*1-Dimensional Advective-Diffusion Model in Porous Media Infusion of therapeutic agents into tissue is makes use of two mass transport modes: advective transport, and molecular diffusion. Bulk infusion into a 0.6% wt agarose phantom was modeled as an infinite, homogenous, and isotropic porous medium saturated with the same solvent used in the infused dye tracer. The source is assumed to be spherical and isotropic with constant flow rate and concentration. The Peclet numberdecreases with power function Pe = 15762t0.337 due to the decrease in mean dye-front pore velocity as V goes to Vfinal. Diffusive mass transport does not become significant during any relevent time period. *Arborizing Fiberoptic Microneedle Catheter We have developed an arborizing catheter that allows multiple slender fused-silica CED cannulae to be deployed within a target volume of the brain via a single needle tract, and tested it in a widely accepted tissue phantom. The arborizing catheter was constructed by bonding and encapsulating seven slender PEEK tubes in a radially symmetric bundle with a progressive helical angle along the length, then grinding a conicle tip where the helical angle is greatest. The catheter was tested by casting 0.6% wt agarose around the device with all needles deployed to a tip-to-tip distance of 4 mm. Phantom temperature was maintained at 26 ± 2°C. 5% wt Indigo Carmine dye was infused at a rate of 0.3 uL/min/needle for 4 hours. N=4 infusions showed a Vd/Vi of 139.774, with a standard deviation of 45.01. This is an order of magnitude greater than single-needle infusions under similar conditions [45]. The arborizer showed the additional benefit of arresting reflux propagating up the lengths of individual needles, which has historically been a weakness of single-needle CED catheter designs. *In Vivo Co-Delivery of Single Walled Carbon Nano-horns and Laser Light to Treat Human Transitional Cell Carcinoma of the Urinary Bladder in a Rodent Model Using a rodent model we explored a treatment method for Transitional Cell Carcinoma (TCC) in the urinary bladder in which Single Walled Carbon Nanohorn (SWNH) solution and 1064 nm laser light are delivered into tumorous tissue via a co-delivery Fiberoptic Microneedle Device (FMD). Preliminary treatment parameters were determined by injecting SWNH solutions with concentrations of 0 mg/mL, 0.17 mg/mL, or 0.255 mg/mL into ex vivo porcine skin and irradiating each for three minutes at laser powers of 500 mW, or 1000 mW. The combination with the greatest temperature increase without burning the tissue, 0.17 mg/mL at 1000 mW, was selected for the in vivo treatment. TCC tumors were induced in a rodent model by injecting a solution of 106 AY27 urothelial carcinoma cells into the lateral aspect of the left hind leg of young, female F344 rats. When tumors reached 5-10 mm3, rats were anesthitized and treated. SWNH solution was injected directly into the tumor and irradiated until the target temperature of 60degC was achieved. The rats were then recovered from anestesia and monitored for 7-14 days, at which point they were humanely sacrificed, and the tumors prepared for histological examination. Histological assessment of areas of FMD treatment correlated well with gross morphological appearance. Foci of tumor necrosis showed sharp (1-2 mm) delineation from areas of viable tumor (not treated) and normal tissue. We believe we have demonstrated the feasibility of using the FMD for treatment of urothelial carcinoma using an animal model of this disease, and are encouraged to continue development of this treatment and testing in larger animal models. / Master of Science

Diffuse Gliome bei Erwachsenen sind aggressive, unheilbare Hirntumore. Humanisierte Mausmodelle helfen, molekulare Mechanismen zu verstehen und therapeutische Ziele zu identifizieren, aber der Vergleich mit Proben von Patienten gestaltet sich schwierig. Ich habe eine computergestützte Plattform namens CAPE entwickelt, um Tumormodelle und Patienten-Expressionsprofile mit Hilfe der nicht-negativen Matrixfaktorisierung zu vergleichen. Die Anwendung von CAPE auf humanisierte Maus-Gliom-Avatar-Modelle (GSA) und diffuse Glioma-Patienten zeigte eine starke Übereinstimmung zwischen den Modellen und dem proneuralen Glioblastom-Subtyp. CAPE hat gezeigt, dass durch die Transplantation der Erwerb neuer Tumorzustände in den Modellen verbessert wurde. Durch die Kombination von reporterbasiertem genetischem Tracing und CAPE zeigte sich, dass eine Untergruppe der in vivo GSA-Populationen mit Patienten zusammenfällt, die astrozytische Merkmale aufweisen. Die Behandlung von GSA-Modellen in vitro mit menschlichem Serum, TNFα oder ionisierender Strahlung führte zu einer Verschiebung in den mesenchymalen Zustand. Einzelzell-Transkriptomik annotierte GSA-Populationen unter verschiedenen Bedingungen und zeigte alle Glioblastomzustände in vivo und bei Aktivierung durch externe Faktoren. Der Vergleich von GSA-Einzelzellpopulationen und Patienten bestätigte diese Identitäten. Die Studie etablierte einen umfassenden Rahmen für die Erprobung und Validierung von Verbesserungen der Tumormodelle, um Patienten besser abzubilden, und erweiterte das Verständnis der Tumorbiologie und Ansprechen auf Therapie. / Adult-type diffuse gliomas are aggressive, incurable adult brain cancers. Humanized mouse models help understand molecular mechanisms and identify therapeutic targets, but comparing them with patient samples is difficult. I developed a computational framework, CAPE, for comparing tumor models and patient expression profiles using non-negative matrix factorization. Applying CAPE to humanized mouse glioma subtype avatar models (GSA) and adult-type diffuse glioma patients revealed a strong resemblance between models and proneural glioblastoma subtype. CAPE showed that transplantation improved new tumor state acquisition in models. Combining genetic tracing reporter phenotypic selection with CAPE showed a subset of in vivo GSA populations clustering with patients having astrocytic-like identities. In vitro treatment of GSA models with human serum, TNFα, or ionizing radiation led to a mesenchymal state shift upon reporter selection. Single-cell transcriptomics annotated GSA populations in different conditions, revealing all glioblastoma states in vivo and upon external factor activation. Comparing GSA single-cell populations and patients confirmed these identities. The study established a comprehensive framework for testing and validating tumor model improvements to resemble patients, advancing tumor biology and treatment response understanding.

High-frequency irreversible electroporation (H-FIRE) is a novel tumor ablation therapeutic that applies bipolar, high-frequency pulsed electric fields to tumors, triggering the formation of irreversible membrane pores and to induce tumor cell death. H-FIRE has demonstrated pre-clinical and clinical utility as a therapeutic for brain tumors, including gliomas. H-FIRE has been shown to induce precise, uniform ablation within the tumor tissue, as well as local changes to the tumor microenvironment and systemic changes to the immune landscape. Namely, disruption of the peritumoral blood-brain barrier (BBB) following H-FIRE ablation of brain tumors, and infiltration and activation of the innate immune system are clinically observed following H-FIRE tumor ablation. Such effects persist long after death of the treated tumor, and therefore an understanding of the mechanisms underlying these local and systemic changes are critical for the development of H-FIRE. Using in vitro models of glioma and lung carcinoma-derived brain metastases, we investigate the interactions between cancer cells that have been ablated with H-FIRE and the brain tumor microenvironments. Specifically, we demonstrate that H-FIRE-treated cancer cells can recover treatment-induced damage and proliferative capacity after treatment with specific electric field doses, while higher doses inhibit such recovery. This suggests that after H-FIRE ablation of brain tumors, tumor cells can still secrete factors to trigger alterations in their local and systemic environments. We then specifically investigate the role of tumor-derived extracellular vesicles (TDEVs) in mediating these changes, namely pBBB disruption and changes in innate immunity. We find that, following H-FIRE ablation of brain cancer cells, treated cells immediately release TDEVs that disrupt the blood-brain barrier (BBB) endothelium in vitro, and are uniquely internalized by cerebral endothelial cells in vitro, despite reduced release of TDEVs after H-FIRE. We further demonstrate that H-FIRE significantly alters the proteomic payloads of TDEVs. When TDEVs released by sham- and H-FIRE-treated glioma cells are delivered to healthy rats, only TDEVs released by H-FIRE-ablated cells are retained in the brain, suggesting changes to TDEV organotropism after H-FIRE ablation of glioma. Further, once retained in the brain, these post-H-FIRE TDEVs cluster near cerebral endothelial cells, similarly to in vitro. Although the TDEVs released by H-FIRE ablated glioma cells do not disrupt the BBB in vivo, Iba1+ cells were increased in the brains of rats that received TDEVs released by H-FIRE-ablated glioma cells. Together, these data suggest that H-FIRE immediately alters the secretion and proteome of TDEVs, facilitating changes in TDEV organotropism and cellular tropism and immune cell recruitment to the tumor microenvironment. Together, this research indicates mechanisms by which tumor cells continue to modulate their local and systemic environments via the action of TDEVs, which is critical information for the continued development of H-FIRE and its optimization with adjuvant therapeutics for the treatment of malignant brain tumors. / Doctor of Philosophy / All cells secrete extracellular vesicles, which are packets of information that function as communication highways between cells. In cancer, tumor-derived extracellular vesicles (TDEVs) reprogram local and distant cells to support tumor growth. However, they have also been shown to change local and systemic functions, such as blood vessel function and immune response, after tumors are treated with therapeutics. Therefore, a full understanding of the role of TDEVs in how tumors communicate with the body after cancer treatment is necessary when developing new anti-cancer therapeutics. Here, in developing high-frequency irreversible electroporation (H-FIRE), a novel anti-tumor therapeutic for the treatment of malignant brain tumors, we explore how TDEVs released by brain cancer cells treated with H-FIRE interact with various cell types and structures in the body, and how these interactions may affect the response to treatment. Using a glioma model of primary brain cancer, and a lung carcinoma model of brain metastases, we first explore how tumor cells may be able to recover from damage after treatment with H-FIRE. We discover that brain cancer cells treated with specific doses of H-FIRE recover cell damage and continue to proliferate, but cells treated with higher doses of H-FIRE cannot recover these functions. The fact that tumor cells may be able to recover after H-FIRE suggests that cancer cells may still secrete factors, such as TDEVs, that interact with cells in the microenvironment after tumor treatment. We investigated the role of TDEVs released by brain cancer cells treated with H-FIRE to determine whether they cause changes in surrounding cells and structures in the brain cancer microenvironment. We determined that brain cancer cells treated with H-FIRE release TDEVs that carry proteins different from those carried by TDEVs routinely released by untreated cells. We further found that these TDEVs disrupt the blood-brain barrier (BBB) endothelium in vitro, and are uniquely internalized by cells of the endothelium. When these TDEVs were administered to the brains of healthy rats, they were retained in the brain, clustered near the endothelium, and recruited immune cells from circulation into the brain. Conversely, TDEVs that were routinely released from the brain cancer cells, in the absence of H-FIRE treatment, exhibited none of these functions. Taken together, these results show that H-FIRE changes TDEVs in numerous ways: after H-FIRE, the TDEVs may gravitate toward particular organs and cell types, and recruit immune cells. All of these changes can impact the overall therapeutic response after H-FIRE, and may also be specifically optimized and targeted with additional therapeutics to make H-FIRE more effective for brain cancer.

En esta tesis se estudian los efectos farmacológicos de derivados lipídicos frente el glioma y el Alzheimer. Los beneficios de este tipo de fármacos, basados en la terapia lipídica de membrana, están asociados con la modulación de la composición y las propiedades fisicoquímicas de membrana. En concreto, el ácido 2-hidroxioleico (2OHOA) es un potente fármaco antitumoral que fue diseñado para regular la composición y la estructura de la membrana lipídica así como la función de importantes proteínas de membrana. Por otro lado, el ácido 2-hidroxiaraquidónico (2OHARA), el ácido 2-hidroxieicosapentaenóico (2OHEPA), y el ácido 2-hidroxidocosahexanóico (2OHDHA) son derivados lipídicos hidroxilados que fueron diseñados en nuestro grupo de investigación para el tratamiento del Alzheimer. Este trabajo se ha basado en el estudio del funcionamiento de estos derivados de ácidos grasos hidroxilados en la modulación de las vías de señalización de la UPR (respuesta a las proteínas mal plegadas) y de la autofagia en células de glioma y células neuronales. / In this thesis, the pharmacological effects of lipid derivatives against glioma and Alzheimer's Disease are studied. The benefits of this type of drugs, which are based on the lipid membrane therapy, are associated with the modulation of the composition and physicochemical properties of membranes. 2-Hydroxyoleic acid (2OHOA) is a potent antitumor drug designed to regulate membrane lipid composition and structure and the function of important membrane proteins. In addition, 2- hydroxyarachidonic acid (2OHARA; LP204A1), 2-hydroxyeicosapentaenoic acid (2OHEPA; LP205A1), and 2-hydroxydocosahexanoic acid (2OHDHA; LP226A1) are new hydroxy derivated lipids designed in our group for the treatment of Alzheimer’s Disease. The main goal of this work was to study how these synthetic hydroxy derivates modulate the unfolded protein response and the autophagy pathways in glioma cells and neuron-like cells for Alzheimer’s Disease.

Changes in gene expression programs play a central role in cancer. Chromosomal aberrations such as deletions, duplications and translocations of DNA segments can lead to highly significant positive correlations of gene expression levels of neighboring genes. This should be utilized to improve the analysis of tumor expression profiles. Here, we develop a novel model class of autoregressive higher-order Hidden Markov Models (HMMs) that carefully exploit local data-dependent chromosomal dependencies to improve the identification of differentially expressed genes in tumor. Autoregressive higher-order HMMs overcome generally existing limitations of standard first-order HMMs in the modeling of dependencies between genes in close chromosomal proximity by the simultaneous usage of higher-order state-transitions and autoregressive emissions as novel model features. We apply autoregressive higher-order HMMs to the analysis of breast cancer and glioma gene expression data and perform in-depth model evaluation studies. We find that autoregressive higher-order HMMs clearly improve the identification of overexpressed genes with underlying gene copy number duplications in breast cancer in comparison to mixture models, standard first- and higher-order HMMs, and other related methods. The performance benefit is attributed to the simultaneous usage of higher-order state-transitions in combination with autoregressive emissions. This benefit could not be reached by using each of these two features independently. We also find that autoregressive higher-order HMMs are better able to identify differentially expressed genes in tumors independent of the underlying gene copy number status in comparison to the majority of related methods. This is further supported by the identification of well-known and of previously unreported hotspots of differential expression in glioblastomas demonstrating the efficacy of autoregressive higher-order HMMs for the analysis of individual tumor expression profiles. Moreover, we reveal interesting novel details of systematic alterations of gene expression levels in known cancer signaling pathways distinguishing oligodendrogliomas, astrocytomas and glioblastomas.

Os gliomas são tumores cerebrais intracraniais caracterizados pelo seu rápido crescimento e pela sua resistência à quimioterapia e radioterapia atuais. Assim, a procura por novos agentes terapêuticos com múltiplos mecanismos de ação têm identificado o ácido <font face=\"symbol\">g-linolênico (GLA), antiinflamatórios não esteroidais (AINEs) e compostos contendo rutênio como possíveis candidatos. Dessa forma, a principal proposta deste projeto foi entender melhor o mecanismo de ação dessas drogas sobre as células C6 de glioma de rato. Foram analisadas proteínas envolvidas no controle do ciclo celular, apoptose, angiogênese, invasão e migração através de RT-PCR e Western Blotting após tratamento in vitro e in vivo. Alterações da expressão de ciclina D1, E2F-1, pRb, p27, p21, p16, p65, c-myc, ERK1/2, nm23 e <font face=\"symbol\">b, MMP-2, Brevican GPI e Secretado, Tenascina-R, Tenascina-C, VEGF-A, Flt1, Flk1, Bax, PPAR<font face=\"symbol\">g, p53, COX-2, EP1, 2, 3 e 4, Ku70 e 80 foram encontradas. Em conclusão, o GLA e o complexo Rutênio-Ibuprofeno possuem múltiplos alvos que levam à inibição da proliferação celular. / Gliomas are intracranial tumors of cerebral origin characterized for its rapid growth and resistance to both conventional chemotherapy and radiotherapy. The search for new therapeutics agents with multiple mechanisms of action has identified <font face=\"symbol\">g-linolenic acid (GLA), nonsteroidal anti-inflammatory drugs (NSAIDs) and ruthenium containing compounds as possible candidates. The aim of this study was to better know the mechanism of action of these drugs on C6 rat glioma cells. Expression of proteins involved in control of the cell cycle, apoptosis, angiogenesis, invasion and migration was analyzed using RT-PCR and Western Blotting methods after treatment in vitro and in vivo. Alterations in cyclin D1, E2F-1, pRb, p27, p21, p16, p65, c-myc, ERK1/2, nm23 e <font face=\"symbol\">b, MMP-2, GPI and Secreted Brevican, Tenascin-R, Tenascin-C, VEGF-A, Flt1, Flk1, Bax, PPAR<font face=\"symbol\">g, p53, COX-2, EP1, 2, 3 and 4, Ku70 and 80 expression were observed. In conclusion, GLA and Ruthenium-Ibuprofen complex has multiple target wich translate into the inhibition of proliferation.

Os gliomas são tumores cerebrais intracraniais caracterizados pelo seu rápido crescimento e pela sua resistência à quimioterapia e radioterapia atuais. Assim, a procura por novos agentes terapêuticos com múltiplos mecanismos de ação têm identificado o ácido <font face=\"symbol\">g-linolênico (GLA), antiinflamatórios não esteroidais (AINEs) e compostos contendo rutênio como possíveis candidatos. Dessa forma, a principal proposta deste projeto foi entender melhor o mecanismo de ação dessas drogas sobre as células C6 de glioma de rato. Foram analisadas proteínas envolvidas no controle do ciclo celular, apoptose, angiogênese, invasão e migração através de RT-PCR e Western Blotting após tratamento in vitro e in vivo. Alterações da expressão de ciclina D1, E2F-1, pRb, p27, p21, p16, p65, c-myc, ERK1/2, nm23 e <font face=\"symbol\">b, MMP-2, Brevican GPI e Secretado, Tenascina-R, Tenascina-C, VEGF-A, Flt1, Flk1, Bax, PPAR<font face=\"symbol\">g, p53, COX-2, EP1, 2, 3 e 4, Ku70 e 80 foram encontradas. Em conclusão, o GLA e o complexo Rutênio-Ibuprofeno possuem múltiplos alvos que levam à inibição da proliferação celular. / Gliomas are intracranial tumors of cerebral origin characterized for its rapid growth and resistance to both conventional chemotherapy and radiotherapy. The search for new therapeutics agents with multiple mechanisms of action has identified <font face=\"symbol\">g-linolenic acid (GLA), nonsteroidal anti-inflammatory drugs (NSAIDs) and ruthenium containing compounds as possible candidates. The aim of this study was to better know the mechanism of action of these drugs on C6 rat glioma cells. Expression of proteins involved in control of the cell cycle, apoptosis, angiogenesis, invasion and migration was analyzed using RT-PCR and Western Blotting methods after treatment in vitro and in vivo. Alterations in cyclin D1, E2F-1, pRb, p27, p21, p16, p65, c-myc, ERK1/2, nm23 e <font face=\"symbol\">b, MMP-2, GPI and Secreted Brevican, Tenascin-R, Tenascin-C, VEGF-A, Flt1, Flk1, Bax, PPAR<font face=\"symbol\">g, p53, COX-2, EP1, 2, 3 and 4, Ku70 and 80 expression were observed. In conclusion, GLA and Ruthenium-Ibuprofen complex has multiple target wich translate into the inhibition of proliferation.

Changes in gene expression programs play a central role in cancer. Chromosomal aberrations such as deletions, duplications and translocations of DNA segments can lead to highly significant positive correlations of gene expression levels of neighboring genes. This should be utilized to improve the analysis of tumor expression profiles. Here, we develop a novel model class of autoregressive higher-order Hidden Markov Models (HMMs) that carefully exploit local data-dependent chromosomal dependencies to improve the identification of differentially expressed genes in tumor. Autoregressive higher-order HMMs overcome generally existing limitations of standard first-order HMMs in the modeling of dependencies between genes in close chromosomal proximity by the simultaneous usage of higher-order state-transitions and autoregressive emissions as novel model features. We apply autoregressive higher-order HMMs to the analysis of breast cancer and glioma gene expression data and perform in-depth model evaluation studies. We find that autoregressive higher-order HMMs clearly improve the identification of overexpressed genes with underlying gene copy number duplications in breast cancer in comparison to mixture models, standard first- and higher-order HMMs, and other related methods. The performance benefit is attributed to the simultaneous usage of higher-order state-transitions in combination with autoregressive emissions. This benefit could not be reached by using each of these two features independently. We also find that autoregressive higher-order HMMs are better able to identify differentially expressed genes in tumors independent of the underlying gene copy number status in comparison to the majority of related methods. This is further supported by the identification of well-known and of previously unreported hotspots of differential expression in glioblastomas demonstrating the efficacy of autoregressive higher-order HMMs for the analysis of individual tumor expression profiles. Moreover, we reveal interesting novel details of systematic alterations of gene expression levels in known cancer signaling pathways distinguishing oligodendrogliomas, astrocytomas and glioblastomas.

No description available.

Malignant brain tumors, known as H3K27-altered diffuse midline glioma (DMG) and H3G34-mutant diffuse hemispheric glioma (DHG), can affect individuals of all ages and are classified as CNS WHO grade 4. We comprehensively characterized 390 H3F3A-mutant diffuse gliomas (201 females, 189 males) arising in pediatric patients (under 20 years old) and adults (20 years and older) evaluated by the CGP program at Foundation Medicine between 2013 and 2020. We assessed information from pathology reports, histopathology review, and clinical data. The cohort included 304 H3K27M-mutant DMG (156 females, 148 males) and 86 H3G34-mutant DHG (45 females, 41 males). Median patient age was 20 years (1–74 years). The frequency of H3K27M-mutant DMG was similar in both pediatric and adult patients in our cohort—48.6% of the patients were over 20 years old, 31.5% over 30, and 18% over 40 at initial diagnosis. FGFR1 hotspot point mutations (N546K and K656E) were exclusively identified in H3K27M-mutant DMG tumors (64/304, 21%; p = 0.0001); these tend to occur in older patients (median age: 32.5 years) and mainly arose in the diencephalon. H3K27M-mutant DMG had higher rates of mutations in NF1 (31.0 vs 8.1%; p = 0.0001) and PIK3CA/PIK3R1 (27.9% vs 15.1%; p = 0.016) compared to H3G34-mutant DHG. However, H3G34-mutant DHG had higher rates of targetable alterations in cell-cycle pathway genes (CDK4 and CDK6 amplification; CDKN2A/B deletion) (27.0 vs 9.0%). Potentially targetable PDGFRA alterations were identified in ~ 20% of both H3G34-mutant DHG and H3K27M-mutant DMG. Overall, in the present study H3K27M-mutant DMG occurred at similar rates in both adult and patient patients. Through our analysis, we were able to identify molecular features characteristic of DMG and DHG. By identifying the recurrent co-mutations including actionable FGFR1 point mutations found in nearly one-third of H3K27M-mutant DMG in young adults, our findings can inform clinical translational studies, patient diagnosis, and clinical trial design.