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Este trabalho descreve a remediação simultânea de dois genes supressores de tumor, CDKN2A e p53, em três linhagens celulares derivadas de glioblastoma multiforme: U87 (CDKN2A-/-, p53wt/wt), U251 (CDKN2A-/-, p53mut/mut) e T98G (CDKN2A-/-, p53mut/mut). A entrega gênica foi mediada por vetor adenoviral bicistrônico contendo o cassete CDKN2AIRESp53, capaz de expressar as duas proteínas simultaneamente. Vetores monocistrônicos também foram testados (AdCDKN2A e Adp53). Visando detectar apoptose, as linhagens receberam o sensor de atividade de caspase-3/7 GFP-DEVD-ssGLUC por transdução lentiviral. Este possui Gaussia luciferase (GLUC) C-terminal, que é secretada após ativação de caspases e pode ser dosada no sobrenadante. Após a marcação, realizaram-se ensaios de viabilidade celular, proliferação, formação de colônias, senescência, ciclo celular e dosagem de GLUC após remediação dos genes supressores de tumor nas linhagens GBMDEVD-GLUC. Com ensaio de viabilidade, observou-se efeito citotóxico do vetor bicistrônico AdCDKN2AIRESp53 maior que a soma dos obtidos com cada tratamento monocistrônico. No ensaio de senescência, o vetor AdCDKN2A resultou na maior indução do fenótipo senescente em todas as linhagens, seguido por Adp53, enquanto AdCDKN2AIRESp53 produziu resultados similares a um desses dois perfis em cada linhagem. Dosagem de GLUC no sobrenadante foi usada como indicador para atividade de caspase-3/7 após tratamento com os vetores supressores de tumor. O controle AdLacZ resultou em atividade de GLUC maior que nas amostras sem vírus (mock), enquanto tratamento com AdCDKN2A obteve resultados maiores que o controle em 72 h nas três linhagens. O vetor AdCDKN2AIRESp53 alcançou, inesperadamente, resultados variados em 72 h. Os dados obtidos neste trabalho indicam que a remediação simultânea de CDKN2A e p53 possui notável ação antiproliferativa tumoral, podendo levar à morte ou à senescência celular. Também é apontado que o sensor de caspase-3/7 GFP-DEVD-ssGLUC é robusto, mas detecta não apenas a indução de apoptose, mas a combinação de todos os processos ativadores de caspases em uma amostra. / This thesis describes the simultaneous remedy of two tumor suppressor genes, CDKN2A and p53, in three glioblastoma multiforme (GBM)-derived cell lines: U87 (CDKN2A-/-, p53wt/wt), U251 (CDKN2A-/-, p53mut/mut) and T98G (CDKN2A-/-, p53mut/mut). Gene delivery was mediated by a bicistronic adenoviral vector bearing the sequence CDKN2AIRESp53, which simultaneously expresses both proteins. Monocistronic vectors were also tested (AdCDKN2A and Adp53). To detect apoptosis, the GBM cell lines received caspase-3/7 sensor GFP-DEVD-ssGLUC via lentiviral transduction. This sensor has a C-terminal Gaussia luciferase (GLUC), which is secreted by the cell after caspase activation and can be measured in the supernatant. After sensorization, functional assays were carried out, including cell viability, proliferation, colony formation, cell senescence, cell cycle and GLUC measure after treatment with the tumor suppressor vectors in GBMDEVD-GLUC lineages. Viability assay with the AdCDKN2AIRESp53 vector resulted in a remarkable cytotoxic effect, greater than the sum of the effects with each monocistronic treatment. In the senescence assay, vector AdCDKN2A yielded the highest induction of cell senescence in all lineages, followed by Adp53, while AdCDKN2AIRESp53 induced results that followed one of these two profiles in each cell line. GLUC measure was an indicator of intracellular caspase-3/7 activity after treatment with the tumor supressor vectors. Control vector AdLacZ resulted in higher GLUC activity than mock treatment in all three cell lines, while AdCDKN2A treatment showed results bigger than control at 72 h in all cell lines. Bicistronic vector AdCDKN2AIRESp53 reached, unexpectedly, varied results at 72 h in all cell lines. Data obtained in this study indicate that simultaneous remedy of CDKN2A and p53 has remarkable antiproliferative activity in GBM cells, resulting in cell death or cell senescence. It is also shown that caspase-3/7 sensor GFP-DEVD-ssGLUC is a robust tool, but its results detect not only a single cellular process, such as apoptosis, but the combination of all caspase-activating processes in a cell population.

Familial Pancreatic Cancer (FPC) is a cancer syndrome characterized by clustering of pancreatic cancer in families, but most FPC cases do not have a known genetic etiology. Understanding genetic predisposition to pancreatic cancer is important for improving screening as well as treatment. The central aim of this thesis is to identify candidate susceptibility genes for FPC, and I used three approaches of increasing resolution. First, based on a candidate-gene approach, I hypothesized that BRCA1 is inactivated by loss-of-heterozygosity in pancreatic adenocarcinoma of germline mutation carriers. I demonstrated that 5/7 pancreatic tumors from BRCA1-mutation carriers show LOH, compared to only 1/9 sporadic tumors, suggesting that BRCA1 inactivation is involved in tumorigenesis in germline mutation carriers. Second, I hypothesized that the germline genomes of FPC subjects differ in copy-number profile from healthy genomes, and that regions affected by rare deletions or duplications in FPC subjects overlap candidate tumor-suppressors or oncogenes. I found no significant difference in the global copy-number profile of FPC and control genomes, but I identified 93 copy-number variable genomic regions unique to FPC subjects, overlapping 88 genes of which several have functional roles in cancer development. I investigated one duplication to sequence the breakpoints, but I found that this duplication did not segregate with disease in the affected family. Third, I hypothesized that in a family with multiple pancreatic cancer patients, genes containing rare variants shared by the affected members constitute susceptibility genes. Using next-generation sequencing to capture most bases in coding regions of the genome, I interrogated the germline exome of three relatives who died of pancreatic cancer and a relative who is healthy at advanced age. I identified a short-list of nine candidate genes with unreported mutations shared by the three affected relatives and absent in the unaffected relative, of which a few had functional relevance to tumorigenesis. I performed Sanger sequencing to screen an unrelated cohort of approximately 70 FPC patients for mutations in the top two candidate genes, but I found no additional rare variants in those genes. In conclusion, I present a list of candidate FPC susceptibility genes for further validation and investigation in future studies.

Familial Pancreatic Cancer (FPC) is a cancer syndrome characterized by clustering of pancreatic cancer in families, but most FPC cases do not have a known genetic etiology. Understanding genetic predisposition to pancreatic cancer is important for improving screening as well as treatment. The central aim of this thesis is to identify candidate susceptibility genes for FPC, and I used three approaches of increasing resolution. First, based on a candidate-gene approach, I hypothesized that BRCA1 is inactivated by loss-of-heterozygosity in pancreatic adenocarcinoma of germline mutation carriers. I demonstrated that 5/7 pancreatic tumors from BRCA1-mutation carriers show LOH, compared to only 1/9 sporadic tumors, suggesting that BRCA1 inactivation is involved in tumorigenesis in germline mutation carriers. Second, I hypothesized that the germline genomes of FPC subjects differ in copy-number profile from healthy genomes, and that regions affected by rare deletions or duplications in FPC subjects overlap candidate tumor-suppressors or oncogenes. I found no significant difference in the global copy-number profile of FPC and control genomes, but I identified 93 copy-number variable genomic regions unique to FPC subjects, overlapping 88 genes of which several have functional roles in cancer development. I investigated one duplication to sequence the breakpoints, but I found that this duplication did not segregate with disease in the affected family. Third, I hypothesized that in a family with multiple pancreatic cancer patients, genes containing rare variants shared by the affected members constitute susceptibility genes. Using next-generation sequencing to capture most bases in coding regions of the genome, I interrogated the germline exome of three relatives who died of pancreatic cancer and a relative who is healthy at advanced age. I identified a short-list of nine candidate genes with unreported mutations shared by the three affected relatives and absent in the unaffected relative, of which a few had functional relevance to tumorigenesis. I performed Sanger sequencing to screen an unrelated cohort of approximately 70 FPC patients for mutations in the top two candidate genes, but I found no additional rare variants in those genes. In conclusion, I present a list of candidate FPC susceptibility genes for further validation and investigation in future studies.

abstract: Cancer is a disease which can affect all animals across the tree of life. Certain species have undergone natural selection to reduce or prevent cancer. Mechanisms to block cancer may include, among others, a species possessing additional paralogues of tumor suppressor genes, or decreasing the number of oncogenes within their genome. To understand cancer prevention patterns across species, I developed a bioinformatic pipeline to identify copies of 545 known tumor suppressor genes and oncogenes across 63 species of mammals. I used phylogenetic regressions to test for associations between cancer gene copy numbers and a species’ life history. I found a significant association between cancer gene copies and species’ longevity quotient. Additional paralogues of tumor suppressor genes and oncogenes is not solely dependent on body size, but rather the balance between body size and longevity. Additionally, there is a significance association between life history traits and genes that are both germline and somatic tumor suppressor genes. The bioinformatic pipeline identified large tumor suppressor gene and oncogene copy numbers in the naked mole rat (Heterocephalus glaber), armadillo (Dasypus novemcinctus), and the two-fingered sloth (Choloepus hoffmanni). These results suggest that increased paralogues of tumor suppressor genes and oncogenes are these species’ modes of cancer resistance. / Dissertation/Thesis / Pipeline results for cancer genes / Phylogenetic regressions with correction tests / Pipeline results for housekeeping genes / Masters Thesis Biology 2019

Ce travail de recherche montre que les différentes sources de polyphénols (polyphénols de vin rouge, jus d'aronia melanocarpa, jus de cassis) ont de puissants effets chemothérapeutiques et chemopréventifs sur différentes lignées de culture cellulaires, mais également in vivo sur un modèle de tumorigenèse. Ces polyphénols inhibent la prolifération des cellules cancéreuses (leucémie lymphoblastique aigüe, cellules souches) en induisant un arrêt du cycle cellulaire et l'apoptose. Les effets anti-cancéreux sont dépendants de l' induction du stress oxydatif mettant en jeu les anions superoxydes et le peroxyde d·hydrogène qui à son tour, activent les voies de signalisation conduisant à une surexpression des gènes suppresseurs de tumeurs comme p73 et p53 et ainsi que caspase 3. Celle étude montre également que les polyphénols contrôlent la prolifération des cellules cancéreuses au niveau épigénétique en diminuant l'expression d'UHRF1 (un intégrateur épigénétique de prolifération). Cependant l'effet anticancéreux de ces polyphénols est sélectif et agit sur les cellules cancéreuses et non sur les cellules normales. Le fractionnement de ces sources riches en polyphénols et les études menées en utilisant des composés purs montrent que les effets anticancéreux sont attribués à plusieurs composés différents. Cette étude montre l' identification de cyanidine-3-glucoside et de cyanidine-3-rutinoside comme source de composés anticancéreux actifs. / This research work shows that different sources of polyphenols (RWPs, AMJ and blackcurrant) have strong chemotherapeutic and chemopreventive effects on several cancer cells lines (acute lymphoblastic leukemia and cancer stem cells) and also in vivo in a model of tumorigenesis in mouse. These polyphenols inhibit the proliferation of various cancer cells by inducing cell cycle arrest and apoptosis. The anti-cancer effect is dependent on the induction of oxidative stress involving superoxide anions and hydrogen peroxide which, in turn, activate the signaling pathways leading to the re-expression of tumor suppressor genes such as p73 and p53 and executor of apoptosis such as caspase 3. This study also shows that polyphenols control the proliferation of cancer cells at epigenetic level by decreasing the expression of UHRF1 (an epigenetic integrator of proliferation). Moreover, the anticancer effect of these polyphenols is selective towards cancer cells and not in normal cells. Fractionation of these rich sources of polyphenols and studies on the commercially available pure products shows that anti-cancer effects of these polyphenols involve several different compounds. This study leads to the identification of cyaniding-3-O-glucoside and cyaniding-3-O-rutinoside as active anticancer compounds.

The development of RNAi based technologies has given researchers the tools to interrogate processes as diverse as cancer biology, metabolism and organ development. Here I employ genome-wide shRNA screens to discover the genes involved in two different processes in carcinogenesis, oncogene-induced senescence [OIS] and epigenetic silencing of tumor suppressor genes [TSGs]. OIS is a poorly studied yet significant tumor suppressing mechanism in normal cells where they enter cell cycle arrest [senescence] or programmed cell death [apoptosis] in the presence of an activated oncogene. Here I employ a genomewide shRNA screen and identify a secreted protein, IGFBP7, that induces senescence and apoptosis in melanocytes upon introduction of the oncogene BRAFV600E. Expression of BRAFV600E in primary cells leads to synthesis and secretion of IGFBP7, which acts through autocrine/paracrine pathways to inhibit BRAF-MEK-ERK signaling and induce senescence and apoptosis. Apoptosis results from IGFBP7-mediated upregulation of BNIP3L, a proapoptotic BCL2 family protein. Recombinant IGFBP7 has potent pro-apoptotic and anti-tumor activity in mouse xenograft models using BRAFV600E-postive melanoma cell lines. Finally, IGFBP7 is epigenetically silenced in human melanoma samples suggesting IGFBP7 expression is a key barrier to melanoma formation. Next I investigated the factors involved in epigenetic silencing in cancer. The TSG p14ARFis inactivated in a wide range of cancers by promoter hypermethylation through unknown mechanisms. To discover p14ARF epigenetic silencing factors, I performed a genome-wide shRNA screen and identified ZNF304, a zinc finger transcription factor that contains a Krüppel-associated box [KRAB] repressor domain. I show that ZNF304 binds to the p14ARF promoter and recruits a KRAB co-repressor complex containing KAP1, SETDB1 and DNMT1 for silencing. We find oncogenic RAS signaling to promote the silencing of p14ARF by USP28-mediated stabilization of ZNF304. In addition I find ZNF304 to be overexpressed in human colorectal cancers and responsible for hypermethylation of over 50 TSGs known as Group 2 CIMP marker genes. My findings establish ZNF304 as a novel oncogene that directs epigenetic silencing and facilitates tumorigenicity in colorectal cancer.

Master of Science / Department of Anatomy and Physiology / Masaaki Tamura / Previous studies have shown that both human and rat umbilical cord matrix mesenchymal stem cells (UCMSC) possess the ability to control the growth of breast carcinoma cells. Comparative analysis of two types of UCMSC suggest that rat UCMSC-dependent growth regulation is significantly stronger than that of human UCMSC. Accordingly, the present study was designed to clarify their different tumoricidal abilities by analyzing gene expression profiles in two types of UCMSC. Gene expression profiles were studied by microarray analysis using Illumina HumanRef-8-V2 and RatRef-12 BeadChip for the respective UCMSC. The gene expression profiles were compared to untreated naïve UCMSC and those co-cultured with species-matched breast carcinoma cells; human UCMSC vs. MDA-231 human carcinoma cells and rat UCMSC vs. Mat B III rat carcinoma cells. The following selection criteria were used for the screening of candidate genes associated with UCMSC-dependent tumoricidal ability; 1) gene expression difference should be at least 1.5 fold between naive UCMSC and those co-cultured with breast carcinoma cells; 2) they must encode secretory proteins and 3) cell growth regulation-related proteins. These analyses screened 17 common genes from human and rat UCMSC. The comparison between the two sets of gene expression profiles identified that two tumor suppressor genes, adipose-differentiation related protein (ADRP) and follistatin (FST), were specifically up-regulated in rat UCMSC, but down-regulated in human UCMSC when they were co-cultured with the corresponding species’ breast carcinoma cells. The suppression of either protein by the addition of a specific neutralizing antibody in co-culture of rat UCMSC with Mat B III cells significantly abrogated UCMSC ability to attenuate the growth of carcinoma cells. Over-expression of both genes by adenovirus vector in human UCMSC enhanced their 4 ability to suppress the growth of MDA-231 cells. In the breast carcinoma lung metastasis model generated with MDA-231 cells, systemic treatment with FST-over-expressing human UCMSC significantly attenuated the tumor burden. These results suggest that both ADRP and FST may play important roles in exhibiting stronger tumoricidal ability in rat UCMSC than human UCMSC and imply that human UCMSC can be transformed into stronger tumoricidal cells by enhancing tumor suppressor gene expression.

Protein product tumor suppressor PALB2 gene plays a major role in pathway of DNA repair of double-strand breaks throught the homologous recombination mechanism. Significance of its pathogenic variants in hereditary forms of breast cancer in BRCA1/2- negative patients in families with multiple breast cancers may be in the Czech Republic comparable with the BRCA2 gene. A role of the PALB2 gene in sporadic breast cancer occurence, which represent 90 - 95 % of all cancers, is still unknown. This thesis focuses on inactivation pathway of tumor suppressor PALB2 in the sporadic breast cancer by a mechanism of allelic loss detecting by loss of heterozygosity (LOH) of corresponding microsatellite markers and hypermethylation of promoter region as the most common mechanisms of inactivation tumor suppressors in early tumorigenesis. In a group of 51 nonselected patients with sporadic breast cancer we found four samples with PALB2 locus allelic loss. These samples were analyzed for somatic mutations. No mutation was found. There is no evidence of promotor hypermethylation in any of the samples. Our data suggest a role of the PALB2 gene inactivation in a minority group of sporadic breast cancers.

Alterações no genoma de células tumorais são eventos comuns durante a carcinogênese. Tais aberrações genômicas - como mutações e variações estruturais - são diretamente relacionadas a detecção e morte de células neoplásicas pelo sistema imune. Além da contribuição da perda de função de genes supressores tumorais (GSTs) no desenvolvimento neoplásico, GSTs também influenciam a resposta imune no câncer. Por exemplo, o GST PTEN afeta diretamente a via interferon através da desfosforilação do fator regulador de interferon 3 (IRF3). No entanto, se mantém inconclusivo se a inativação de PTEN diretamente influencia a resposta imune através de IRF3 ou por provocar altos níveis de instabilidade genômica. Para responder essa questão, conduzimos uma análise PanCancer de 33 tipos tumorais da coorte The Cancer Genome Atlas para identificar se existem associações entre a inativação do gene PTEN e alterações genômicas específicas que podem suprimir ou ativar a resposta imune antitumoral. O status de inativação de PTEN foi determinado a partir de dados de variação no número de cópias e presença de mutações de ponto. Nesse estudo, investigamos o efeito da inativação de PTEN nas alterações genômicas de tumores e na abundância de 22 células do sistema imune derivadas do algoritmo CIBERSORT. Observamos que a inativação de PTEN foi significantemente associada com níveis elevados de aneuploidia, mutações, e heterogeneidade intratumoral. Além disso, nossos achados mostraram que a inativação de PTEN é altamente específica para cada tipo tumoral. Da mesma maneira, observamos que pacientes com tumores PTEN-inativos podem apresentar variações na resposta a imunoterapia. Tal observação deriva da correlação significativa entre a inativação de PTEN e a expressão dos alvos terapêuticos proteína programada 1 da morte celular (PD1), seu ligante (PDL1), e indoleamina 2,3 dioxigenase (IDO1). Na análise PanCancer, a inativação de PTEN também foi significativamente associada à composição de células do sistema imune no microambiente tumoral, incluindo células T regulatórias (Treg) e células CD8+. A partir desses achados, conduzimos uma análise aprofundada de tumores de próstata primários e metastáticos com a perda de PTEN. Através de uma análise in silico, nós observamos que tumores primários e metastáticos apresentam maiores densidades de Treg quando há perda da proteína PTEN. Nós também observamos que, dependendo do local de metástase prostática, a deficiência de PTEN é associada a um perfil de células imunes supressivas no microambiente tumoral. A partir da análise de uma coorte brasileira composta por 94 tumores primários de próstata, observamos que a perda de PTEN se associa a uma maior densidade de Tregs e uma maior expressão da proteína imunossupressora IDO1. Além disso, tumores PTEN-deficientes com altas densidades de Tregs apresentaram o pior prognóstico entre pacientes. Coletivamente, nós demonstramos que a inativação de PTEN é associada a um estado imunossuprimido no microambiente tumoral. Ademais, a perda de PTEN possivelmente se associa a resposta imune antitumoral através da combinação de duas diferentes vias - uma dependente de IRF3 e outra relacionada ao efeito no genoma de células cancerosas. Ensaios funcionais são necessários para validar os achados desse estudo; porém, sugerimos que a avaliação do status de inativação de PTEN pode ter alto potencial para discernir pacientes que responderão à imunoterapia. / Cancer-cell genomes undergo several abnormalities during carcinogenesis. Indeed, many of the tumor-specific genomic changes, such as mutations and chromosomal aberrations, are related to how the host immune system responds to detect and kill tumor cells. In addition to these general effects, loss of function of specific tumor suppressor genes (TSG) contributes to tumor development and progression and at the same time also regulates several facets of the immune response in cancer. For instance, the TSG phosphatase and tensin homolog (PTEN) was shown to directly regulate the anti-viral interferon response by licensing the interferon regulatory factor 3 (IRF3). However, it is still unclear whether PTEN directly influences the immune response through the interferon network or by provoking higher levels of genomic instability. To address this question, we conducted a PanCancer analysis of 33 tumor types from The Cancer Genome Atlas to determine whether there were associations between PTEN inactivation and specific genomic features that are linked to immunosuppressive states in cancer. PTEN inactivation status was determined by combining copy number and point mutation data. Then, we performed a parallel analysis of genomic instability and immune-cell abundances derived from the CIBERSORT algorithm comparing PTEN deficient to intact tumors. We found that PTEN inactivation was strongly associated with enhanced levels of aneuploidy, mutation load, immunogenic mutations, and tumor heterogeneity. Furthermore, we found that the outcome of PTEN inactivation status was highly specific to each tumor type and the induced changes appeared to lead to variation in immune responses in different cancers. Response to current immunotherapeutic approaches depends on the expression of targeted immune checkpoints, and we found that tumors with PTEN deficiency had altered expression of programmed death protein 1 (PD1), its ligand (PDL1), and the immunosuppressive protein indoleamine 2,3-dioxygenase (IDO1). We also found that PTEN inactivation led to a distinct immune-cell composition in the tumor microenvironment, including regulatory T cells and CD8+ T cells. Lastly, we performed an in-depth analysis of the immune-cell content of prostate tumors that harbored PTEN protein loss. Through an in silico analysis of 622 tumors, we found that both primary and metastatic lesions had higher densities of regulatory T cells when PTEN was lost. Then, the analysis of 94 primary prostate tumors from Brazil demonstrated that PTEN protein loss was significantly associated with high Treg density and IDO1 protein expression. Moreover, PTEN-null tumors with high Treg density exhibited the worse outcome among patients. We also found that, depending on the prostate cancer metastatic site, PTEN deficiency was linked to variation in the immunosuppressive immune cell landscape. Collectively, we show that PTEN inactivation associates with the anti-tumor immune response likely through direct avenues (via licensing of IRF3) and indirectly by influencing the genome of cancer cells. Functional studies are required to validate our in silico findings; however, we speculate that determining PTEN inactivation status may allow clinicians to distinguish patients that are more likely to respond to current immunotherapies.