Master of Science / Department of Electrical and Computer Engineering / Punit Prakash / Thermal therapies employing interstitial microwave applicators for hyperthermia or ablation are in clinical use for treatment of cancer and benign disease in various organs. However, treatment of targets in proximity to critical structures with currently available devices is risky due to unfocused deposition of energy into tissue. For successful treatment, complete thermal coverage of the tumor and margin of surrounding healthy tissue must be achieved, while precluding damage to critical structures. This thesis investigates two approaches to increase precision of microwave thermal therapy. Chapter 2 investigates a novel coaxial antenna design for microwave ablation (MWA) employing a hemi-cylinderical reflector to achieve a directional heating pattern. A proof of concept antenna with an S₁₁ of -29 dB at 2.45 GHz was used in ex vivo experiments to characterize the antennas’ heating pattern with varying input power and geometry of the reflector. Ablation zones up to 20 mm radially were observed in the forward direction, with minimal heating (less than 4 mm) behind the reflector. Chapter 3 investigates the use of magnetic nanoparticles (MNP) of varying size and geometry for enhancing microwave tissue heating. A conventional dipole, operating at 2.45 GHz and radiating 15 W, was inserted into a 20 mm radius sphere of distributed MNPs and heating measurements were taken 5 mm, 10 mm, and 15 mm radially away. A heating rate of 0.08°C/s was observed at 10 mm, an increase of 2-4 times that of the control measurement. These approaches provide strong potential for improving spatial control of tissue heating with interstitial and catheter-based microwave antennas.

Master of Science / Department of Electrical and Computer Engineering / Punit Prakash / Microwave ablation (MWA) is a minimally invasive thermal therapy predominantly used in the treatment of localized cancer. Previous studies have demonstrated clinical use of MWA for treating lung tumors, however, these procedures have relied upon the use of rigid percutaneous MWA applicators which can limit the range of accessible tumors and may have inherent disadvantages for use in lung tissue. The objective of this work was to develop and characterize a bronchoscopic MWA applicator suitable for use in a system that enables bronchoscopic transparencymal nodule access (BTPNA). A 3D coupled FEM electromagnetic-heat transfer model was implemented to optimize the antenna design and evaluate the expected ablation size and shape. A prototype device was fabricated and experimentally evaluated in ex vivo tissue to verify simulation results and demonstrate proof-of-concept. Simulated and experimental results indicate the proposed device could create ablation zones 19.3 – 31.0 mm in diameter with 30 – 45 W of power applied for 5 – 10 minutes. Future bronchoscopic MWA applicators based on the design proposed in this study could allow physicians an even less invasive treatment option for lung cancer with increased accuracy and efficacy and reduced risk of procedural complications immediately following a positive bronchoscopic lung biopsy.

This project studies the removal of non-anatomical objects from medical images. During tumor ablation procedures, the ablation probes appear in the image, hindering the performance of segmentation, registration, and dose computation algorithms. These algorithms can also be affected by artifacts and noise generated by body implants. Image inpainting methods allow the completion of the missing or distorted regions, generating realistic structures coherent with the rest of the image. During the last decade, the study of image inpainting methods has accelerated due to advances in deep learning and the increase in the consumption of multimedia content. Models applying generative adversarial networks have excelled at the task of image synthesis. However, there has not been much study done on medical image inpainting. In this project, a new inpainting method is proposed for recovering missing information from medical images. This method consists of a two-stage model, where a coarse network is followed by a refinement network, both of which are U-Nets. The refinement network is trained together with a discriminator, providing adversarial learning. The model is trained on a dataset of CT images of the liver and, in order the mimic the areas where information is missing, regular and irregular shaped masks are applied. The trained models are compared both quantitatively and qualitatively. Due to the lack of standards and accurate metrics in image inpainting tasks, results cannot be easily compared to current approaches. However, qualitative analysis of the inpainted images shows promising results. In addition, this project identifies the Frechet Inception Distance as a more valid metric than older metrics commonly used for evaluation of image inpainting models. In conclusion, this project provides an inpainting model for medical images, which could be used during tumor ablation procedures and for noise and artifact elimination. Future research could include implementing a 3D model to provide more coherent results for inpainting patients - a stack of images - instead of single images. / I detta projekt undersöks metoder för avlägsnande av icke-anatomiska föremål från medicinska bilder. Bilder tagna under ablationsbehandling av tumörer innehåller själva ablationsnålen, denna kan hindra segmenterings-, registrerings-och dosberäknings-algoritmer för att uppnå önska resultat. Dessa algoritmer kan också påverkas av artefakter och brus som genereras av olika metallimplantat. Bildifyllningsmetoder gör det möjligt att ersätta regioner som saknar eller innehåller inkorrekt bilddata, med realistiska strukturer som är sammanhängande med resten av bilden. Under det senaste decenniet har intresset för metoder för bildifyllning accelererat på grund av framsteg inom djupinlärning och ökad konsumtion av multimediainnehåll. Modeller som använder generative adversarial networks har utmärkt sig i bildsynteseringsuppgifter. Det har dock inte gjorts så många studier gällande bildifyllning av medicinska bilder. I detta projekt föreslås en ny bildifyllningsmetod för att återställa regioner med inkorrekt information i medicinska bilder. Denna metod består av ett tvåstegsnätverk, där ett första nätverk följs av ett förfiningsnätverk, båda av typen U-net. Förfiningsnätverk tränas tillsammans med ett diskriminatornätverk. Modellen tränas på ett dataset av CT-bilder av levern. För att efterlikna de områden där information saknas, applicerades masker av olika former. De färdigtränade modellerna jämfördes både kvantitativt och kvalitativt. På grund av bristen på standarder och noggranna mätvärden för bildifyllningsmetoder, kan resultaten inte enkelt jämföras med existerande metoder. Men kvalitativ analys av de målade bilderna visar ganska lovande resultat. Modellen presterar som bäst i områden inte innehåller komplexa strukturer. Sammanfattningsvis har en fungerande bildifyllningsmetod för medicinska bilder skapats och som kan användas vid tumörablation och för eliminering av bildartefakter. Framtida forskning kan inkludera implementering av en 3D-modell för att ge mer sammanhängande resultat.

Brain tumors are among the most devastating types of solid tumors to treat. Standard of care for glioblastoma (GBMs), the most aggressive form of primary brain tumors, has failed to improve the current survival rates in the past decades. Despite many other solid tumors, recent advances in cancer immunotherapies have also shown disappointing outcomes in GBMs. The heterogenous nature of GBMs, the immunosuppressive tumor microenvironment and the restrictive role of blood brain barrier (BBB) are some of the main challenges faced for treating GBMs. Electroporation-based treatments have demonstrated promising results, treating preclinical models of GBMs. It has been shown that low and high frequency irreversible electroporation treatments shift the immunosuppressive tumor microenvironment and reversibly open large areas of blood brain barrier (BBB). In this dissertation, in vitro cell culture models are utilized to study electroporation-based treatments for achieving a more optimized treatment for glioblastoma. We are proposing to utilize the immunomodulatory effects of electroporation treatments to improve the outcomes of immunotherapies in the brain. / Doctor of Philosophy / Despite the current advancements in treating solid tumors, brain tumors remain among the most difficult cancers to treat. The special structure of the brain as an organ as well as tumor complexity can lead to treatment failure. It is also known that infiltration of the immune cells within the tumor mass is limited due to the tumor's immunosuppressive nature. Hence, the use of newly advancing immunotherapy techniques is limited in the brain. Local treatments have become one of the most promising tools against brain tumors. Such treatments include methods that use excessive heating of the tissue to kill the tumors. Relying on heat for tissue destruction could damage the critical structures near the tumor and will reduce the favorable immune response after the treatment. A new treatment modality known as electroporation has been introduced for non-thermal treatment of brain tumors. Due to its non-thermal nature, electroporation treatments will allow for sparing of critical structures and can lead to a more robust immune response comparing to thermal treatment modalities. In this dissertation, we utilize electroporation-based treatments to try to overcome some of the challenges associated with treating brain tumors such as tumor heterogeneity and immune suppression.

Glioblastoma Multiforme (GBM) is a highly aggressive and prevalent brain tumor with an average 5-year survival rate of approximately 6.9%. Its complex pathophysiology, characterized by the capacity to invade surrounding tissues beyond the visible tumor margin, intratumor heterogeneity, hypoxic core, and the presence of the blood-brain barrier (BBB) that restricts the penetration of large therapeutic agents, all pose formidable challenges for effective therapeutic intervention. The standard of care for GBM has thus far exhibited limited success, and patients often face a poor prognosis. Electroporation-based therapies, such as irreversible electroporation (IRE), have emerged as promising alternatives to conventional treatments. By utilizing high amplitude pulsed electric fields, IRE is able to permeabilize cells, disrupt the BBB, and induce non thermal ablation of soft tissues. However, IRE is oftentimes accompanied by undesirable secondary effects such as muscle contractions, complex anesthetic protocols, and susceptibility to electrical heterogeneities, which have impeded its clinical translation. To address these limitations, high-frequency IRE (H-FIRE) was developed. H-FIRE employs short bursts of bipolar pulses, similar in duration to the cell charging time constant, enabling the desired tissue ablation while minimizing nerve excitation and muscle contractions. Additionally, H-FIRE reduces susceptibility to electrical heterogeneities, allowing for more predictable treatment volumes, thus enhancing the feasibility of clinical translation. This dissertation investigates H-FIRE for targeting malignant gliomas while looking into improved efficacy when administering the therapy in conjunction with other treatment forms and technologies. Specifically, the presented work focuses on several key areas: (1) determining the effect of pulsing protocol and geometric configuration selection on the biological outcomes from electroporation; (2) using a tumor bearing rodent glioma model to evaluate the effects of H-FIRE as a standalone therapy and as a combinatorial therapy with liposomal doxorubicin; (3) investigating the effects of waveform shape on biological outcomes; (4) utilizing real-time Fourier Analysis SpecTroscopy (FAST) to accurately model rises in temperature during treatment; and (5) modifying real-time FAST methods to determine treatment endpoints for safe and effective ablation volumes. / Doctor of Philosophy / Glioblastoma Multiforme (GBM) is one of the deadliest tumors, with an overall five-year survival rate of approximately 6.9%. Unfortunately, it also holds the position of being the most prevalent malignant brain tumor, constituting nearly 50.1% of all primary malignant brain tumor diagnoses. Despite its widespread occurrence, there has been limited success in improving survival rates. The tumor's infiltrative nature and its location behind the blood-brain barrier (BBB), which often screens out large drug molecules like chemotherapeutics, contribute significantly to these unfavorable treatment outcomes. This dissertation explores the potential of high-frequency irreversible electroporation (H-FIRE) as a solution to these challenges. H-FIRE employs bursts of pulsed electric fields to induce nanoscale defects in the cell membrane. The response to these defects may involve temporary pores that facilitate the uptake of therapeutic molecules into the cell, or larger and longer lasting pores that disrupt cell homeostasis, ultimately leading to cell death. Furthermore, this pulsed field therapy has shown success in enabling molecules to bypass the BBB. Thus, this dissertation aims to elucidate the various biophysical phenomena associated with H-FIRE, shedding light on how to manipulate treatment protocols to maximize BBB disruption and enhance therapy when used in conjunction with combinatorial agents. Additionally, this work aims to further develop technologies to provide real-time feedback, ensuring the safe and effective delivery of the treatment. Through these efforts, this dissertation aspires to offer valuable insights into optimizing H-FIRE for the treatment of malignant gliomas and advancing the understanding of combinatorial therapies in this specific context.

Malignant gliomas (MG), most notably glioblastoma multiforme (GBM), are among the most aggressive of all malignancies. High-grade variants of this type of brain cancer are generally considered incurable with singular or multimodal therapies. Many patients with GBM die within one year of diagnosis, and the 5-year survival rate in people is approximately 10%. Despite extensive research in diagnostic and therapeutic technologies, very few developments have emerged that significantly improve survival over the last seven decades. Irreversible electroporation (IRE) is a new non-thermal focal tissue ablation technique that uses low-energy electric pulses to destabilize cell membranes, thus achieving tissue death. The procedure is minimally invasive and is performed through small electrodes inserted into the tissue with treatment duration of about one minute. The pulses create an electric field that induces an increase in the resting transmembrane potential (TMP) of the cells in the tissue. The induced increase in the TMP is dependent on the electric pulse parameters. Depending on the magnitude of the induced TMP the electric pulses can have no effect, transiently increase membrane permeability or cause spontaneous death. In this dissertation we hypothesize that irreversible electroporation is capable of ablating normal (gray and white matter) and pathological (MG and/or GBM) brain tissue in a highly focused non-thermal manner that is modulated through pulse parameters and electrode configuration. Through a comprehensive experimental and numerical investigation, we tested and attained results strongly supporting our hypothesis. Specifically, we developed numerical models that were capable of simulating an entire IRE treatment protocol and would take into account pulse parameters (e.g. duration, frequency, repetition rate and strength) in addition to the dynamic changes in tissue electrical conductivity due to electroporation and joule heating, as well as biologically relevant processes such as blood perfusion and metabolic heat. We also provided a method to isolate the IRE effects from undesired thermal damage in models that were validated with real-time temperature measurements during the delivery of the pulses. Finally we outlined a procedure to use 3D volumetric reconstructions of IRE lesions using patient specific MRI scans in conjunction with the models described for establishing field thresholds or performing treatment planning prior to the surgical procedure; thus supplying the readers with the tools and understanding necessary to design appropriate treatment protocols for their specific application. Experimentally we presented the first systematic in vivo study of IRE in normal canine brain and the multimodal treatment of a canine MG patient. We confirmed that the procedure can be applied safely in the brain and was well tolerated clinically. The lesions created with IRE were sub-millimeter in resolution and we achieved 75% tumor volume reduction within 3 days post-IRE in the patient. In addition to the sharp delineation between necrotic and normal brain, the treatments spared the major blood vessels, making it appropriate for treatment of tumors adjacent to, or enveloping critical vascular structures. We believe that irreversible electroporation will play a key role in the treatment of intracranial disorders including malignant brain cancer in which the intent is to focally kill undesired tissue while minimizing damage to surrounding healthy tissue. / Ph. D.

PURPOSE: Thermal ablation therapy is an emerging local cancer treatment to destroy cancer tissue using heat. However variations in blood flow and energy absorption rates make it extremely challenging to monitor thermal changes. Insufficient ablation may lead to recurrence of the cancer while excessive ablation may damage adjacent healthy tissues. Ultrasound could be a convenient and inexpensive imaging modality for real-time monitoring of the ablation. For the development and optimization of these methods, it is essential to have ground truth data and a reliable and quantitative validation technique before beginning clinical trials on humans. In this dissertation, my primary focus was to solve the image-to-physical space registration problem using stereotactic fiducials that provide accurate correlation of ultrasound and pathology (ground truth) images. METHOD: A previously developed validation test-bed prototype was evaluated using phantom experiments to identify the shortcomings and limitations. In order to develop an improved validation platform, a simulator was implemented for evaluating registration methods as well as different line fiducial structures. New fiducial line structures were proposed, and new methods were implemented to overcome the limitations of the old system. The new methods were then tested using simulation results and phantom studies. Phantom experiments were conducted to improve the visibility of fiducials, as well as the quality of acquired ultrasound and pathology image datasets. RESULTS: The new system outperforms the previous one in terms of accuracy, robustness, and simplicity. The new registration method is robust to missing fiducials. I also achieved complete fiducial visibility in all images. Enhancing the tissue fixation medium improved the ultrasound data quality. The quality of pathology images were improved by a new imaging method. Simulation results show improvement in pose recovery accuracy using my proposed fiducial structure. This was validated by phantom studies reducing spatial misalignment between the US and pathology image sets. CONCLUSION: A new generation of test-bed was developed that provides a reliable and quantitative validation technique for evaluating and optimizing ablation monitoring methods. / Thesis (Master, Computing) -- Queen's University, 2011-09-29 20:31:55.159

This thesis project serves to fill experimental gaps needed to advance the goal of performing pre-clinical trials using an orthotopic rat glioblastoma model to evaluate the efficacy of high-frequency electroporation (H-FIRE) and QUAD-CTX tumor receptor-targeted cytotoxic conjugate therapies, individually and in combination, in selectively and thoroughly treating glioblastoma multiforme. In order to achieve this, an appropriate model must be developed and characterized. I have transduced F98 rat glioma cells to express red-shifted firefly luciferase, which will facilitate longitudinal tumor monitoring in vivo through bioluminescent imaging. I have characterized their response to H-FIRE relative to DI TNC1 rat astrocytes. I have demonstrated the presence of the molecular targets of QUAD in F98 cells. The in vitro characterization of this model has enabled preclinical studies of this promising glioblastoma therapy in an immunocompetent rat model, an important step before advancing ultimately to clinical human trials. / Master of Science / Treating glioblastoma multiforme (GBM), a form of cancer found in the brain, has not been very successful; patients rarely live two years following diagnosis, and there have been no major breakthrough advances in treatment to improve this outlook for decades. We have been working on two treatments which we hope to combine. The first is high-frequency electroporation (H-FIRE), which uses electrical pulses to kill GBM cells while leaving healthy cells alive and blood vessels intact. The second is QUAD-CTX, which combines a toxin with two types of protein that attach to other proteins that are more common on the surface of GBM cells than healthy cells. We have shown these to be effective at disproportionately killing human GBM cells growing in a lab setting. Before H-FIRE and QUAD-CTX may be tested on humans, we need to show them to be effective in an animal model, specifically rats. I have chosen rat glioma cells that will behave similarly to human GBM and a rat species that will not have an immune response to them. I have made these cells bioluminescent so that we may monitor the tumors as they grow and respond to our treatments. I have also shown that QUAD-CTX kills these rat glioma cells, as does H-FIRE. Because of this work, we are ready to begin testing these two treatments in rats.

Glioblastoma (GBM) is the most common and deadliest of the malignant primary brain tumors in humans, with a reported 5-year survival rate of only 6.8% despite years of extensive research. Failure to improve local tumor control rates and overall patient outcome is attributed to GBM's inherent therapeutic resistance. Marked heterogeneity, extensive local invasion within the brain parenchyma, and profound immunosuppression within the tumor microenvironment (TME) are some of the unique features that drive GBM therapeutic resistance. Furthermore, tumor cells are sequestered behind the blood-brain barrier (BBB), limiting delivery of effective therapeutics and immune cell infiltration into the local tumor. Electroporation-based therapies, such as irreversible electroporation (IRE) and second generation, high-frequency IRE (H-FIRE) represent attractive alternative approaches to standard GBM therapy given their ability to induce transient BBB disruption (BBBD), achieve non-thermal tumor cell ablation and stimulate local and systemic anti-tumor immune responses without significant morbidity. The following work explores the use of H-FIRE to overcome GBM-induced therapeutic resistance and improve treatment success. Chapter 1 opens with an overview of GBM and known barriers to treatment success. Here, we emphasize the utility of spontaneous canine gliomas as an ideal translational model for investigations into novel treatment approaches. Chapter 2 introduces novel ablation methods (i.e. IRE/H-FIRE) capable of targeting treatment-resistant cancer stem cells. The focus of Chapter 3 is to highlight IRE applications in a variety of spontaneous tumor types. In Chapter 4, we investigate the feasibility and local immunologic response of percutaneous H-FIRE for treatment of primary liver tumors using a spontaneous canine hepatocellular carcinoma (HCC) model. In chapter 5, we characterize the mechanisms of H-FIRE-mediated BBBD in an in vivo healthy rodent model. In Chapter 6, we characterize the local and systemic immune responses to intracranial H-FIRE in rodent and canine glioma models to enhance the translational value of our work. Collectively, our work demonstrates the potential for H-FIRE to overcome therapeutic resistance in GBM, thereby supporting its use as a novel, alternative treatment approach to standard therapy. / Doctor of Philosophy / Glioblastoma (GBM) is the most common and deadliest form of primary brain cancer in humans, with only 6.8% of people surviving 5-years after their diagnosis. GBM is characterized by a number of unique features that make it resistant to standard treatments, such as surgery, radiation and chemotherapy. Examples include: (1) extensive invasion of tumor cells into the brain, making complete removal via surgery very difficult; (2) tumor cells are protected by a structure called the blood-brain barrier (BBB), which restricts the entry of most drugs (i.e. chemotherapy) and many immune cells, into the brain, thereby preventing them from reaching tumor cells; (3) tumor cells produce substances that block the immune system from being able to detect the tumor itself, which allows it to continue to grow undetected. High-frequency irreversible electroporation (H-FIRE) represents a new approach for the treatment of GBM. H-FIRE uses electric pulses to temporarily or permanently injure cell membranes without the use of heat, which allows for very precise treatment. The following work explores the ways in which H-FIRE can interfere with specific GBM features that drive its resistance to treatment. Here, we demonstrate that H-FIRE is capable of temporarily disrupting the BBB and characterize the mechanisms by which this occurs. This allows for drugs and immune cells within the blood to enter the brain and access the tumor cells, particularly those extending beyond the visible tumor mass and invading the brain. We also illustrate the potential for H-FIRE treatment within the brain to stimulate local and systemic immune responses by causing the release of proteins from injured cells. Similar to a vaccine, these proteins are recognized by the immune system, which becomes primed to help fight off cancer cells within the body. The end result is an anti-tumor immune response. Collectively, this work supports the use of H-FIRE as an alternative treatment approach to standard therapy for GBM given its potential to overcome certain causes of treatment resistance.