Clark-Swanson, Kamala

Abstract INTRODUCTION The quantification of intratumoral heterogeneity – through radiomics-based approaches - can help resolve the regionally distinct genetic drug targets that may co-exist within a single Glioblastoma (GBM) tumor. While this offers potential diagnostic value under the paradigm of individualized oncology, clinical decision-making must also consider the degree of uncertainty associated with each model. In this study, we evaluate the performance of a novel machine-learning (ML) algorithm, called Gaussian Process (GP) modeling, that can quantify the impact of multiple sources of uncertainty in ML model development and prediction accuracy, including variabilities in the copy number measurement, radiomics features, training sample characteristics, and training sample size. METHOD We collected 95 image-localized biopsies from 25 primary GBM patients. We coregistered stereotactic locations with preoperative multi-parametric MRI features (conventional MRI, DSC perfusion, Diffusion Tensor Imaging) to generate spatially matched pairs of MRI and copy number variants (CNV) for for each biopsy. We developed a Gaussian Process (GP) model to predict CNV for Epidermal Growth Factor Receptor (EGFR) based on MRI radiomic features in each patient. We used leave-one-patient-out cross validation to quantify prediction accuracy and model uncertainty. Spatial prediction and uncertainty (p-value) maps were overlaid to help visualize regional genetic variation of EGFR and uncertainty of the radiomic predictions. RESULT: The initial GP radiomics model for EGFR amplification (CNV > 3.5) produced a sensitivity of 0.8 and specificity of 0.8. Samples/regions associated with high uncertainty (p-value >0.05) correlated with either 1) extrapolation of radiomic features from the training set-defined feature space or 2) insufficient training samples in the feature space. CONCLUSION We present a ML-based model that quantifies spatial genetic heterogeneity in GBM, while also estimating model uncertainties that result from multi-source data variabilities. This approach lays the groundwork for prospective clinical integration of modeling-based diagnostic approaches in the paradigm of individualized medicine.

Abstract High-grade gliomas (HGGs) nearly always recur after standard initial treatment, and the resulting mixture of recurrent tumor and treatment-induced reactive changes presents major diagnostic challenges. Anatomical imaging, such as MRI, cannot adequately distinguish progressive disease from treatment effect (pseudo-progression). Furthermore, there is marked intra-tumoral heterogeneity, such that some areas of a tumor may demonstrate necrotic treatment effect and others frank recurrence. Due to this difficulty reliably differentiating between these two clinical findings, analytic methods using multiple modalities are necessary to further our understanding of this disease process. To this end, we sought to correlate radiographic, histopathologic and molecular features of surgically sampled post-treatment suspected recurrence to identify markers distinguishing tumor growth from treatment effect. We performed Stimulated Raman Histology (SRH) imaging and highly multiplexed RNA-sequencing (PLATE-seq) on 84 MRI-localized biopsies from 39 patients with clinically suspected recurrent HGG. The SRH images were classified as recurrent tumor or gliotic/reactive tissue using a convolutional neural network trained on an independent cohort including a large set of recurrent HGG, and an automated cell-counting algorithm was used to quantify cellularity from the SRH image of each sample. Differential gene expression analysis of the PLATE-seq data was used to identify gene sets that distinguish recurrent tumor from treatment effect, and single sample gene set variation analysis (GSVA) was used to further assess the molecular and cellular composition of each MRI-localized sample. The histopathologic and molecular features of each sample were also correlated with the MRI features of the corresponding biopsy sites, and this data is currently being used to train machine learning models that predict the distribution of recurrent tumor and treatment-induced reactive changes within a patient’s radiographic lesion. These predictive radiomic models will help to guide neurosurgical sampling, and improve our ability to monitor glioma progression and response to therapy.

Abstract Background : Sex is recognized as a significant determinant of outcome among glioblastoma patients, but the relative prognostic importance of glioblastoma features has not been thoroughly explored for sex differences. Methods : Combining multi-modal MR images, biomathematical models, and patient clinical information, this investigation assesses which pretreatment variables have a sex-specific impact on the survival of glioblastoma patients (299 males and 195 females). Results : Among males, tumor (T1Gd) radius was a predictor of overall survival (HR=1.027, p=0.044). Among females, higher tumor cell net invasion rate was a significant detriment to overall survival (HR=1.011, p<0.001). Female extreme survivors had significantly smaller tumors (T1Gd) (p=0.010 t-test), but tumor size was not correlated with female overall survival (p=0.955 CPH). Both male and female extreme survivors had significantly lower tumor cell net proliferation rates than other patients (M p=0.004, F p=0.001, t-test). Additionally, extent of resection, tumor laterality, and IDH1 mutation status were also found to have sex-specific effects on overall survival. Conclusion : Despite similar distributions of the MR imaging parameters between males and females, there was a sex-specific difference in how these parameters related to outcomes.

Abstract Background: Sex is recognized as a significant determinant of outcome among glioblastoma patients, but the relative prognostic importance of glioblastoma features has not been thoroughly explored for sex differences. Methods: Combining multi-modal MR images, biomathematical models, and patient clinical information, this investigation assesses which pretreatment variables have a sex-specific impact on the survival of glioblastoma patients (299 males and 195 females). Results: Among males, tumor (T1Gd) radius was a predictor of overall survival (HR=1.027, p=0.044). Among females, higher tumor cell net invasion rate was a significant detriment to overall survival (HR=1.011, p<0.001). Female extreme survivors had significantly smaller tumors (T1Gd) (p=0.010 t-test), but tumor size was not correlated with female overall survival (p=0.955 CPH). Both male and female extreme survivors had significantly lower tumor cell net proliferation rates than other patients (M p=0.004, F p=0.001, t-test). Additionally, extent of resection, tumor laterality, and IDH1 mutation status were also found to have sex-specific effects on overall survival. Conclusion: Despite similar distributions of the MR imaging parameters between males and females, there was a sex-specific difference in how these parameters related to outcomes.

PurposeDespite the intra- and intertumoral heterogeneity seen in glioblastoma multiforme (GBM), there is little definitive data on the underlying cause of the differences in patient survivals. Serial imaging assessment of tumor growth allows quantification of tumor growth kinetics (TGK) measured in terms of changes in the velocity of radial expansion seen on imaging. Because a systematic study of this entire TGK phenotype—growth before treatment and during each treatment to recurrence —has never been coordinately studied in GBMs, we sought to identify whether patients cluster into discrete groups on the basis of their TGK.Patients and MethodsFrom our multi-institutional database, we identified 48 patients who underwent maximally safe resection followed by radiotherapy with imaging follow-up through the time of recurrence. The patients were then clustered into two groups through a k-means algorithm taking as input only the TGK before and during treatment.ResultsThere was a significant survival difference between the clusters ( P = .003). Paradoxically, patients among the long-lived cluster had significantly larger tumors at diagnosis ( P = .027) and faster growth before treatment ( P = .003) but demonstrated a better response to adjuvant chemotherapy ( P = .048). A predictive model was built to identify which cluster patients would likely fall into on the basis of information that would be available to clinicians immediately after radiotherapy (accuracy, 90.3%).ConclusionDichotomizing the heterogeneity of GBMs into two populations—one faster growing yet more responsive with increased survival and one slower growing yet less responsive with shorter survival—suggests that many patients who receive standard-of-care treatments may get better benefit from select alternative treatments.

Abstract Purpose: Investigate the utility of patient-specific spatial predictions of tumor cell density from a bio-mathematical model. Introduction: Glioblastomas (GBMs) are the most malignant of all primary brain tumors. While it is known there is always a non-detectable portion of the tumor, current techniques of monitoring GBM progression, imaging and initial histological assessment, are not able to reliably estimate the tumor invasion past the enhancing region on T2-Weighted (T2W) imaging. Over the last two decades, a large effort has been made to create a simple patient-specific mathematical model of gliomas. The resulting model, referred to as the Proliferation-Invasion (PI) model, is based on two key parameters, the net growth rate, ρ, and the dispersal coefficient, D. In this model, the ratio of D/ρ is related to degree of invasion and the product D*ρ, is related to the speed of growth. The intuitive understanding provided by this model has been able to provide patient-specific understanding of disease kinetics enabling prediction of outcomes following surgical resection, radiation and the development of a prognostic response metric. Previous literature utilizing this model has been based on the assumption that what is seen on the pretreatment T1-Weighted contrast-enhanced (T1Gd) and T2W, images correspond to an 80% and 16% tumor cell density threshold respectively. This assumption allows for an estimate of D/ρ from a single time point of imaging. While these values were based on extensive experience, for ethical and technical reasons, they have never been rigorously investigated histologically. Recent technological advances have made it possible for surgeons to use an MRI to guide the acquisition of tissue making it possible to know with a good degree of accuracy where on the MR image the histological specimen comes from. Methods: Model Calibration : To estimate D/ρ for each patient, we assume abnormalities on the T1Gd and T2W images correspond to an 80% and 16% tumor cell density threshold respectively. We then utilize a Bayesian calibration approach based on adaptive grid refinement while holding the velocity constant to find the most likely value of D/ρ to match the observed radial measurements. Three-Dimensional Density Maps : Given a gray/white segmentation and an estimate for D/ρ, we can build a tumor cell density prediction in the patient's anatomy using the Eikonal equations and the modified Fast Marching Method (FMM) algorithm presented by Konukoglu et al. Patient Cohort : Eighteen patients were recruited with clinically suspected GBM undergoing preoperative stereotactic MRI for surgical resection with IRB approval Barrow Neurological Institute and Mayo Clinic in Arizona. Surgical Biopsy : Pre-operative conventional MRI, including T1Gd and T2W, was utilized to guide stereotactic biopsies. An average of 5–6 tissue specimens were acquired from each tumor by using stereotactic surgical localization, following the smallest possible diameter craniotomies to minimize brain shift. Histological Analysis : 4 μm tissue sections were stained with hematoxylin and eosin (H&E) for neuropathology review. H&E slides were reviewed by a neuropathologist. The percent tumor nuclei in the field was estimated. Results and Conclusion: Our analysis showed that the intuitive ordering of diffuse to nodular tumor profiles from the PI model is consistent with the histologic data. Further, utilizing the histologic data, limitations to a universal threshold cutoff of the T2/FLAIR region are specified and a better threshold cutoff value is suggested. We hope that this paper will lead to more studies of this kind resulting in more accurate ways to predict the spatial distribution of GBM tumor cells from medical imaging. Such advances could revolutionize surgical procedures and radiation therapy and may enable additional insights into tumor kinetic differences meaningful for treatment. Citation Format: Andrea Hawkins-Daarud, Lauren DeGirolamo, Joshua Jacobs, Kamala Clark-Swanson, Jennifer M. Eschbacher, Kris A. Smith, Peter Nakaji, Leslie C. Baxter, John P. Karis, Teresa Wu, J. Ross Mitchell, Jing Li, Leland Hu, Kristin R. Swanson. Histologic evidence for a bio-mathematical model of glioblastoma invasion. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A08.