Biopsy is a standard practice in the diagnosis and treatment of many cancers. Despite its integral role in cancer diagnosis, in some instances, the biopsy tool facilitates metastasis by transferring cancerous cells attached to its exterior into the healthy tissue or the blood circulation during its retraction from the tumor. These few cancer cells can then serve as seeds for the malignant tumor to grow in the healthy tissue. Cauterization using extreme heat or cold can destroy cells in the region and minimize the chance of seeding but this can be an inexact process that increases damage to otherwise healthy tissue and prolongs healing time following a biopsy procedure. In our laboratory, we have developed the concept of a new smart biopsy tool that can reduce the chance of cancer cell dissemination during a biopsy. This tool improves on the conventional biopsy needle by introducing an impedance sensor on the biopsy tool which is housed in a sliding sheath. Due to the significant difference in the electrical conductivity of the tumor and the healthy tissue, the sensor is able to distinguish between the two and locate the exact tumor interface. The protective sheath placed around the instrumented biopsy tool and above the interface isolates the healthy tissue and prevents or at least minimizes the transfer of tumor cells. Delivering an RF dose through the sheath can kill any malignant cells that might be lurking around the interface. This thesis, in particular, will concentrate on the development of the design, fabrication and calibration of the impedance sensor and its integration with the biopsy tool. The impedance sensor essentially consists of conductive electrodes sandwiched between insulating layers. They are built on thin-film polymer, Polyimide, using conventional microfabrication techniques. These sensors are further calibrated to estimate the cell constant. Once calibrated, these probes are used to measure the conductivity of porcine tissues, and in-house prepared agar phantoms. / Master of Science

Yes / A sub-population of cells named cancer stem cells (CSCs) that initiate and promote tumour growth have been demonstrated to exist in several malignancies including colon carcinoma. The objective of our pilot study was to isolate CD133+CD26+CD44+ CSCs from patient colon tumours, culture spheres or organoids and observe their proliferation in primary cultures. Parallel cultures of non-cancer controls from colon normal lining and nonadenomatous polyps were set up. Magnetic activated cell sorting was used to isolate CD133+CD26+CD44+ cell populations followed by primary cell culturing under stem cell culture conditions. Number, cells/organoid and daughter generations of organoids were calculated using phase contrast microscope. Trypan blue exclusion method was used to test the viability of the cells. Both colon tumour and colon non-adenomatous polyp formed floating organoids in suspension; however non-adenomatous polyp cultures did not show self-renewal properties for more than 1 passage. Normal colon singlecell suspension did not create organoids. Metastatic colon tumours rapidly produce cancer cell organoids in less than 24 hours in larger numbers compared to non-metastatic colon tumours (1-3 weeks). Metastatic colon tumour organoids have the ability for proliferation for upto five daughter generations in primary culture compared to three generations for those grown from non-metastatic tumours. This in vitro CSC organoid model will help study colon cancer biology, in particular providing a valuable source of primary cell-derived tissue for studying personalized molecular profiling using ‘omics strategies to direct therapeutic intervention.

This diploma thesis is focused on preparation of liposome by relatively new method called nanofluidisation. This method allows the controlled preparation of small unilamellar liposomes in one step. In my thesis I was dealing with optimalization of liposomes preparation which carry hydrophobic cytostatics using this method. Cytotoxic effect of liposomes carrying hydrophobic cytostatics in vitro on cell lines A549 and MCF-7 was determined. In cytotoxicyty test I compared the effect of hydrophobic cytostatics (paclitaxel and derivates of vitamin E specifically alfa-Tos, alfa-TEA) that were incorporated into liposomes prepared via nanofluidisation method and lipid film hydration method. Moreover, a technology of lyophilisation in the presence of cryoprotectants for preparation of liposomes using the method of nanofluidisation was developed.

<p dir="ltr">Cancer biological mechanisms are a vastly researched area in the field, yet they are not well understood in the various contexts in which cancer is found. Cancerous tumors often exist in harsh, stressful environments for normal cells, but cancer cells can thrive in these conditions. The tumor microenvironment (TME) typically has low oxygen levels (hypoxia), high acidity, and low nutrition. Exposure to the TME leads to many metabolic changes in the cells, enabling cancer to continue proliferating and migrating. However, these metabolic changes are not well understood, especially at the single-cell level. The ability to monitor cells in real time to determine the physical characteristics they undergo is critical to understanding the impact of these metabolic changes. Conventional methods focus on determining the genomic and proteomic changes in large numbers of cells, which may be overlooked if the changes are homogeneous across samples. In this work, we demonstrate the power of using multiple imaging techniques in combination with biochemical methods to visualize metabolic changes and determine the causes in various cancer cells under extreme hypoxia conditions.</p><p dir="ltr">The changes in the microtubule network that occur under hypoxia at the single-cell level are not widely researched. The use of confocal fluorescence microscopy can determine microtubule polymerization in conjunction with eGFP-transfected EB3, a protein that assists in microtubule polymerization. We have determined that hypoxic HeLa cells produce finger-like protrusions when exposed to hypoxia that help with cell migration and, ultimately, cancer cell metastasis. The formation of these protrusions is facilitated by localized mitochondria activities in the protrusions.</p><p dir="ltr">The metabolic changes in lipid droplets (LDs) under hypoxia at the single-cell level remain an elusive topic. The use of stimulated Raman spectroscopy (SRS) and coherent anti-Stokes Raman scattering (CARS) can determine the quantity and spatial-temporal distribution of LDs in cancer cells. We have found that LDs redistribute to the endoplasmic reticulum (ER) and increase in intensity in hypoxic MIA PaCa-2 and A549 cells. Time-lapse CARS microscopy revealed a release-accumulate process of these LDs on ER in hypoxia. We also studied the impact of carbon sources on LD formation and found that MIA PaCa2 cells prefer direct lipid uptake while glucose is also essential to reduce lipotoxicity. The use of hyperspectral stimulated Raman scattering (hSRS) also reveals that the content of the LDs changes to include less cholesteryl ester and a decrease in lipid saturation level.</p><p dir="ltr">Collectively, these findings shed new light on the understanding of cytoskeleton dynamics and lipid metabolism in hypoxic conditions. The discoveries made within this research would lead to better treatment strategies for effective treatment of hypoxia-resistant cancer cells.</p>

Despite significant advances in cancer treatment, clinical response remains suboptimal and there is a continued requirement for improved chemotherapeutics. The attrition rate for new therapies is high, due principally to lack of in vivo efficacy and poor pharmacodynamics. Consequently better systems are required to determine in vivo preclinical efficiency and drug-target interactions. Engineering of cancer cells to express fluorescent or bioluminescent proteins, either endogenously or under the control of specific gene promoters, and their detection by noninvasive optical imaging has the potential to improve preclinical drug development. In this study, a panel of colorectal cancer cell lines were engineered to express fluorescent and luminescent proteins either constitutively or under control of gene-promoters for the DNA damage response gene p53 or the cell cycle regulator p21, both important pharmacodynamic sensors. These cell lines were characterised for their potential as in vivo models of primary and metastatic tumour therapy response, several showing significant potential. In addition to the development of these models, this study also addressed the pharmacokinetics of different luciferase substrates and identified optimal temporal and dose characteristics for each. Furthermore, a new application for bioluminescent imaging was developed and validated for use in preclinical evaluation of vascular disrupting agents, a new generation of cancer therapeutic. This study demonstrates that despite the dynamic and variable nature of fluorescent and bioluminescent imaging, reproducible results can be obtained if appropriate precautions are taken. The models developed herein will expedite cancer drug development whilst reducing and refining the use of animals in research.

The mammalian E2F family of transcription factors plays a crucial role in the regulation of cellular proliferation, apoptosis and differentiation. E2F7 and E2F8 are the most recently identified family members and have unusual features that distinguish them from other members in the E2F family, including two distinct DNA-binding domains that bind to DNA in a DP-independent manner. E2F7 and E2F8 have been shown to be transcriptional repressors. However, the mechanism by which E2F7 represses E2F responsive gene expression remains to be elucidated. The results presented here provide the first insight into the E2F7-mediated transcriptional mechanism. E2F7 was shown to contain a CtBP binding motif and form a complex with CtBP in both HeLa and MCF7 cells. An E2F7 deletion mutant lacking the CtBP binding motif was unable to form a complex with CtBP and repress the transcription of E2F target genes in luciferase assays, suggesting that this motif is essential for E2F7-dependent repression. Furthermore, the E2F7-CtBP complex was shown to be stable under different types of damage, such as following etoposide and UV treatment, and under different cell redox states. Interestingly, however, E2F7 was unable to repress the transcriptional activity of E2F target genes following treatment with the CtBP substrate MTOB. Moreover, E2F7 endogenous immunoprecipitations showed that E2F7 forms a complex with the chromatin-modifying enzymes HDAC1, HDAC2 and LSD1 and the co-repressor CoREST. Interestingly, via chromatin immunoprecipitations, E2F7 was shown to recruit these co-repressors to a subset of E2F-responsive promoters where they affect the activity of these promoters in a target gene-specific manner. Furthermore, results presented here suggest that CtBP could play a dual role in E2F7 function, not only being involved in E2F7-mediated repression but also in the repression of E2F7 itself as siRNA mediated CtBP depletion was shown to cause an upregulation of E2F7 protein levels. These results implicate a repertoire of co-repressors in a target gene-specific E2F7 repression mechanism, and as such define a new level of complexity in cell cycle control.

Epidermal growth factor receptor (EGFR) is frequently overexpressed in the majority of triple negative breast cancer patients (TNBC). However, the molecular determinants behind their limited response to EGFR-targeted therapies are poorly understood. Here, both the acute and chronic responses of TNBC to the EGFR-targeted therapy, cetuximab (CTX), have been investigated. The expression of EGFR has been analyzed in a cohort of 2000 breast cancer tumours from the public dataset as well as in a panel of breast cancer cell lines. Furthermore, the response of TNBC cell lines to CTX has been investigated using conventional biochemical methods. Finally, a comprehensive transcriptomic profiling of an acquired CTX-resistant TNBC model by RNA sequencing has been performed to understand the molecular determinants of acquired CTX resistance. The results confirmed that EGFR is highly expressed in TNBC in comparison to non-TNBC breast cancer tumours and cell lines, which was associated with adverse clinical outcomes. Targeting EGFR in TNBC cell lines using CTX failed to completely inhibit the EGFR signalling pathway and was associated with an increase in ADAMs-mediated release of endogenous EGFR ligands, EGF and TGFα. Inhibition of ADAMs (ADAM10 and ADAM17) significantly enhanced the anti tumour efficacy of CTX both in vitro and in vivo. Furthermore, transcriptomic profiling of the acquired CTX-resistant TNBC cell line (MDA-MB-468CR) revealed an activation of several key oncogenic pathways and genes, including the TGFβ/BMP pathway. Blocking BMP receptors (BMPRs) restored the sensitivity of resistant cells to CTX treatment. Collectively, current findings offer alternative strategies that could enhance the CTX response in TNBC. We further reported that simultaneous targeting of both EGFR and BMPR pathways could overcome CTX resistance, which might have important implications for the treatment of TNBC.

Em mulheres, o câncer de mama é o tipo mais incidente depois do tumor de pele não melanoma e é a principal causa de morte por câncer. Apesar dos avanços já alcançados na caracterização da doença, a busca por novos marcadores moleculares para diagnóstico, tratamento e entendimento molecular da doença é de extrema importância. Estudos em nosso laboratório apontaram a proteína EMC1 (do inglês, Endoplasmic Reticulum Complex 1) como relacionada a propriedades malignas em linhagens celulares de câncer de mama e melanoma, assim como aumento no crescimento tumoral em ensaios in vivo. Despertou-se, então, o interesse em nosso laboratório, no estudo das outras proteínas do complexo EMC. Este estudo atual, busca analisar dados em larga escala do banco TCGA em um painel de 32 tipos tumorais, e aponta associação da expressão de diversas proteínas EMCs a pior sobrevida dos pacientes. O gene EMC2, que se localiza na região cromossômica altamente amplificada em diversos tumores (8q23.1), se destaca pela intensidade de pacientes com superexpressão em câncer de mama (40%). Em linhagens desse tipo tumoral, o knockdown de EMC2 aponta redução na taxa proliferativa, assim como associação à progressão do ciclo celular na fase M, quando feito o protocolo de sincronização utilizando a droga nocodazol. Em conjunto, nossos dados sugerem que o complexo EMC pode favorecer o desenvolvimento de tumores e influenciar em sua malignidade. Além disso, a proteína EMC2 parece apresentar funções relacionadas a proliferação e possivelmente, ciclo celular. / In woman, the breast cancer is the most incidence type after skin tumor non melanoma and it is a main cause of cancer death. Despite the advances already achieved in the disease caracterization, the search for novel molecular biomarkers to diagnostic, treatment and disease knowledge is extremely importante. In vitro approaches pointed Endoplasmic Reticulum Complex 1 (EMC1) involvement in malignant properties in breast cancer and melanoma cell lines, and increase in tumor growth in a in vivo assay. It highlighted the study of the other members of EMC complex. In this study, we used a large-scale database from TCGA in a range of 32 tumoral types, and showed association in EMC expression and poor surviving curve. The EMC2 gene, localized in a high amplified chromosome region in cancer (8q23.1), have a interesting upregulation level in breast cancer (40%). In knockdown EMC2 cell lines, the proliferation is less intense and progression in M phase, in a nocodazole sincronization assay, is impaired. Together, the data suggest that the EMC complex favors the tumour development and the EMC2 protein seens to play a role in proliferation and maybe in cell cycle.

O ácido linoleico conjugado (CLA), um grupo de isômeros do ácido linoleico, é encontrado no leite e na carne de animais ruminantes, e apresenta propriedades anticarcinogênica, antidiabética, antiadipogênica e antiaterogênica. Neste trabalho de doutorado estudou-se o efeito do CLA (cis-9, trans-11) em duas linhagens de células de câncer de mama, MCF-7 e MDA-MB-231, com a técnica de RMN denominada HR-MAS (High Resolution Magic Angle Spinning). O HR-MAS foi usado para identificar e quantificar os principais metabólitos das linhagens e também foi eficiente para observar mudanças significativas na variação dos metabólitos em função da adição de CLA ao meio de cultura. As células de câncer de mama, MCF-7 submetidas a 100 &micro;M CLA tiveram aumento significativo do sinal de acetona. Esse padrão não foi observado para a MDA-MB-231. Também se observou que o teor de fosfocolina decresceu em ambas as linhagens celulares quando tratadas com 100 &micro;M CLA. Mediante esses resultados e simulação por modelagem molecular propôs-se que o CLA pode atuar inibindo a ação da enzima HMG-CoA redutase (HMGR), de maneira similar as estatinas. Ao se ligar a HMGR, o CLA impede a ligação do HMG-CoA (substrato), impedindo a sua conversão para mevalonato e consequentemente a biossíntese do colesterol. O HMG-CoA é então convertido para acetoacetato e posteriormente a acetona. Esse mecanismo pode explicar tanto o aumento da acetona quanto a redução da fosfocolina, uma vez que há controle positivo mútuo entre o colesterol e os fosfolipídios. Desta forma, pode-se concluir que a inibição da HMGR pelo CLA pode ser uma demonstração do mecanismo bioquímico tanto de sua ação anticarcinogênica quando das atividades antidiabética, antiadipogênica e antiaterogênica, relatadas na literatura. Neste trabalho também foi demonstrada a potencialidade do processamento dos sinais de HR-MAS no domínio do tempo pelo método de diagonalização filtrada. Essa técnica foi capaz de obter espectros de alta resolução, sem necessidade de supressão do sinal da água e filtro de T2, para suprimir linhas largas. / Conjugated linoleic acid (CLA), a group of isomers of linoleic acid,is found in milk and meat of ruminant animals, which have anticarcinogenic, antidiabetic, antiatherogenic and anthiadipogenic properties. In this thesis the effect of CLA (cis-9, trans-11) in two cell lines of breast cancer, MCF-7 and MDA-MB-231 was studied High Resolution Magic Angle Spinning (HR-MAS) NMR technique. HR-MAS was used to identify and quantify the metabolites of the two cells and was effective to observe significant changes in metabolites due to the addition of CLA to the culture medium. The breast cancer cells, MCF-7 subjected to 100 &micro;M CLA had a significantly higher acetone signal. This pattern was not observed for MDA-MB-231. It was noted that the content of phosphocholine decreased in both cell lines treated with 100 &micro;M CLA. Given these results and simulation with molecular modeling we are suggesting that CLA inhibits the enzyme HMG-CoA reductase (HMGR), similar to statins. By binding to HMGR, CLA prevents binding of the HMG-CoA (substrate), preventing their conversion to mevalonate, and consequently the cholesterol biosynthesis. The HMG-CoA is then converted to acetoacetate and then acetone. This mechanism explains the increase of acetone and decreased of phosphocholine, since there is mutual positive control with cholesterol and phospholipids. Therefore, the inhibition of HMGR by CLA may be the biochemical explanation for its anticarcinogenic activities as well as antidiabetic, antiatherogenic and antiadipogenic properties reported in the literature. It was also demonstrated the capability of Filter Diagonalization Method (FDM) to process time domain HR-MAS signals. FDM was able to obtain high-resolution spectra without the water suppression and T2 filter.

O adenocarcinoma ductal pancreático (PDAC, pancreatic ductal adenocarcinoma), o tipo mais prevalente de câncer do pâncreas, é uma neoplasia extremamente agressiva e com elevado índice de letalidade. Há uma necessidade premente de identificação de vulnerabilidades no PDAC que possam ser exploradas como alvos terapêuticos, e a utilização de modelos pré-clínicos que recapitulem a complexidade biológica e heterogeneidade clínica da doença é um aspecto central para a realização dessa tarefa. Os xenotransplantes de tecido tumoral derivado de pacientes (PDX, patient-derived tumor tissue xenografts), realizados em camundongos imunodeficientes, replicam com grande similaridade as principais características do tumor original e, assim, constituem uma ferramenta valiosa para o teste de drogas e estudos funcionais. Neste trabalho, 17 amostras cirúrgicas de PDAC humano foram implantadas subcutaneamente em camundongos nude atímicos. Sete tumores (41%) foram enxertados com sucesso e têm sido mantidos em sucessivas gerações de animais receptores. O exame histológico de seis desses xenoenxertos identificou características morfológicas compatíveis com os padrões reconhecidos no PDAC humano, assim como uma consistente similaridade de seu status de diferenciação histológica em relação aos perfis verificados nos tumoresoriginais. O cultivo in vitro de células derivadas de um dos xenotumores resultou em uma nova linhagem de câncer de pâncreas, com morfologia e cinética de crescimento comparáveis às de outras linhagens celulares de câncer pancreático. O potencial tumorigênico dessa nova linhagem foi validado in vivo, com uma consistente formação de tumores após inoculação em camundongos nude. A fim de aproveitar esse recurso para a investigação de potenciais alvos terapêuticos no PDAC, um rastreamento de vulnerabilidades moleculares foi realizado por meio de silenciamento gênico em larga-escala com RNA de interferência (RNAi). Uma biblioteca lentiviral de 4492 shRNAs (short hairpin RNAs), alvejando cerca de 350 genes envolvidos na regulação epigenética, foi empregada para a triagem de genes de suscetibilidade nas células derivadas de PDX, e em outras cinco linhagens tumorais pancreáticas (AsPC-1, BxPC-3, Capan-1, MIA PaCa-2 e PANC-1). Inicialmente, foi realizada uma série de experimentos preliminares, visando à amplificação e controle de qualidade da biblioteca de silenciamento, à produção de vetores lentivirais e à padronização das condições experimentais para a transdução e seleção das células-alvo. Apenas três das linhagens avaliadas (AsPC-1, MIA PaCa-2 e PANC-1) mostraram-se permissíveis à transdução pelos vetores lentivirais, e foram assim utilizadas no screening de alvos epigenéticos. A análise dos dados obtidos nesse ensaio está em curso e os resultados serão utilizados para a definição de potenciais alvos candidatos. Em conclusão, recursos valiosos para apoiar a pesquisa sobre o câncer de pâncreas foram desenvolvidos. A coleção de PDXs estabelecida, bem como a linhagem celular recém-derivada, constituem uma fonte permanente e estável de células de PDAC para análises moleculares e estudos funcionais que busquem elucidar aspectos da doença ainda pouco compreendidos. Adicionalmente, os reagentes gerados e a expertise adquirida com os ensaiosrealizados com a biblioteca de shRNAs contra alvos epigenéticos serão de grande utilidade em futuras investigações para identificar genes com funções importantes na manutenção do fenótipo tumoral, e consequentemente com potencial para serem explorados terapeuticamente. / Pancreatic ductal adenocarcinoma (PDAC), the most prevalent type of pancreatic cancer, is a highly aggressive and lethal neoplasm. There is a pressing need to identify vulnerabilities in PDAC suited to be exploited as therapeutic targets, and the use of preclinical models recapitulating the biological complexity and clinical heterogeneity of the disease is central to this task. Patient-derived tumor tissue xenografts (PDX), established in immunodeficient mice, replicate with great similarity the main characteristics of the original tumor and thus constitute a valuable tool for drug testing and functional studies. In this work, 17 surgical samples of human PDAC were implanted subcutaneously in athymic nude mice. Seven tumors (41%) were successfully grafted and have been maintained through successive generations of recipient animals. Histological examination of six of these xenografts identified morphological characteristics compatible with the recognized patterns of human PDAC, as well as a consistent similarity of their histological differentiation status in relation to the profiles verified in the original tumors. In vitro culture of cells derived from one of these xenografts resulted in a new pancreatic cancer cell line, with morphology and growth kinetics comparable to those of other pancreatic tumor cells. The tumorigenic potential of this freshly derived cell line was validated in vivo, with a consistent tumor formation following inoculation into nude mice. To take advantage ofthis resource to investigate potential therapeutic targets in PDAC, a screening of molecular vulnerabilities was performed through large-scale gene silencing with RNA interference (RNAi). A lentiviral library containing 4492 short hairpin RNAs (shRNAs), targeting about 350 genes involved in epigenetic regulation, was employed for the search of susceptibility genes in the PDX-derived cells and in other five pancreatic tumor cell lines (AsPC-1, BxPC -3, Capan-1, MIA PaCa-2 and PANC-1). Initially, a series of preliminary experiments were carried out aiming at the amplification and quality control of the silencing library, production of lentiviral vectors and adjustment of the experimental conditions for transduction and selection of the target cells. Only three of the cell lines evaluated (AsPC-1, MIA PaCa-2 and PANC-1) were permissible for transduction by the lentiviral vectors, and were accordingly used in the screening of epigenetic targets. The analysis of data obtained in this trial is ongoing and the results will be used for definition of potential candidate targets. In conclusion, valuable resources to support research on pancreatic cancer have been developed. The established collection of PDXs as well as the newly derived cell line constitutes a permanent and stable source of PDAC cells for molecular analyzes and functional studies seeking to elucidate aspects of this disease that are still poorly understood. Additionally, both the reagents generated and the expertise gained from the RNAi assay against epigenetic targets will have inordinate usefulness in future investigations to identify genes with major functions in maintaining the malignant phenotype, and consequently with the potential to be exploited therapeutically.