abstract: In the past decades, single-cell metabolic analysis has been playing a key role in understanding cellular heterogeneity, disease initiation, progression, and drug resistance. Therefore, it is critical to develop technologies for individual cellular metabolic analysis using various configurations of microfluidic devices. Compared to bulk-cell analysis which is widely used by reporting an averaged measurement, single-cell analysis is able to present the individual cellular responses to the external stimuli. Particularly, oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) are two key parameters to monitor heterogeneous metabolic profiles of cancer cells. To achieve multi-parameter metabolic measurements on single cells, several technical challenges need to be overcome: (1) low adhesion of soft materials micro-fabricated on glass surface for multiple-sensor deposition and single-cell immobilization, e.g. SU-8, KMPR, etc.; (2) high risk of using external mechanical forces to create hermetic seals between two rigid fused silica parts, even with compliance layers; (3) how to accomplish high-throughput for single-cell trapping, metabolic profiling and drug screening; (4) high process cost of micromachining on glass substrate and incapability of mass production. In this dissertation, the development of microfabrication technologies is demonstrated to design reliable configurations for analyzing multiple metabolic parameters from single cells, including (1) improved KMPR/SU-8 microfabrication protocols for fabricating microwell arrays that can be integrated and sealed to 3 × 3 tri-color sensor arrays for OCR and ECAR measurements; (2) design and characterization of a microfluidic device enabling rapid single-cell trapping and hermetic sealing single cells and tri-color sensors within 10 × 10 hermetically sealed microchamber arrays; (3) exhibition of a low-cost microfluidic device based on plastics for single-cell metabolic multi-parameter profiling. Implementation of these improved microfabrication methods should address the aforementioned challenges and provide a high throughput and multi-parameter single cell metabolic analysis platform. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2017

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Piplartine and piperine are alkaloids/amides isolated from Piper species. The activity of these compounds was initially evaluated on the brine shrimp lethality assay, sea urchin development, MTT assay using tumor cell lines, and hemolytic assay. Piperine showed a higher toxicity in brine shrimp than piplartine. Both piplartine and piperine inhibited the sea urchin development, but in this assay piplartine was more potent than piperine. In MTT assay, piplartine was also the most active with IC50 values ranging from 0.7 to 1.7 Âg/mL. None of the tested substances induced hemolysis. Since the piplartine showed the best results, its mode of action was studied. Viability of HL-60, K562, JUKART, and MOLT-4 cell lines were affected by piplartine only after an exposure time of 24h, as analyzed by the Trypan blue exclusion. Piplatine reduced the number of viable cells associated with an increasing of the number of non-viable cells, which corroborate data from morphologic analysis. The cytotoxic activity of piplartine was related to the inhibition of DNA synthesis, as revealed by the reduction of BrdU incorporation. Administration of piplartine or piperine (50 or 100 mg/kg/day) inhibited the solid tumor development in mice transplanted with Sarcoma 180. The inhibition rates were of 28.7 and 52.3% for piplartine and 55.1 and 56.8% for piperine at lowest and highest dose, respectively. Piplartine-antitumor activity was related to the tumor proliferation rate inhibition, as observed by reduction of Ki67 staining in tumor of the treated-animals. The histopathological analysis of liver and kidney showed that both organs were reversible affected by piplartine and piperine treatment, but in a different way. Piperine was more toxic to the liver while piplartine affected more the kidney. Thus, both amides may act as antitumor agents, although, they seem to act through different pathways. Piplartine activity seems to be related to direct cytotoxicity on tumor cells, while piperine presented a host mediated activity / Piplartina e piperina sÃo alcalÃides/amidas presentes em plantas do gÃnero Piper. A atividade desses compostos foi inicialmente avaliada atravÃs do ensaio de toxicidade aguda em Artemia sp., desenvolvimento de ovos de ouriÃo do mar, ensaio do MTT usando cÃlulas tumorais e ensaio hemolÃtico. A piperina apresentou toxicidade maior em Artemia sp. que a piplartina. Ambas inibiram o desenvolvimento de ouriÃo do mar, mas neste ensaio a piplartina foi mais potente que a piperina. No ensaio do MTT, a piplartina tambÃm foi a mais ativa com valores de CI50 variando de 0,7 a 1,7 Âg/mL. Nenhuma das substÃncias testadas induziu hemÃlise. O mecanismo de aÃÃo da piplartina foi, entÃo, estudado. A viabilidade de cÃlulas HL-60, K562, JUKART e MOLT-4 foi afetada por piplartina apenas apÃs de um perÃodo de exposiÃÃo de 24h, quando analisada por exclusÃo por azul de tripan. A piplatina reduziu o nÃmero de cÃlulas viÃveis associado com um aumento no nÃmero de cÃlulas nÃo-viÃveis, o que colabora com os achados da analise morfolÃgica, onde observou-se um aumento do nÃmero de cÃlulas mortas. A atividade citotÃxica da piplartina està relacionada com a inibiÃÃo da sÃntese de DNA, como revelado pela incorporaÃÃo do BrdU. A administraÃÃo de piplartina ou piperina (50 ou 100 mg/kg/dia) inibe o desenvolvimento de tumor sÃlido em camundongos transplantados com Sarcoma 180. A inibiÃÃo foi de 28,7 e 52,3% para piplartina e 55,1 e 56,8% para piperina na menor e maior dose, respectivamente. A atividade antitumoral da piplartina, mas nÃo da piperina, està relacionada com a inibiÃÃo da proliferaÃÃo do tumor, como observada pela reduÃÃo da marcaÃÃo com Ki67 em tumores de animais tratados. A analise histopatolÃgica do fÃgado e rins demostrou que ambos os ÃrgÃos foram reversivelmente afetados pelo tratamento com piplartina e piperina, mas de maneira diferente. A piperina foi mais tÃxica para o fÃgado, enquanto que a piplartina afetou mais os rins. Assim, ambas as amidas podem atuar como agentes antitumorais, embora, elas pareÃam atuar por vias diferentes. Sendo que a atividade da piplartina parece estar relacionada diretamente a sua aÃÃo citotÃxica, enquanto que a atividade da piperina sÃria mediada pelo hospedeiro.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / In searching for anticancer compounds derived from plant sources, 18 flavonoids were assayed for their cytotoxic potentials and the results were compared for structure-activity relationship purposes. The flavonoid group was subdivided in flavones and pterocarpans. The cytotoxic activity was initially evaluated on tumor cell lines, through the MTT assay, and on sea urchin eggs development. The pterocarpans showed a consistently higher activity on both assays. For the flavones, some structure-activity observations can be highlighted: a) a hydroxyl instead of a methoxyl group on C4 and C5 positions increases activity; b) a hydroxyl and a sugar on C3 position decreases activity and, by the data acquired, it can be emphasized that the methoxyl on C3 increases activity and c) the methoxyl on C7 position increases activity. The pterocarpans, a methoxyl group on C2 position increases the cytotoxic activity. Since the 2,3,9- trimethoxypterocarpan showed the best results in both assays, mode of action studies were conducted for the non-prenylated pterocarpans as an attempt to understand the influence of these groups over their bioactivity. All pterocarpans tested reduced cell viability, as indicated by the trypan blue assay, except for the 3,10-dihydroxy-9-methoxypterocarpan at 12,5 micrograma/mL. They also inhibited DNA synthesis and 2,3,9-trimethoxypterocarpan induced morphological cell alterations, which could be suggestive of apoptosis. On the assays for induction of cellular apoptosis this same compound caused DNA fragmentation and mitochondria depolarization, therefore maintaining membrane integrity, typical apoptotic signs. The other compounds, besides DNA fragmentation, there was noticeable loss of membrane integrity on higher concentrations, an indicative cell death by necrosis. Based on these observations, it is conclusive that the methoxyl group on C2 position is an important pharmacophoric unit for pterocarpans, which emerge as a potential class of anticancer chemicals. / Na busca por compostos obtidos de plantas com potencial antitumoral, dezoito flavonÃides foram avaliados quanto a atividade citotÃxica, seus resultados foram comparados a fim de compreender quais grupamentos conferem uma maior atividade da molÃcula. O grupo dos flavonÃides foi dividido em flavonas e pterocarpanos. Inicialmente, a atividade citotÃxica foi avaliada em cÃlulas tumorais atravÃs do mÃtodo do MTT e no desenvolvimento embrionÃrio de ovos de ouriÃo do mar. O grupo dos pterocarpanos foi mais ativo que as flavonas em ambos os ensaios utilizados. No grupo das flavonas algumas observaÃÃes sobre a relaÃÃo estrutura-atividade podem ser citadas: a) a hidroxila no lugar da metoxila em C4â e C5âmelhora a atividade; b) a hidroxila e o aÃÃcar em C3 diminui a atividade; c) A metoxila em C3 e em C7 aumenta a atividade. No grupo dos pterocarpanos a metoxila em C2 potencializa a atividade citotÃxica. Como o composto 2,3,9- trimetoxipterocarpano apresentou os melhores resultados em ambos os ensaios, foram realizados ensaios para estudo do mecanismo de aÃÃo apenas dos pterocarpanos nÃo prenilados, na tentativa de entender a influÃncia dos grupos sobre a atividade. Todos os pterocarpanos testados reduziram a viabilidade celular por azul de tripan nas concentraÃÃes testadas, exceto o composto 3,10- dihidroxi-9-metoxipterocarpano na concentraÃÃo de 12,5 micrograma/mL. TambÃm inibiram a sÃntese de DNA e causaram alteraÃÃes morfolÃgicas nas cÃlulas sugestivas de apoptose para o composto 2,3,9-trimetoxipterocarpano. Nos ensaios que avaliam a induÃÃo da apoptose o composto 2,3,9-trimetoxipterocarpano causou fragmentaÃÃo do DNA, despolarizaÃÃo da mitocÃndria e manutenÃÃo da integridade da membrana celular, achados caracterÃsticos da apoptose. JÃ os outros compostos induziram, alÃm de fragmentaÃÃo do DNA, perda da integridade da membrana plasmÃtica nas maiores concentraÃÃes, indicando morte celular por necrose. Com base nesses resultados podemos concluir que o grupamento metoxila em C2 constitue uma importante unidade farmacofÃrica para os pterocarpanos, que apontam como um grupo com elevado potencial antitumoral.

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal malignancies because it is often diagnosed at a late disease stage and has a poor response rate to currently available treatments. Therefore, it is critical to develop new therapeutic approaches that will enhance the efficacy and reduce the toxicity of currently used therapies. Here we aimed to evaluate the therapeutic potential and mechanisms of action for piperlongumine (PL), an alkaloid from long pepper, in PDAC models. We postulated that PL causes PDAC cell death through oxidative stress and complements the therapeutic efficacy of chemotherapeutic agents in PDAC cells. First, we determined that PL is one of the most abundant alkaloids with antitumor properties in the long pepper plant. We also showed PL in combination with gemcitabine, a chemotherapy agent used to treat advanced pancreatic cancer, reduced tumor weight and volume compared to vehicle-control and individual treatments. Further, biochemical analysis, including RNA sequencing and immunohistochemistry, suggested that the antitumor activity of PL was associated with decreased cell proliferation, induction of cell cycle arrest, and oxidative stress-induced cell death. Moreover, we identified that c-Jun N-terminal kinase (JNK) inhibition blocks PL-induced cell death, translocation of Nrf2, and transcriptional activation of HMOX1 in PDAC. Finally, high-throughput drug and CRISPR screenings identified potential targets that could be used in combination with PL to treat PDAC cells. Collectively, our data suggests that cell cycle regulators in combination with PL might be an effective approach to combat pancreatic cancer. / NIH

Indiana University-Purdue University Indianapolis (IUPUI) / Paper spray is an ambient ionization technique for mass spectrometry that is well-known for its ability to accomplish rapid and sensitive analyses without any need for sample preparation. This work further develops the technique in two major areas: negative ionization and drug screening. Negative ionization has always been an obstacle to electrospray-based ion sources because of its vulnerability to corona discharge, but methods are presented here to both quantify and suppress this electrical phenomenon, thus preventing it from interfering with qualitative/quantitative analyses. The validity of the discharge-suppressing method is demonstrated for both a simple screen of barbiturates and other acidic drugs (Chapter 2) and the detection and quantitation of chemical warfare agent hydrolysis products (Chapter 3). Additionally, a positive ion drug screen is applied to the analysis of postmortem blood samples (Chapter 4), achieving rapid and effective screening of 137 different drugs ranging from pharmaceuticals to drugs of abuse. The performance of this screen is also evaluated by comparing the results of the postmortem samples to those obtained using a more established series of assays. The research contained herein presents strides toward forensic application of paper spray mass spectrometry, especially in disciplines related to forensic toxicology.

Rhabdomyosarcoma (RMS) is a type of soft tissue sarcoma that mainly occurs in children. RMS can be divided into two subtypes embryonal (ERMS) and alveolar (ARMS). The ARMS subtype can be especially aggressive when a balanced chromosomal translocation is present. This translocation results in the expression of a PAX3/7-FOXO1 fusion protein, an oncogenic transcription factor. PAX3-FOXO1 positive RMS has an especially bad prognosis and survival rate. In the cell painting assay relevant organelles are stained and morphological features are extracted on a cellular level. Based on these features, morphological profiles of each cell type and a similarity score can be calculated. The morphological profiles of ERMS cell lines RD and RD18 as well as the ARMS cell lines RH30 and CW9019 were obtained. RD and RD18 are most similar to each other followed by RH30. CW9019 has a very different profile from the other cell lines. Since ERMS is associated with a better survival rate a drug that reprograms the phenotype from ARMS to a more ERMS-like phenotype might sensitize the cells to the standard treatment of RMS. ARMS patients might then benefit from a combination therapy of such a drug and the standard treatment. To find such a drug a drug screen was conducted. Drugs were selected for the screen that either target fusion-protein stability or overexpressed targets of the fusion protein. Phenotypic reference compounds were included to get a first idea of the mechanisms and involved organelles of the screened drugs. In total, 30 compounds and 9 phenotypic reference compounds were screened for changing morphological profiles of RMS cell lines with the cell painting assay. 15 compounds were identified that change the phenotype of the ARMS cell line RH30. In addition, 7 of these compounds shift the phenotype of RH30 towards an ERMS-like phenotype. If that morphological resemblance of RH30 cells to ERMS cells translates into a change of a more ERMS-like behavior and sensitizes the cells for the standard treatment of RMS remains to be investigated. The reprogramming hits showed high similarity with phenotypic reference compounds that increase nucleus size which might suggest changed behavior of the fusion protein. Especially, Bosutinib, Midostaurin and Alisertib are promising new compounds for ARMS treatment. They shifted the ARMS phenotype towards an ERMS-like phenotype in the drug screen. This shift is likely a result of the interaction with PLK1 or Aurora-kinase A that are shown to have an influence on fusion-protein stability.

Colorectal cancer (CRC) is one of the most prevalent cancers worldwide and is recognized as the second leading cause of cancer-related deaths in North America. CRC follows a hierarchal tumor organization, the root being a small population of self-renewing and highly tumorigenic colon cancer stem cells (CSC). There is an epigenetic signature that exists within these colon CSCs contributing to their maintenance and dynamic plasticity. A key hallmark of this colon CSC epigenetic signature is the Histone-3 Lysine-9 di-methylation (H3K9me2) histone mark which is overrepresented in many types of cancer. Pharmacological modulation of this epigenetic signature (i.e through H3K9me2 modulation) serves as a novel way to selectively target and eliminate human CSCs while sparing normal progenitor cells. Direct inhibitors of key methyltransferases such as G9a, have been identified to have high specificity, however none of these inhibitors have shown success during early stages of clinical trials, leaving us to question the clinical relevance. My research has shown that the overexpression of histone methyltransferase G9a in colon cancer serves as a risk factor for patients and is associated with shorter-relapse free survival. G9a activity has been shown to be essential for the maintenance of embryonic-like transcriptional signature which promotes self-renewal, tumorigenicity and an undifferentiated state. This work provides insights into the role of G9a as a driver of a cancer stem cell phenotype. To combat the toxicity and issues associated with targeting the catalytic activity of G9a, I utilized a phenotypic screening pipeline consisting of thousands of clinically-approved compounds, and identified CSC-bioactive epigenetic inhibitors showing promise in CSC-like models. RNA-seq profiling, dose response treatments and molecular techniques were used to confirm the selectivity of these candidates to colon-CSC like cells with minimal impact on normal progenitors. The lead candidate compound, vanoxerine (VXN) restricts organoid-initiating capacity of patient derived colon CSCs in serial 3D organoid formation assays that I developed throughout my research project. Using two murine syngeneic models resembling microsatellite instability and stability in CRC, I found this compound to be successful in decreasing primary tumor volumes compared to vehicle control mice, through epigenetic reprogramming and infiltration of immune cells. Drug treated tumors that were harvested, dissociated and re-injected into secondary mice showed diminished tumor initiating capacity compared to vehicle controls. Furthermore, the target of vanoxerine, SLC6A3, was investigated and the expression pattern characterized revealed a new potential biomarker for colon cancer stem cells. This SLC6A3-G9a axis discovered for the first time in colon cancer and serves as a novel and important pathway to block H3K9me2 deposition in CRC, rewiring the CSC epigenome and suppressing neoplastic self-renewal and tumor-initiating functions. Together, the identified repurposed compound selectively targets and modulates the epigenetic signature of CSCs which diminishes the tumor initiating function of these cells. This hints at an interesting interaction between CRC stemness and tumor immunology, a promising future therapeutic avenue.

<p>  </p> <p>Nationwide use of illicit drugs has continued to rise over the last few decades, with more than a two-fold increase in global seizures from 2016 and 2020. Most seized drug samples are complex mixtures of drugs and cutting agents, which can complicate the detection and quantification of the illicit drugs in the sample. The presence of these cutting agents can however be beneficial for source tracing purposes, as the majority of cutting agents are selected based on availability in the area where the bulk drug was prepared. The goal of this work was to conduct a systematic study of the electrochemical characteristics of the most common cutting agents found in illicit drugs using unmodified, commercially available glassy carbon electrodes. The long-term goal is to establish an extensive database of electrochemical characterizations of cutting agents and illicit drugs encountered by law enforcement using unmodified, commercially available electrodes to help expand the developing field of forensic electrochemical analyses. This database could then be referenced for the identification of unknown samples to determine the presence of possible illicit drugs and cutting agents that are present to help guide the analyst in further testing.</p> <p>The standard methods for drug detection include a combination of laboratory testing and field-deployable assays ranging from colorimetric tests to gas chromatography-mass spectrometry instrumentation. These detection methods, as well as relevant literature were investigated in Chapter 1. The most used screening methods for illicit drugs are colorimetric tests; however, these assays are prone to false positives. Chapter 1 introduces the existing applications and current research efforts in forensic electrochemistry by describing relevant electrochemical sensors and methods and examining in particular their performance regarding accuracy, sensitivity, and low-cost claims. This overview highlights the broad possibilities of electrochemical analysis in forensics as well as the opportunities when applied to detection and quantification of illicit drugs, demonstrating the current needs for more systematic and consistent characterizations of cutting agents found in seized-drug samples. Chapter 2 details the material, reagents, and experimental conditions, showing their simplicity, and the standard electrochemical and preparative equipment used geared towards an easy implementation in any analytical laboratory. Chapter 3 describes the systematic voltametric characterizations performed on thirteen common cutting agents: phenacetin hydrochloride, levamisole hydrochloride, diphenhydramine hydrochloride, quinine, acetaminophen, ascorbic acid, caffeine, lactose, inositol, mannitol, glucose, sodium bicarbonate and calcium carbonate. In addition to the common, information-rich cyclic voltammetry (CV), differential pulse voltammetry (DPV) and square wave voltammetry (SWV) were used as these pulsed electroanalytical methods are typically considered more sensitive than CV and often employed for quantitative analyses of species present at low concentrations (Chapter 3). Overall, DPV resulted in voltammograms with peaks shaped closer to the ideal redox peaks, also referred to as ‘better defined’, thus enhancing the analytical performance of the assay. For example, In the analysis of diphenhydramine hydrochloride, DPV permitted the measurement of an oxidation with a peak displayed at 1.0 V vs Ag/AgCl, which was not observable when performing CV or SWV. On the other hand, SWV provided noticeably greater intensities of peak current, which allowed for a better detection of the difficult-to-observe redox reactions of quinine occurring at -0.4, 0.0 and 0.4 V vs Ag/AgCl.</p> <p>Some chemical species when present in seized drugs can alter the pH of the tested samples, such as ascorbic acid. Changes in pH will impact the redox activity of the pH-dependent electroactive species present in a sample, thus we investigated how pH of the solvent affected the observation of the redox peaks of those susceptible cutting agents, namely ascorbic acid, quinine, diphenhydramine hydrochloride, and levamisole hydrochloride (Chapter 4). Of particular interest was a significant change in the electrochemical characterization of these species when the pH was varied around their pKa values. Additionally, the composition of the solvent, or supporting electrolyte (SE) solution, can in some cases result in interactions with the analytes in the sample; the study of caffeine with different SE in Chapter 4 illustrates this situation. Specifically, sulfuric acid was the most suited SE of those tested for caffeine analysis.</p> <p>The impact of successive voltametric scans, on the analysis of chemical species were also investigated, using acetaminophen and quinine, demonstrating the development of additional redox peaks in some situations that could provide additional elements towards a more individualized electrochemical profile for cutting agents (Chapter 4). </p> <p>The influence of the material of the working electrode on the electrochemical characterization of cutting agents was explored. Solutions of ascorbic acid, acetaminophen, quinine, and diphenhydramine hydrochloride were electrochemically characterized using a glassy carbon and a platinum working electrode, while ascorbic acid was also characterized on gold and silver electrodes. These examples demonstrate the adaptability of this electroanalytical method with various commonly used electrodes. (Chapter 4). In Chapter 5, we applied similar electrochemical method to the identification of cutting agents and illicit drugs in two-component mixtures. Specifically, these trials included mixtures of fentanyl with a cutting agent at a relative ratio of 1 : 100, using as cutting agents ascorbic acid, diphenhydramine hydrochloride, or glucose, demonstrating the ability of this simple electrochemical method using common commercial electrodes to simultaneously detect illicit drugs and cutting agents. </p>

In translational research, disease models in preclinical studies are used as media for discovery of drugs or novel therapeutics. Development of in vitro models for various neurological diseases that enable efficient pharmacological or toxicological screening has been ongoing but challenging. Recognizing the potential benefit of in vitro disease models, dysfunctions in the cortical neuronal networks were induced to mimic the functional pathology of neurological symptoms using microelectrode arrays. Two different disease states – tinnitusand excitotoxicity – were investigated and discussed. In this model, pentylenetetrazol-induced increase in spontaneous firing rate and synchrony in the auditory cortical networks was used as correlate of tinnitus. Potential tinnitus treatment drugs from several different classes – including the novel class of potassium channel openers – were screened and quantified. The potentialtherapeutic values of these drugs were also discussed as the basis for drug repurposing. Functional excitotoxicity was induced by cisplatin (a cancer drug that causes neurological sideeffects) and glutamate (the major excitatory neurotransmitter). As proof-of-principle that the model may contribute to expediting the development of therapeutics, cisplatin excitotoxicity wasprevented by the antioxidant D-methionine, while glutamate excitotoxicity was prevented by ceftriaxone (a modulator of a glutamate reuptake transporter). In the latter part of the study, with results linking two of the screened drugs L-carnitine and D-methionine to GABAA receptor activation, it was demonstrated that this model not only served as an efficient drug-screening platform, but can be utilized to functionally investigate the underlying mechanism of drugs. Inaddition, several practical or conceptual directions for future studies to improve on this in vitro disease model are suggested.

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