Submitted by ANDRÉ LUIS GIACOMETTI CONCEIÇÃO null (andre4487@gmail.com) on 2016-03-08T12:40:30Z No. of bitstreams: 1 Arquivo_Completo_-_Tese_Doutorado_-_André_Luis_Giacometti_Conceição.pdf: 1296182 bytes, checksum: 29c1b4fbebefc1b96e79210f433f4d2f (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-09T16:44:10Z (GMT) No. of bitstreams: 1 conceicao_alg_dr_sjrp.pdf: 1296182 bytes, checksum: 29c1b4fbebefc1b96e79210f433f4d2f (MD5) / Made available in DSpace on 2016-03-09T16:44:10Z (GMT). No. of bitstreams: 1 conceicao_alg_dr_sjrp.pdf: 1296182 bytes, checksum: 29c1b4fbebefc1b96e79210f433f4d2f (MD5) Previous issue date: 2016-02-16 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O carcinoma renal de células claras (ccRCC) é o mais comum dos subtipos histológicos de carcinoma renal. Este carcinoma é histologicamente caracterizado pela presença de células com citoplasma claro e abundante. O processo inicial de metástase pode ser atribuída à transição epitélio mesênquima (EMT). Neste estudo, buscou-se identificar genes diferencialmente expressos em ccRCC, construindo assim um perfil molecular para este tumor. Nós selecionamos genes descritos na literatura que apresentam relação com EMT, diferenciação e proliferação celular. Analisou-se por PCR quantitativo e imuno-histoquímica a expressão dos genes e suas proteínas, respectivamente, e os possíveis mecanismos epigenético que regulam a sua expressão em amostras de ccRCC e linhagem celular. Os genes OCLN e GAS1 foram encontrados com baixa expressão em ccRCC, e nós sugerimos que o miR-122 e miR- 34a podem regular sua expressão, respectivamente, neste tipo de câncer. Além disso, mostramos, por qPCR e imuno-histoquímica, a alta expressão de SLC2A1 foi significantemente alta em ccRCC. O conjunto de genes identificados neste estudo possibilita a compreensão das bases moleculares e de desenvolvimento do ccRCC. / Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of kidney cancer. This carcinoma is histologically characterized by the presence of clear and abundant cytoplasm. The initial process of ccRCC metastatic tumor formation can be attributed to epithelial- mesenchymal transition (EMT). In this study, we sought to identify genes differentially expressed in ccRCC and build a molecular profile of this cancer. We selected genes described in the literature to be related to EMT, cellular differentiation and proliferation. We analyzed the gene and protein expression by quantitative PCR and immunohistochemistry, respectively, and examined possible epigenetic mechanisms that regulate their expression in ccRCC samples and cell lines. OCLN and GAS1 genes were under-expressed in ccRCC, and we report that miR-122 and miR- 34a, respectively, may regulate their expression in this cancer. Furthermore, we showed by quantitative PCR (qPCR) and immunohistochemistry that SLC2A1 was significantly over-expressed in ccRCC. The set of genes identified in this study furthers our understanding of the molecular basis and development of ccRCC. / FAPESP: 2012/08853-0

>Magister Scientiae - MSc / Kidney cancers, of which clear cell renal cell carcinoma comprises an estimated 70%, have been placed amongst the top ten most common cancers in both males and females. With a mortality rate that exceeds 40%, kidney cancer is considered the most lethal cancer of the genitourinary system. Despite advances in its treatment, the mortality- and incidence rates across all stages of the disease have continued to climb. Since the release of the Human Genome Project in the early 2000’s, most genetics studies have focused on the protein coding region of the human genome, which accounts for a mere 2% of the entire genome. It has been suggested that diverting our focus to the other 98% of the genome, which was previously dismissed as non-functional “junk DNA”, could possibly contribute significantly to our understanding of the underlying mechanisms of complex diseases.In this study a whole genome sequencing somatic mutation data set from the International Cancer Genome Consortium was used. The non-coding somatic mutations within the promoter, intronic, 5-prime untranslated and 3-prime untranslated regions of clear cell renal cell carcinoma-implicated genes were extracted and submitted to RegulomDB for their functional annotation.As expected, most of the variants were located within the intronic regions and only a small subset of identified variants was predicted to be deleterious. Although the variants all belonged to a selected subset of kidney cancer-associated genes, the genes frequently mutated in the non-coding regions were not the same genes that were frequently mutated in the whole exome studies (where the focus is on the coding sequences). This indicates that with whole genome sequencing studies a new set of genes/variants previously unassociated with the clear cell renal cell carcinoma could be identified. In addition, most of the non-coding somatic variants fell within multiple transcriptions factor binding sites. Since many of these variants were also deleterious (as predicted by RegulomDB), this suggests that mutations in the non-coding regions could contribute to disease due to their role in transcription factor binding site disruptions and their subsequent impact on transcriptional regulation. The substantial overlap between the genes with the most aberrantly methylated variants and the genes with the most transcription factor binding site disruptions signifies a potential link between differential methylation and transcription factor binding site affinities. In contrast to the upregulated DNA methylation generally seen in promoter methylation studies, all of the significant hits in this study were hypomethylated, with the subsequent up-regulation of the genes of interest, suggesting that in the clear cell renal cell carcinoma, aberrant methylation may play a role in activating proto-oncogenes, rather than the silencing of genes. When a cross-analysis was carried out between the gene expression patterns and the transcription factor binding site disruptions, the non-coding somatic variants and differential methylation profiles, the genes affected again showed a clear overlap. Interestingly, most of the variants were not present in the 1000genomes data and thus represent novel mutations, which possibly occurred as a result of genomic instability. However, identifying novel variants are always promising, since they epitomise the possibility of developing pioneering ways to target diseases. The numerous detrimental effects a single non-coding mutation can have on other genomic processes have been demonstrated in this study and therefore validate the inclusion of non-coding regions of the genome in genetic studies in order to study complex multifactorial diseases. / National Research Foundation (NRF) and DAAD

Resumo: O tumor renal é a mais letal das doenças urológicas. É uma doença histologicamente heterogênea, sendo o carcinoma renal de células claras o subtipo histológico mais comum. Embora a nefrectomia e imunoterapia sejam tratamentos bem estabelecidos, aproximadamente 30% dos pacientes tratados são acometidos por metástases. Alterações na expressão gênica e na inativação transcricional, devido ao mecanismo de metilação, são evidentes em células cancerosas. A metilação do DNA é um evento epigenético intimamente relacionado com o silenciamento da expressão gênica, e está envolvida em vários processos, dentre eles, a carcinogênese. Dessa forma, este trabalho teve como objetivos investigar se os genes selecionados, GPC3, CRABP2, KTN1 e ADAM23 apresentam expressão alterada nas amostras tumorais, verificar se a expressão gênica está associada com a progressão tumoral, e analisar o padrão de metilação de ilhas CpGs. Os quatro genes selecionados foram validados pela técnica de PCR em Tempo Real. Para validação desses genes foram utilizadas 35 amostras de carcinoma renal de células claras e 35 amostras de córtex renal normal. Os genes GPC3, CRABP2, KTN1 e ADAM23 apresentaram redução de expressão significativa em amostras de carcinoma renal de células claras quando comparadas ao pool de amostras de córtex renal normal. Observou-se que a redução da expressão do gene ADAM23 está diretamente relacionada com o avanço do estadiamento tumoral. Foi observada uma freqüência elevada de hipermetilação do gene ADAM23, entretanto, não houve associação do padrão de metilação com os dados clínicos. A análise da expressão gênica e dos mecanismos responsáveis pela inativação transcricional dos genes CRABP2, KTN1 e ADAM23, estudados pela primeira vez em carcinoma renal, e GPC3, podem fornecer informações relevantes para o conhecimento e desenvolvimento do carcinoma renal de células claras. / Abstract: The renal tumor, which is the most lethal of urological diseases, is a histologically heterogeneous disease, and the clear cell renal cell carcinoma the most common histological subtype. Although the treatment of nephrectomy and immunotherapy are established, approximately 30% of patients are affected by metastases. Changes in gene expression and transcriptional inactivation, due to the methylation mechanism are evident in cancer cells. The DNA methylation is an epigenetic event closely related to the silencing of gene expression, and is involved in several cases, including the carcinogenesis. The aim of this study was to investigate the gene expression of GPC3, CRABP2, KTN1 and ADAM23, check if gene expression was associated with tumor progression and analyze methylation pattern of CpG island. The four selected genes were validated by the quantitative RT-PCR. Thirty five samples of clear cell renal cell carcinoma and 35 samples of normal renal cortex were used for validation. The genes GPC3, CRABP2, KTN1 and ADAM23 showed significant reduction of expression in samples of clear cell renal cell carcinoma when compared to a pool of samples of normal renal cortex. It was observed that the lower expression of ADAM23 is directly related to the advancement of the tumor staging. Despite the high frequency of hypermethylation of ADAM23, there was no association with the methylation pattern of the clinical data. The analysis of gene expression and the mechanisms responsible for the transcriptional inactivation of genes CRABP2, KTN1 and ADAM23, first studied in clear cell renal cell carcinoma, and GPC3, may provide relevant information for the clear cell renal cell carcinoma understanding and development. / Orientador: Paula Rahal / Coorientador: Paulo Peitl Júnior / Banca: Ana Elizabete Silva / Banca: Andréia Machado Leopoldino / Mestre

Le carcinome rénal à cellules claires (ccRCC) est la tumeur du rein la plus fréquente. Il se caractérise par une inactivation fréquente du gène suppresseur de tumeur VHL retrouvée dans 70% des tumeurs conduisant à une transcription des gènes cibles du facteur de transcription HIF dont le VEGF. Il s’agit d’une tumeur agressive métastatique chez 50% des patients. Le sunitinib, un inhibiteur des récepteurs tyrosine kinase anti-angiogénique, est actuellement le plus utilisé en 1ère ligne malgré 30% des patients qui progressent rapidement. L’avènement d’un nouvel anti-angiogénique ciblant MET (cabozantinib) et d’immunomodulateurs (anticorps anti-PD-1, nivolumab) rend cruciale la découverte de facteurs prédictifs de réponse au traitement. Dans une 1ére partie, nous avons étudié une série rétrospective de 98 ccRCC consécutifs pour lesquels nous souhaitions étudiés le statut VHL complet et le corréler à l’expression de PD-L1. De plus, alors que le pronostic est différent entre ccRCC métastatiques synchrones (d’emblée) et métachrones (à distance), leur phénotype n’avait jamais été comparé. Pour cela, nous avons effectué une analyse histologique des principaux facteurs pronostiques, immunohistochimique (CAIX, VEGF, PAR3, PD-1 et PD-L1) et moléculaire (statut complet VHL : délétion, mutation et méthylation du promoteur) corrélée à la survie spécifique. Nous avons démontré que le statut VHL non-inactivé (niVHL) était associé à la présence de métastases synchrones, une composante sarcomatoïde, un infiltrat lymphocytaire dense, une surexpression de VEGF, une expression de PD-L1 et à un mauvais pronostic. Nous avons aussi comparé les phénotypes des ccRCC métastatiques métachrones et synchrones. Ces derniers étaient associés à une  composante sarcomatoïde, une expression cytoplasmique de PAR-3, une surexpression de VEGFA, un statut niVHL et à un mauvais pronostic depuis le diagnostic des métastases. Dans une 2ème partie, nous avons étudié une série rétrospective de 90 ccRCC métastatiques consécutifs traités par sunitinib en première ligne afin d’identifier des facteurs prédictifs de réponse ou de résistance. Nous avons utilisé les mêmes techniques que précédemment avec en plus le statut MET (mutation en NGS et expression en IHC). Les patients ont été classés en résistants primaires, intermédiaires et longs répondeurs en fonction de la durée de leur réponse évaluée par des critères radiologiques (RECIST). Nous avons aussi caractérisé le profil génétique de 73 ccRCC de cette série par CGH array pour lesquels nous disposions de congélation. Les patients résistants primaires avaient plus souvent un mauvais pronostic (score de Heng), des métastases hépatiques, une infiltration de la graisse hilaire. Sur le plan cytogénétique, leurs tumeurs présentaient des altérations génétiques plus nombreuses tant au niveau des gains que des pertes. Parmi ces altérations récurrentes, étaient décrites les gains du 5p, 7p, 8q22.1-qter et la perte de la région 6q21-q25.3. Le modèle de Cox multivarié mettait en évidence 4 facteurs indépendants : le score de Heng, des métastases hépatiques, une infiltration de la graisse hilaire et le gain du 8q qui intégrés dans un nomogramme pronostique avaient un c-index de 0.74 et 0.77 pour la survie sans progression et la survie globale. En conclusion, notre étude a permis d’identifier un sous-type de ccRCC avec un statut niVHL de mauvais pronostic qu’il conviendrait d’étudier de manière plus approfondie sur le plan génomique. De plus, nous avons montré une différence de phénotype entre les ccRCC des patients métastatiques synchrones et métachrones alors que leur prise en charge est actuellement équivalente. Enfin nous avons mis en évidence un nomogramme pronostique dans les ccRCC métastatiques traités par sunitinib en 1ère line. Ce nomogramme s’il est confirmé par une étude prospective plus large pourrait avoir un impact clinique important dans la sélection des patients les plus à même de bénéficier des anti-angiogéniques. / Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer. It is characterized by frequent inactivation of the tumor suppressor gene VHL found in 70% of tumors leading to the transcription of HIF transcription factor target genes such as VEGF. This is an aggressive tumor with 50% of metastatic patients. Sunitinib, an inhibitor of receptor tyrosine kinase antiangiogenic, is currently the most used in 1st line despite 30% of patients who progress quickly. The advent of a new anti-angiogenic targeting MET (cabozantinib) and immunomodulators (anti-PD-1 antibody, nivolumab) makes crucial discovery of predictors of response to treatment. In the first part, we studied a retrospective study of 98 consecutive ccRCC. We assessed complete VHL status and correlated it with the expression of PD-L1. Moreover, while the prognosis is different between ccRCC synchronous metastatic and metachronous, their phenotype have never been compared. In this purpose, we performed an analysis of the main pathological prognostic factors, immunohistochemical markers (CAIX, VEGF, PAR3, PD-1 and PD-L1) and molecular (VHL status: deletion, mutation and promoter methylation) correlated with specific survival. We demonstrated that non-inactivated VHL tumors (niVHL) were associated with the presence of synchronous metastases, sarcomatoid component, a dense lymphocytic infiltrate, an overexpression of VEGF, an expression of PD-L1 and a poor prognosis. We also compared the phenotypes of metachronous and synchronous metastatic ccRCC. The first ones were associated with sarcomatoid component, cytoplasmic expression of PAR-3 overexpression VEGFA and niVHL status and a poor prognosis even from the diagnosis of metastases. In the second part, we studied a retrospective study of 90 consecutive metastatic ccRCC treated with first line sunitinib to identify predictors of response or resistance. We used the same techniques as above plus the MET status (mutation in Next-Generation sequencing and expression by IHC). Patients were classified as primary-refractory, intermediate and long-term responders depending on the duration of their response as assessed by radiological criteria (RECIST). We also characterized the genetic profile of 73 ccRCC of this series by CGH array for which we had frozen tumor. Primary refractory patients often had poor prognosis (Heng criteria), liver metastases, infiltration of the hilar fat. Cytogenetically, their tumors had many more genetic alterations, both gains as losses. These recurrent alterations were gains of 5p, 7p, 8q22.1-qter and loss of 6q21-q25.3 region. The multivariate Cox model highlighted four independent factors: the score of Heng, liver metastases, infiltration of the hilar fat and gain of 8q which integrated into a prognostic nomogram had a c-index of 0.74 for survival progression-free survival and 0.77 for overall survival. In conclusion, our study identified a subtype of ccRCC with a poor prognosis with niVHL status that should be explored at the genomic level. Furthermore, we showed a phenotype difference between ccRCC synchronous and metachronous metastatic patients whereas their care is currently the same. Finally we have identified a prognostic nomogram in metastatic ccRCC treated with sunitinib in the first line. This nomogram if confirmed by a larger prospective study could have a significant clinical impact in the selection of patients most likely to benefit from anti-angiogenic therapy.

Carcinoma de Células Renais (CCR) representa uma família de tumores distintos com evolução clínica imprevisível. Uma variedade de moléculas tem sido avaliada como marcadores prognósticos para CCR. Ciclina D1, uma proteína reguladora do ciclo celular, encontra-se superexpressa em vários tumores primários. Nosso objetivo é avaliar sua expressão como marcador prognóstico em CCR. Antes disso, traçamos um perfil clínico e histopatológico da amostra e verificamos sua relação com os fatores prognósticos considerados clássicos pela literatura. 109 espécimes de pacientes diagnosticados com CCR foram obtidos entre 2005 e 2010 no Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto USP e submetidos à análise imunoistoquímica juntamente com 07 amostras de tecido renal normal. A maior parte das características epidemiológicas e clínicas de nossa amostra foi similar àquelas descritas na literatura mundial. Houve predomínio do gênero masculino, da raça branca, com idade próxima a 60 anos, frequência de pacientes assintomáticos em torno de 36% e grande prevalência do CCR de células claras (71,55%). A mortalidade específica da doença foi de 13,76%, sendo o CCR de células claras o tipo mais frequente entre os óbitos e casos metastáticos. Os casos que exibiram má evolução clínica, definida pela ocorrência de metástase e/ou óbito por CCR (22,01%), estiveram associados à presença de sintomas ao diagnóstico, maior tamanho tumoral, grupo de estágio alto (III ou IV), grau nuclear de Fuhrman alto (3 ou 4), presença de necrose e de diferenciação sarcomatóide no tumor, além de outros fatores histológicos desfavoráveis (p < 0,01). Isso indica que as variáveis utilizadas na avaliação de prognóstico em países desenvolvidos podem ser aplicadas aos nossos pacientes. Não houve expressão imunoistoquímica de Ciclina D1 nos casos de tecido renal normal. Observou-se heterogeneidade de marcação nuclear intratumoral no total de casos e menor expressão proteica entre os CCR papilífero e cromófobo. Pacientes com tumores com Ciclina D1baixa (até 30% de células positivas) apresentaram má evolução clínica (p = 0,03), maior tamanho tumoral (p = 0,01), presença de sintomas ao diagnóstico (p = 0,04), grau nuclear alto (p = 0,001), presença de necrose (p = 0,004) e de diferenciação sarcomatóide (p = 0,04) no tumor, além de menor sobrevida sem metástase e/ou óbito por CCR (p = 0,03). Após análise multivariada, a expressão de Ciclina D1 não apresentou valor prognóstico independente para má evolução clínica, embora tenha aumentado levemente a acurácia prognóstica do modelo adotado. Em todas as análises realizadas para o CCR de células claras isoladamente, observamos significância estatística semelhante à do total de casos (CCR). Nosso estudo demonstrou que: a proteína Ciclina D1 encontra-se superexpressa em CCR; os tipos de CCR parecem exibir diferentes padrões de marcação imunoistoquímica da Ciclina D1; alta marcação da proteína (acima de 30% de células positivas) esteve associada à boa evolução clínica e à maioria dos fatores prognósticos favoráveis bem estabelecidos na literatura. Novas investigações são necessárias para descobrir que mecanismos levam a seu acúmulo nas células neoplásicas e quais outros eventos podem estar contribuindo para a progressão da doença. / Renal Cell Carcinoma (RCC) is a family of distinct tumors with unpredictable clinical outcome. A variety of molecules have been evaluated as prognostic markers for RCC. Cyclin D1, a cell cycle regulatory protein, is overexpressed in several primary tumors. Our purpose is to evaluate its expression as a prognostic marker in RCC. Before that, we drew a clinical and histopathological profile of the sample and verified its relationship with prognostic factors regarded as classics in literature. 109 specimens from patients diagnosed with RCC were obtained between 2005 and 2010 at Hospital das Clínicas - Ribeirão Preto School of Medicine USP and submitted to immunohistochemical analysis, along with 07 normal kidney tissue samples. Most epidemiological and clinical characteristics of our sample were similar to those described in the literature. There was a predominance of male, Caucasian, aged about 60 years, the frequency of asymptomatic patients around 36%, and high prevalence of clear cell RCC (71.55%). The disease-specific mortality was 13.76%, being the clear cell RCC the most frequent type among deaths and metastatic cases. Cases that exhibited poor clinical outcome, defined by the occurrence of metastasis and/or death by RCC (22.01%), were related to the presence of symptoms at diagnosis, larger tumor size, high stage group (III or IV), high Fuhrman nuclear grade (3 or 4), presence of necrosis and sarcomatoid differentiation in the tumor and other unfavorable histological factors (p < 0.01). This indicates that the variables used in the assessment of prognosis in developed countries can be applied to our patients. There was no immunohistochemical expression of Cyclin D1 in cases of normal kidney tissue. There was intratumoral heterogeneity in nuclear staining in all cases and lower protein expression among papillary and chromophobe RCC. Patients with Cyclin D1low tumors (up to 30% positive cells) showed poor clinical outcome (p = 0.03), larger tumor size (p = 0.01), presence of symptoms at diagnosis (p = 0.04), high nuclear grade (p = 0.001), presence of necrosis (p = 0.004) and sarcomatoid differentiation (p = 0.04) in the tumor and lower survival without metastasis and/or death by RCC (p = 0.03). After multivariate analysis, the expression of Cyclin D1 showed no independent prognostic value for poor clinical outcome, although it has slightly increased the prognostic accuracy of the model adopted. In all analyzes performed for clear cell RCC alone, we observed statistical significance similar to that of the total cases (RCC). Our study showed that: Cyclin D1 protein is overexpressed in RCC; RCC types seem to exhibit different patterns of immunohistochemical staining for Cyclin D1; high protein expression (over 30% positive cells) was related to good clinical outcome and to most favorable prognostic factors well established in the literature. Further investigations are necessary to reveal which mechanisms lead to its accumulation in neoplastic cells and what other events might be contributing to the progression of the disease.

Le syndrome von Hippel Lindau (VHL) prédispose au développement de multiples tumeurs hautement vascularisées, telles que des hémangioblastomes rétiniens ou du système nerveux central, des phéochromocytomes et des carcinomes rénaux à cellules claires (CCRCC). Les patients atteints de ce syndrome sont porteurs d’une mutation du gène VHL. Ce gène, composé de trois exons, est transcrit en deux ARN messagers par épissage alternatif de l’exon 2. L’ARNm composé des 3 exons (variant #1) est la forme majoritairement exprimée par rapport à l’ARNm dépourvu de l’exon 2 (variant #2). Toutefois, une diminution du ratio variant #1/variant #2 a été essentiellement décrite dans deux situations : (i) dans les tissus embryonnaires humains et en particulier le rein, et (ii) dans certains CCRCC. Ces données suggèrent un rôle potentiel de ce variant #2 dans la tumorigenèse rénale. Deux protéines, pVHL213 et pVHL160, sont produites à partir du variant #1 et elles agissent comme suppresseurs de tumeur. Au début de ce travail, l’expression de l’isoforme protéique pVHL172 produite à partir du variant #2 restait à démontrer et sa fonction était inconnue. Les travaux effectués au cours de cette thèse ont permis de mettre en évidence l’expression de pVHL172 dans des lignées cellulaires et dans des tissus tumoraux grâce à un nouvel anticorps monoclonal de souris dirigé contre les trois isoformes protéiques humaines de pVHL. Pour savoir si l’isoforme pVHL172 a un rôle de suppresseur de tumeur, des lignées cellulaires tumorales rénales exprimant stablement cette protéine ont été établies puis des expériences de xénogreffes de ces cellules chez la souris ont été réalisées. Non seulement pVHL172 n’inhibe pas la formation de tumeurs mais son expression induit un phénotype tumoral plus agressif avec une composante sarcomatoïde plus importante ainsi qu’une vascularisation immature plus conséquente que dans les tumeurs contrôles (n’exprimant pas pVHL). De plus, pVHL172 augmente l’expression des métalloprotéases de matrice MMP1 et MMP13, en partie via l’activation de la voie de signalisation Smad-dépendante du TGF-β. Par ailleurs, des partenaires protéiques de cette protéine ont été recherchés par une analyse protéomique différentielle. Les réseaux d’interaction réalisés à partir des protéines identifiées concernent entre autres la régulation de la matrice extracellulaire et le contrôle qualité des protéines. En conclusion, ce travail a montré que le gène VHL produit des isoformes protéiques avec des fonctions distinctes voire antagonistes, ce qui implique que la balance de leur expression influencerait la progression tumorale rénale. Chez certains patients, une augmentation de l’expression de pVHL172 pourrait être corrélée à une pathologie plus sévère. Ce travail montre l’intérêt de poursuivre l’étude des fonctions de cette protéine pour une meilleure compréhension de son implication dans le cancer du rein et dans la maladie VHL afin d’envisager de nouvelles approches thérapeutiques. / VHL disease predisposes to the development of multiple and highly vascularized tumors, including central nervous system and retinal haemangioblastomas, phaeochromocytomas and clear cell renal cell carcinomas (ccRCCs). Patients with VHL disease harbor a mutant allele of the VHL gene. This gene is transcribed into two mRNAs by alternative splicing of the exon 2. The mRNA variant #1 composed of 3 exons usually predominates over the mRNA variant #2 lacking exon 2. A decrease of the variant #1/variant #2 ratio was however described in 2 situations: (i) in embryonic tissues, particularly in the kidney, and (ii) in some ccRCCs. These data suggest a potential role for the variant #2 in kidney tumorigenesis. pVHL213 and pVHL160 are the two proteins encoded by the mRNA variant #1 and act as tumor suppressors. At the beginning of this Ph.D. project, the expression of pVHL172 isoform encoded by the mRNA variant #2 remained to be established and its function was unknown. The experiments performed during this Ph.D. shed light on pVHL172 expression in cell lines and in tumor tissues using a newly produced mouse monoclonal antibody recognizing the three human pVHL isoforms. To examine if pVHL172 had a tumor suppressor function, human kidney tumor cell lines stably expressing this isoform were established, characterized and then grafted in mice. pVHL172 not only inhibits tumor formation, but its expression also induces a more aggressive phenotype with a higher sarcomatoid component and a more immature vasculature compared to control tumors (that do not express any pVHL). Moreover, pVHL172 increases the matrix metalloproteases MMP1 and MMP13 expression, partly by the activation of the Smad-dependent TGF-β signalling pathway. Besides, we looked for protein partners of pVHL172 by a differential proteomic analysis and showed that interaction networks obtained with the identified proteins are related to extracellular matrix regulation and protein quality control. To conclude, this work demonstrated that the VHL gene encodes protein isoforms with distinct and even antagonistic functions. The balance of expression of these isoforms is likely to influence kidney tumor progression. For some patients, an increase of pVHL172 expression could be correlated with a more severe pathology. This work shows the importance of further studying this isoform’s functions to better understand its involvement in kidney cancer and in VHL disease, so that new therapeutic approaches could be developed.

Carcinoma de Células Renais (CCR) representa uma família de tumores distintos com evolução clínica imprevisível. Uma variedade de moléculas tem sido avaliada como marcadores prognósticos para CCR. Ciclina D1, uma proteína reguladora do ciclo celular, encontra-se superexpressa em vários tumores primários. Nosso objetivo é avaliar sua expressão como marcador prognóstico em CCR. Antes disso, traçamos um perfil clínico e histopatológico da amostra e verificamos sua relação com os fatores prognósticos considerados clássicos pela literatura. 109 espécimes de pacientes diagnosticados com CCR foram obtidos entre 2005 e 2010 no Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto USP e submetidos à análise imunoistoquímica juntamente com 07 amostras de tecido renal normal. A maior parte das características epidemiológicas e clínicas de nossa amostra foi similar àquelas descritas na literatura mundial. Houve predomínio do gênero masculino, da raça branca, com idade próxima a 60 anos, frequência de pacientes assintomáticos em torno de 36% e grande prevalência do CCR de células claras (71,55%). A mortalidade específica da doença foi de 13,76%, sendo o CCR de células claras o tipo mais frequente entre os óbitos e casos metastáticos. Os casos que exibiram má evolução clínica, definida pela ocorrência de metástase e/ou óbito por CCR (22,01%), estiveram associados à presença de sintomas ao diagnóstico, maior tamanho tumoral, grupo de estágio alto (III ou IV), grau nuclear de Fuhrman alto (3 ou 4), presença de necrose e de diferenciação sarcomatóide no tumor, além de outros fatores histológicos desfavoráveis (p < 0,01). Isso indica que as variáveis utilizadas na avaliação de prognóstico em países desenvolvidos podem ser aplicadas aos nossos pacientes. Não houve expressão imunoistoquímica de Ciclina D1 nos casos de tecido renal normal. Observou-se heterogeneidade de marcação nuclear intratumoral no total de casos e menor expressão proteica entre os CCR papilífero e cromófobo. Pacientes com tumores com Ciclina D1baixa (até 30% de células positivas) apresentaram má evolução clínica (p = 0,03), maior tamanho tumoral (p = 0,01), presença de sintomas ao diagnóstico (p = 0,04), grau nuclear alto (p = 0,001), presença de necrose (p = 0,004) e de diferenciação sarcomatóide (p = 0,04) no tumor, além de menor sobrevida sem metástase e/ou óbito por CCR (p = 0,03). Após análise multivariada, a expressão de Ciclina D1 não apresentou valor prognóstico independente para má evolução clínica, embora tenha aumentado levemente a acurácia prognóstica do modelo adotado. Em todas as análises realizadas para o CCR de células claras isoladamente, observamos significância estatística semelhante à do total de casos (CCR). Nosso estudo demonstrou que: a proteína Ciclina D1 encontra-se superexpressa em CCR; os tipos de CCR parecem exibir diferentes padrões de marcação imunoistoquímica da Ciclina D1; alta marcação da proteína (acima de 30% de células positivas) esteve associada à boa evolução clínica e à maioria dos fatores prognósticos favoráveis bem estabelecidos na literatura. Novas investigações são necessárias para descobrir que mecanismos levam a seu acúmulo nas células neoplásicas e quais outros eventos podem estar contribuindo para a progressão da doença. / Renal Cell Carcinoma (RCC) is a family of distinct tumors with unpredictable clinical outcome. A variety of molecules have been evaluated as prognostic markers for RCC. Cyclin D1, a cell cycle regulatory protein, is overexpressed in several primary tumors. Our purpose is to evaluate its expression as a prognostic marker in RCC. Before that, we drew a clinical and histopathological profile of the sample and verified its relationship with prognostic factors regarded as classics in literature. 109 specimens from patients diagnosed with RCC were obtained between 2005 and 2010 at Hospital das Clínicas - Ribeirão Preto School of Medicine USP and submitted to immunohistochemical analysis, along with 07 normal kidney tissue samples. Most epidemiological and clinical characteristics of our sample were similar to those described in the literature. There was a predominance of male, Caucasian, aged about 60 years, the frequency of asymptomatic patients around 36%, and high prevalence of clear cell RCC (71.55%). The disease-specific mortality was 13.76%, being the clear cell RCC the most frequent type among deaths and metastatic cases. Cases that exhibited poor clinical outcome, defined by the occurrence of metastasis and/or death by RCC (22.01%), were related to the presence of symptoms at diagnosis, larger tumor size, high stage group (III or IV), high Fuhrman nuclear grade (3 or 4), presence of necrosis and sarcomatoid differentiation in the tumor and other unfavorable histological factors (p < 0.01). This indicates that the variables used in the assessment of prognosis in developed countries can be applied to our patients. There was no immunohistochemical expression of Cyclin D1 in cases of normal kidney tissue. There was intratumoral heterogeneity in nuclear staining in all cases and lower protein expression among papillary and chromophobe RCC. Patients with Cyclin D1low tumors (up to 30% positive cells) showed poor clinical outcome (p = 0.03), larger tumor size (p = 0.01), presence of symptoms at diagnosis (p = 0.04), high nuclear grade (p = 0.001), presence of necrosis (p = 0.004) and sarcomatoid differentiation (p = 0.04) in the tumor and lower survival without metastasis and/or death by RCC (p = 0.03). After multivariate analysis, the expression of Cyclin D1 showed no independent prognostic value for poor clinical outcome, although it has slightly increased the prognostic accuracy of the model adopted. In all analyzes performed for clear cell RCC alone, we observed statistical significance similar to that of the total cases (RCC). Our study showed that: Cyclin D1 protein is overexpressed in RCC; RCC types seem to exhibit different patterns of immunohistochemical staining for Cyclin D1; high protein expression (over 30% positive cells) was related to good clinical outcome and to most favorable prognostic factors well established in the literature. Further investigations are necessary to reveal which mechanisms lead to its accumulation in neoplastic cells and what other events might be contributing to the progression of the disease.

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Made available in DSpace on 2014-06-11T19:26:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-02-19Bitstream added on 2014-06-13T19:53:57Z : No. of bitstreams: 1 pires_lc_me_sjrp.pdf: 2393717 bytes, checksum: a2b9ac8071136c02761c529a8ecaecef (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Os dados de seqüência genômicas humanas depositados em bancos públicos têm fornecido uma oportunidade sem precedentes para pesquisadores decifrarem a funcionalidade do genoma humano. Essas informações são extremamente valiosas na prevenção, diagnóstico e tratamento do câncer. O Cancer Genome Anatomy Project (CGAP), o Gene Expression Omnibus (GEO), o Genome Data Mining (GDM) e o Babelomics funtional analysis of genome-scale experiments representam quatro importantes ferramentas para o estudo da genética funcional. O objetivo do presente trabalho foi o de explorar bancos de dados públicos para selecionar e validar a expressão de genes relacionados com o desenvolvimento e a progressão de carcinoma renal de células claras (CRcc). Utilizando ferramentas de bioinformática foi analisada a expressão gênica diferencial entre duas bibliotecas de SAGE elaboradas a partir de tecidos renais normais e de CRcc. Os resultados obtidos demonstraram alterações na expressão de genes participantes de importantes vias metabólicas. Baseando-se nessas análises, os genes CDK7, CLDN1, CSTB, EPC2 e ZNF706 foram selecionados e a expressão gênica diferencial desses foi avaliada por PCR em tempo real em 35 amostras de pacientes portadores de CRcc em diferentes estágios de progressão da doença e 1 amostra metastática. Paralelamente, utilizando-se a metodologia de RaSH foram elaboradas bibliotecas subtrativas entre o tecido neoplásico e o tecidos normal, sendo selecionados os genes MATR3 e PITPNB. O ZNF706 apresentou super expressão em relação aos tecidos normais, nas amostras tumorais analisadas independentemente do grau de evolução tumoral. O mesmo comportamento foi apresentado pelo gene CSTB, sendo que os maiores níveis de expressão foram observados nas amostras de estágio III de progressão tumoral. O gene CDK7 apresentou níveis de expressão dependente do grau de evolução da... / The data of human genomic sequences available in public database have provided an unpredictable opportunity for researchers to decipher the utility of human genome. This information is extremely valuable in prevention, diagnosis and cancer treatment. The Cancer Genome Anatomy Project (CGAP), the Gene expression Omnibus (GEO), the Genome Data Mining (GDM) and the Babelomics Functional Analysis of Genome-Scale Experiments do represent four important tools for functional genetics studies. This work aimed to explore public database to select and validate expression of genes related to development and progression of Clear Cell Renal Cell Carcinoma (ccRCC). The differential gene expression of two SAGE libraries from normal renal tissues and ccRCC was analyzed using bioinformatics tools. The results showed altered gene expression pattern in genes that participate in important metabolic pathways. Based on these analysis, the genes CDK7, CLDN1, CSTB, EPC2 and ZNF706 were selected and their differential gene expression was evaluated by Real Time PCR in 35 tissue samples from patients with ccRCC in different stages of disease progression and one metastatic sample. Simultaneously through RaSH methodology were elaborated subtractive libraries between normal and neoplasic tissues so the genes MATR3 and PITPNB were selected. The ZNF706 presented over expression in tumor tissues independent of tumor progression grade. The same behavior was presented by CSTB where the higher expression levels were observed in samples from stage IV of tumor progression. The CDK7 gene presented expression levels dependent of disease evolution grade where the lowers levels were in stages I, II, III and presented over expression in samples from stage IV and retroperitoneal metastasis. This result shows a clear relationship between CDK7 expression and the aggressiveness of ccRCC and suggests that this gene... (Complete abstract click electronic access below)

Made available in DSpace on 2014-06-11T19:26:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-02-18Bitstream added on 2014-06-13T19:12:52Z : No. of bitstreams: 1 valsechi_mc_me_sjrp_parcial.pdf: 574533 bytes, checksum: a4733296b652ce8ac3b0aa3af78e4e48 (MD5) Bitstreams deleted on 2015-01-16T10:37:46Z: valsechi_mc_me_sjrp_parcial.pdf,Bitstream added on 2015-01-16T10:38:34Z : No. of bitstreams: 1 000590383.pdf: 1465270 bytes, checksum: 6abb1c740c0eb28b1d1eb0e5696f75a3 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O tumor renal é a mais letal das doenças urológicas. É uma doença histologicamente heterogênea, sendo o carcinoma renal de células claras o subtipo histológico mais comum. Embora a nefrectomia e imunoterapia sejam tratamentos bem estabelecidos, aproximadamente 30% dos pacientes tratados são acometidos por metástases. Alterações na expressão gênica e na inativação transcricional, devido ao mecanismo de metilação, são evidentes em células cancerosas. A metilação do DNA é um evento epigenético intimamente relacionado com o silenciamento da expressão gênica, e está envolvida em vários processos, dentre eles, a carcinogênese. Dessa forma, este trabalho teve como objetivos investigar se os genes selecionados, GPC3, CRABP2, KTN1 e ADAM23 apresentam expressão alterada nas amostras tumorais, verificar se a expressão gênica está associada com a progressão tumoral, e analisar o padrão de metilação de ilhas CpGs. Os quatro genes selecionados foram validados pela técnica de PCR em Tempo Real. Para validação desses genes foram utilizadas 35 amostras de carcinoma renal de células claras e 35 amostras de córtex renal normal. Os genes GPC3, CRABP2, KTN1 e ADAM23 apresentaram redução de expressão significativa em amostras de carcinoma renal de células claras quando comparadas ao pool de amostras de córtex renal normal. Observou-se que a redução da expressão do gene ADAM23 está diretamente relacionada com o avanço do estadiamento tumoral. Foi observada uma freqüência elevada de hipermetilação do gene ADAM23, entretanto, não houve associação do padrão de metilação com os dados clínicos. A análise da expressão gênica e dos mecanismos responsáveis pela inativação transcricional dos genes CRABP2, KTN1 e ADAM23, estudados pela primeira vez em carcinoma renal, e GPC3, podem fornecer informações relevantes para o conhecimento e desenvolvimento do carcinoma renal de células claras. / The renal tumor, which is the most lethal of urological diseases, is a histologically heterogeneous disease, and the clear cell renal cell carcinoma the most common histological subtype. Although the treatment of nephrectomy and immunotherapy are established, approximately 30% of patients are affected by metastases. Changes in gene expression and transcriptional inactivation, due to the methylation mechanism are evident in cancer cells. The DNA methylation is an epigenetic event closely related to the silencing of gene expression, and is involved in several cases, including the carcinogenesis. The aim of this study was to investigate the gene expression of GPC3, CRABP2, KTN1 and ADAM23, check if gene expression was associated with tumor progression and analyze methylation pattern of CpG island. The four selected genes were validated by the quantitative RT-PCR. Thirty five samples of clear cell renal cell carcinoma and 35 samples of normal renal cortex were used for validation. The genes GPC3, CRABP2, KTN1 and ADAM23 showed significant reduction of expression in samples of clear cell renal cell carcinoma when compared to a pool of samples of normal renal cortex. It was observed that the lower expression of ADAM23 is directly related to the advancement of the tumor staging. Despite the high frequency of hypermethylation of ADAM23, there was no association with the methylation pattern of the clinical data. The analysis of gene expression and the mechanisms responsible for the transcriptional inactivation of genes CRABP2, KTN1 and ADAM23, first studied in clear cell renal cell carcinoma, and GPC3, may provide relevant information for the clear cell renal cell carcinoma understanding and development.