth detection was only 14 months for CAD compared to 44 months for current standard of care radiological evaluation (p < 0.001). Using CAD, accurate detection of tumor enlargement was possible with a median of only 57% change in the tumor volume as compared to a median of 174% change of volume necessary to diagnose tumor growth using standard of care clinical methods (p < 0.001). In the radiologically stable group, CAD facilitated growth detection in 13 out of 22 patients. CAD did not detect growth in the imaging abnormality group. The main limitation of this study was its retrospective design; nevertheless, the results depict the current state of a gold standard in clinical practice that allowed a significant increase in tumor volumes from baseline before detection. Such large increases in tumor volume would not be permitted in a prospective design. The number of glioma patients (n = 56) is a limitation; however, it is equivalent to the number of patients in phase II clinical trials.

CONCLUSIONS

The current practice of visual comparison of longitudinal MRI scans is associated with significant delays in detecting growth of low-grade gliomas. Our findings support the idea that physicians aided by CAD detect growth at significantly smaller volumes than physicians using visual comparison alone. This study does not answer the questions whether to treat or not and which treatment modality is optimal. Nonetheless, early growth detection sets the stage for future clinical studies that address these questions and whether early therapeutic interventions prolong survival and improve quality of life.

Therapeutic Systems and Technologies: State-of-the-Art Applications, Opportunities, and Challenges

In this review, we present current state-of-the-art developments and challenges in the areas of thermal therapy, ultrasound tomography, image-guided therapies, ocular drug delivery, and robotic devices in neurorehabilitation. Additionally, intellectual property and regulatory aspects pertaining to therapeutic systems and technologies are addressed.

Progress Towards Computational 3-D Multicellular Systems Biology

Tumors cannot be understood in isolation from their microenvironment. Tumor and stromal cells change phenotype based upon biochemical and biophysical inputs from their surroundings, even as they interact with and remodel the microenvironment. Cancer should be investigated as an adaptive, multicellular system in a dynamical microenvironment. Computational modeling offers the potential to detangle this complex system, but the modeling platform must ideally account for tumor heterogeneity, substrate and signaling factor biotransport, cell and tissue biophysics, tissue and vascular remodeling, microvascular and interstitial flow, and links between all these sub-systems. Such a platform should leverage high-throughput experimental data, while using open data standards for reproducibility. In this chapter, we review advances by our groups in these key areas, particularly in advanced models of tissue mechanics and interstitial flow, open source simulation software, high-throughput phenotypic screening, and multicellular data standards. In the future, we expect a transformation of computational cancer biology from individual groups modeling isolated parts of cancer, to coalitions of groups combining compatible tools to simulate the 3-D multicellular systems biology of cancer tissues.

Using computational phantoms to improve delivery of Tumor Treating Fields (TTFields) to patients

This paper reviews the state-of-the-art in simulation-based studies of Tumor Treating Fields (TTFields) and highlights major aspects of TTFields in which simulation-based studies could affect clinical outcomes. A major challenge is how to simulate multiple scenarios rapidly for TTFields delivery. Overcoming this challenge will enable a better understanding of how TTFields distribution is correlated with disease progression, leading to better transducer array designs and field optimization procedures, ultimately improving patient outcomes.

Key rates for the grades and transformation ability of glioma: model simulations and clinical cases

Tumor progression to higher grade is a fundamental property of cancer. The malignant advancement of the pathological features may either develop during the later stages of cancer growth (natural evolution) or it may necessitate new mutations or molecular events that alter the rates of growth, dispersion, or neovascularization (transformation). Here, we model the pathological and radiological features of grades 2-4 gliomas at the times of diagnosis and death and study grade development and the progression to higher grades. We perform a retrospective review of clinical cases based on model predictions. Simulations uncover two unusual patterns of glioma progression, which are supported by clinical cases: (1) some grades 2 and 3 gliomas lack the ability of progression to higher grades, and (2) grade 3 glioma may evolve to GBM in a few weeks. All 13 gliomas that recurred at the same grade carry either the IDH1-R132H or the ATRX mutation. All (five of five) grade 3 tumors are 1p/19q co-deleted, IDH1-R132H mutated and ATRX wt. Furthermore, three of seven grade 2 gliomas are both IDH1-R132H mutated and ATRX mutated. Simulations replicate the good prognosis of secondary GBM. The results support the hypothesis that constant rates of dispersion, proliferation, and angiogenesis prescribe either a natural evolution or the inability to progress to higher grades. Furthermore, the accrual of molecular events that change a tumor's ability to infiltrate, proliferate or neovascularize may transform the glioma either into a more aggressive tumor at the same grade or elevate its grade.

Personalized Radiotherapy Planning Based on a Computational Tumor Growth Model

In this article, we propose a proof of concept for the automatic planning of personalized radiotherapy for brain tumors. A computational model of glioblastoma growth is combined with an exponential cell survival model to describe the effect of radiotherapy. The model is personalized to the magnetic resonance images (MRIs) of a given patient. It takes into account the uncertainty in the model parameters, together with the uncertainty in the MRI segmentations. The computed probability distribution over tumor cell densities, together with the cell survival model, is used to define the prescription dose distribution, which is the basis for subsequent Intensity Modulated Radiation Therapy (IMRT) planning. Depending on the clinical data available, we compare three different scenarios to personalize the model. First, we consider a single MRI acquisition before therapy, as it would usually be the case in clinical routine. Second, we use two MRI acquisitions at two distinct time points in order to personalize the model and plan radiotherapy. Third, we include the uncertainty in the segmentation process. We present the application of our approach on two patients diagnosed with high grade glioma. We introduce two methods to derive the radiotherapy prescription dose distribution, which are based on minimizing integral tumor cell survival using the maximum a posteriori or the expected tumor cell density. We show how our method allows the user to compute a patient specific radiotherapy planning conformal to the tumor infiltration. We further present extensions of the method in order to spare adjacent organs at risk by re-distributing the dose. The presented approach and its proof of concept may help in the future to better target the tumor and spare organs at risk.

Role of mathematical medicine in gastrointestinal carcinoma: Current status and perspectives

Mathematical medicine has already played an important role in clinical and basic research as a major interdisciplinary branch of medicine. Mathematical medicine has an important role not only in imaging diagnosis, image storage and transmission in gastrointestinal (GI) cancer, but also in tumor precision therapy. Specifically, in the field of minimally invasive treatment such as precise ablation, 3-dimension modeling, navigation, and surgical simulation significantly improve the therapeutic safety and efficiency in GI cancer. In addition, in the era of big data, data analysis and individualized therapy using mathematical medicine will become a trend in the future, offering an effective method for diagnosing and treating GI cancer and promoting clinical and scientific research.

Single Cell Mathematical Model Successfully Replicates Key Features of GBM: Go-Or-Grow Is Not Necessary

Glioblastoma (GBM) is a malignant brain tumor that continues to be associated with neurological morbidity and poor survival times. Brain invasion is a fundamental property of malignant glioma cells. The Go-or-Grow (GoG) phenotype proposes that cancer cell motility and proliferation are mutually exclusive. Here, we construct and apply a single glioma cell mathematical model that includes motility and angiogenesis and lacks the GoG phenotype. Simulations replicate key features of GBM including its multilayer structure (i.e.edema, enhancement, and necrosis), its progression patterns associated with bevacizumab treatment, and replicate the survival times of GBM treated or untreated with bevacizumab. These results suggest that the GoG phenotype is not a necessary property for the formation of the multilayer structure, recurrence patterns, and the poor survival times of patients diagnosed with GBM.

MRI Based Bayesian Personalization of a Tumor Growth Model

The mathematical modeling of brain tumor growth has been the topic of numerous research studies. Most of this work focuses on the reaction-diffusion model, which suggests that the diffusion coefficient and the proliferation rate can be related to clinically relevant information. However, estimating the parameters of the reaction-diffusion model is difficult because of the lack of identifiability of the parameters, the uncertainty in the tumor segmentations, and the model approximation, which cannot perfectly capture the complex dynamics of the tumor evolution. Our approach aims at analyzing the uncertainty in the patient specific parameters of a tumor growth model, by sampling from the posterior probability of the parameters knowing the magnetic resonance images of a given patient. The estimation of the posterior probability is based on: 1) a highly parallelized implementation of the reaction-diffusion equation using the Lattice Boltzmann Method (LBM), and 2) a high acceptance rate Monte Carlo technique called Gaussian Process Hamiltonian Monte Carlo (GPHMC). We compare this personalization approach with two commonly used methods based on the spherical asymptotic analysis of the reaction-diffusion model, and on a derivative-free optimization algorithm. We demonstrate the performance of the method on synthetic data, and on seven patients with a glioblastoma, the most aggressive primary brain tumor. This Bayesian personalization produces more informative results. In particular, it provides samples from the regions of interest and highlights the presence of several modes for some patients. In contrast, previous approaches based on optimization strategies fail to reveal the presence of different modes, and correlation between parameters.