Submitted by Israel Vieira Neto (israel.vieiraneto@ufpe.br) on 2015-03-05T18:13:15Z No. of bitstreams: 2 Eduardo Ramalho.pdf: 538304 bytes, checksum: e4a30cf566174291fcd76bbfacaf4eff (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-03-05T18:13:15Z (GMT). No. of bitstreams: 2 Eduardo Ramalho.pdf: 538304 bytes, checksum: e4a30cf566174291fcd76bbfacaf4eff (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2012 / CAPES / Sabe-se que os genes p53, BRCA1 e BRCA2 apresentam a característica em comum de serem considerados supressores tumorais. Eventos genéticos e epigenéticos são frequentes ao longo de todo o genoma humano. Mutações somáticas são passíveis de ocorrer nas regiões codificantes de genes específicos, alterando sua sequência e gerando proteínas mutantes, as quais resultam numa alteração de sua capacidade funcional ou até mesmo a perda dela. Este trabalho objetivou avaliar alterações epigenéticas nas regiões promotoras dos genes BRCA1 e BRCA2 através da técnica de PCR para Metilação Específica (MSP) e correlacionar mutações pontuais nos exons 4 e 7 do gene p53 como fator de risco para o carcinoma ductal invasivo (CDI) de mama na população feminina do Recife atendida no Hospital das Clínicas (HCUFPE). Cinquenta biópsias de mama diagnosticadas com CDI fixadas em formalina e embebidas em parafina foram obtidas do Setor de Anatomia Patológica do HC-PE e cinco amostras de tecido mamário de mulheres submetidas à mastectomia estética foram usadas como controle normal. O DNA das amostras foram extraídos e, então, amplificados por MSP. Para avaliação do perfil mutacional utilizou-se a técnica de PCR-RFLP (Restriction Fragment Length Polymorphism) com as enzimas BstUI e HaeIII para verificação dos polimorfismos nos exons 4 e 7, respectivamente. A frequência no padrão de metilação para o gene BRCA2 foi de 46,9% enquanto a frequência de mutações pontuais nos códons 72 (exon 4) e 249 (exon 7) do gene p53 foram de 91,8% e 8,1%, respectivamente. Para o BRCA1 os resultados obtidos foram inconsistentes quanto ao seu padrão de metilação. Os resultados mostraram que o polimorfismo do códon 72 apresentou-se estatisticamente significante para metástase podendo ser utilizado como um potencial biomarcador auxiliar no diagnóstico de carcinoma ductal invasivo de mama humana.

Abstract In the present study, mutations in BRCA1 and BRCA2, the two major genes predisposing individuals to hereditary breast and ovarian cancer, were screened in Finnish and Turkish cancer families. Germline BRCA1 mutations were found in 7% (6/88) and BRCA2 mutations in 6% (5/88) of the Finnish families studied in Oulu. Two distinct BRCA1 (3745delT, 4216nt-2A→G) and three BRCA2 (999delTCAAA, 6503delTT, 9346nt-2A→G) mutations were identified, all of which are recurrently found in Finland. In the 15 Turkish cancer families studied, 5382insC and 5622C→T were detected in BRCA1, and 3414delTCAG in BRCA2. The novel 3414del4 mutation was found in a family with a case of male breast cancer. In order to determine their ages and origin, 9 recurrent Finnish BRCA1 and BRCA2 mutations were studied further as regards haplotype conservation. Common origins approximately 18–80 generations (400–1600 years) ago were demonstrated for all studied mutations by partial haplotype sharing. The majority of the mutations showed geographical clustering, supporting the theory of regional founder effects. Four of the nine mutations are unique for Finland, whereas five have also been seen elsewhere. Mutations in the 5' end of BRCA1 tend to predispose individuals to ovarian cancer and those found in the 3' end to breast cancer. The age of ovarian cancer onset was significantly lower for BRCA1 (51 years) than for BRCA2 mutation carriers (61 years). Germline TP53 mutations were sought in the Finnish breast cancer families found to be negative after BRCA1 and BRCA2 screening but who exhibited some phenotypic features of the Li-Fraumeni syndrome. The Asn235Ser was found in a family displaying Li-Fraumeni syndrome phenotype and the Tyr220Cys in a family with a milder Li-Fraumeni-like phenotype. The nature of both mutations as cancer-predisposing alterations was supported by means of loss of heterozygosity (LOH) and p53 immunohistochemistry studies. Regional clustering of BRCA1 and BRCA2 founder mutations enables targeted genetic tests including especially those mutations characteristic of the birthplace of each patient. Additional genes are likely to explain a large proportion of the inherited susceptibility to breast cancer in particular. Germline TP53 mutations are expected to be found in the breast cancer families with other clinical features seen in the Li-Fraumeni syndrome.

Germ-line mutations within the breast cancer susceptibility genes, BRCA1 and BRCA2 are responsible for inherited susceptibility to breast and ovarian cancer. A wide spectrum of pathogenic mutations has been identified within both genes, but alterations within these genes occur far less frequently than originally believed. A large number of breast cancer families that showed linkage to BRCA1 were not found to carry a pathogenic BRCA1 mutation following the use of “classical” PCR based assays. In 1997, a large genomic rearrangement was reported within BRCA1, using Southern blotting. Numerous groups then employed semi-/quantitative methods to determine the presence and/or frequency of such alterations. This search extended the mutation spectrum of this gene, and to date at least 69 unique rearrangements have been reported. The contribution of these alterations to the burden of breast/ovarian cancer differs greatly between populations ranging from 0% to 36% of all BRCA1 mutations in the Finnish and Dutch populations respectively. Mutation screening has previously indicated that small mutations within the two BRCA genes are responsible for 59% of breast/ovarian cancer susceptibility in South Africa. To determine whether large rearrangements contribute to breast cancer susceptibility in South Africa, 74 BRCA1/2 small mutation negative patients from 58 breast / ovarian cancer families were screened for large intragenic BRCA1 rearrangements using Multiplex Ligation-dependent Probe Amplification (MLPA). In this first study of large genomic rearrangements within BRCA1 in South Africa, three genomic aberrations were detected. A deletion of exon 22 (IVS21-36del510) was identified in a Dutch immigrant. This deletion represents one of the Dutch founder mutations. Both exons 23 and 24 were found deleted in a South African family of Greek ancestry. The breakpoints of this deletion were not characterized. Simultaneous deletions of these two exons (where the breakpoints could not be characterized) have been reported in the Italian and Spanish populations. One of the genomic aberrations detected by MLPA in the present study erroneously appeared as a deletion of exon 18. Sequence analysis of this variant identified it as a single base pair substitution (c.5215G_A). This variant (R1699Q) has been reported previously, but its pathological significance is unconfirmed. In total, two large genomic rearrangements were detected in two families, of which only one is a South African, of Greek ancestry. This indicates that such mutations play a small role (1.75%; 1/57) in familial breast / ovarian cancer in South Africa (Dutch immigrant excluded). No rearrangements were identified in the Afrikaner population, indicating that such mutations do not contribute to the burden of familial breast/ovarian cancer in this population (0/40). The remaining South African breast/ovarian cancer risk may to some extent be explained by large rearrangements within BRCA2, or by mutations in other low penetrance breast cancer susceptibility gene(s). BRCA2 will now be screened by MLPA, followed by mutation screening of genes such as p53 and CHEK2 in high-risk families. / Dissertation (MSc)--University of Pretoria, 2011. / Genetics / unrestricted

No description available.

Clinical trials are currently exploring the combinations of P ARP inhibitors and immunotherapies in the treatment of ovarian cancer, but their effects on the ovarian tumour microenvironment (TME) remain unclear. Here, we investigate how olaparib, PD-L1 monoclonal antibodies and their combination can influence TME composition and survival of tumour-bearing mice. We further explored how BRCA mutations can influence the response to therapy. Olaparib and combination therapies similarly improved the median survival of Brca1- and Brca2-deficient tumour-bearing mice. Anti-PD-L1 monotherapy improved the survival of mice with Brca1-null tumours, but not Brca2-null tumours. A detailed analysis of the TME revealed that the olaparib monotherapy resulted in a large number of immunosuppressive and immunomodulatory effects in the more inflamed Brca1-deficient TME but not Brca2-deficient tumours. Anti-PD-L1 treatment was mostly immunosuppressive, resulting in a systemic reduction of cytokines and a compensatory increase of PD-L1. The results of the combination therapy generally resembled the effects of one or both of the monotherapies, along with unique changes observed in certain immune populations. In-silico analysis of RNA-seq also revealed numerous differences between Brca-mutated tumour models. In summary, these findings shed light on the influence of novel therapeutics and BRCA mutations on the ovarian TME.

No description available.

The research presented in this thesis aims to uncover the intricate manner in which BRCA1 interacts with RNAP II during mRNA production utilizing a unique microchip system developed in our lab. We were first able to prove the effectiveness of our tunable system using a breast cancer model of patient derived triple negative breast cancer (TNBC) cells. Here we switched out different mammalian antibodies and collected images of the same structure from different angles. This served many purposes: (1) it proved the system could be tuned for specific uses; (2) it demonstrated that all subunits were present in the complex; (3) it eliminated the need for the tilt function allowing for a less intensive computational procedure. In the BRCA1 wild type cell line we were able to incorporate into our 3D reconstruction, atomic models of the BRCA1-BARD1 heterodimer and the RNAP II core in regions of major unoccupied density. Other areas of minor missing density were overlaid with a short strand of DNA and ubiquitin moieties, which proved agreement with Co-IPs. Next we sought to compare the wild type structure with a BRCA1 mutant variety. Using these techniques, we determined the 3D structure of the mutated complex. After further analysis slight differences were detected between the two complexes, especially in the placement of the atomic models. Overall we were able to determine structural abnormalities that occur when a mutation is present in BRCA1 that may have future applications for targetable therapy in TNBC patients. Moreover, by using TNBC as the disease model, we have created a platform that can be used to evaluate other human diseases due to the tunable nature of our microchip system. / Master of Science

BRCA1 est l’un des deux gènes majeur de prédisposition au cancer du sein. Les multiples partenaires protéiques de BRCA1 lui confèrent de nombreuses fonctions par lesquelles elle peut assurer la surveillance de l’intégrité cellulaire. L’équipe dans laquelle j’ai mené ma thèse a identifié un nouveau partenaire protéique de BRCA1, la protéine de liaison au poly(A) des ARN messagers PABP1, et a ainsi mis en lumière l’implication de BRCA1 dans la régulation de la traduction [1]. Durant ma thèse, j’ai étudié cette nouvelle fonction de BRCA1 et essayé de comprendre si, et comment, elle pourrait contribuer à son rôle de suppresseur de tumeur. J’ai tout d’abord montré que BRCA1 est associée avec la fraction ribosomique des cellules, et plus particulièrement à la fraction subpolysomique, ce qui pourrait indiquer sa participation à l’initiation de la traduction. De plus, nos résultats indiquent que BRCA1 pourrait participer à un complexe non canonique d’initiation de la traduction. Dans la mesure où BRCA1 n’est pas un facteur canonique d’initiation de la traduction, il est peu probable qu’elle intervienne dans la traduction de tous les ARNm. Notre hypothèse est qu’elle pourrait réguler la traduction d’ARNm spécifiques codant pour des protéines impliquées dans ses différentes fonctions de surveillance de l’intégrité cellulaire. Afin d’identifier les cibles traductionnelles de BRCA1, j’ai réalisé une analyse transcriptomique comparative du contenu des polysomes de cellules épithéliales mammaires MCF7 exprimant de façon transitoire un ARN interférent dirigé contre BRCA1 ou contrôle. Parmi les ARNm cibles de l’activité traductionnelle de BRCA1, beaucoup codent effectivement pour des protéines impliquées dans les fonctions auxquelles elle participe. Ce travail confirme que la participation de BRCA1 à la régulation de la traduction pourrait être une autre voie par laquelle BRCA1 exerce son rôle de suppresseur de tumeur. De plus, l’analyse des cibles traductionnelle de BRCA1 pourrait conduire à l’identification de nouvelles fonctions de cette protéine ainsi qu’à la découverte de marqueurs tumoraux ou de cibles thérapeutiques pour les patients porteurs d’une mutation de BRCA1 / BRCA1 is one of the two major genes of breast cancer susceptibility. The numerous binding partners of BRCA1 allow it to participate to several cellular pathways which globally contribute to its cell surveillance capacity. The team in which I performed my PhD identified a new bindind partner of BRCA1, the Poly(A)-Binding Protein 1 and, consequently, a new function of this tumor suppressor, namely, the translation regulation [1]. During my PhD, I studied this new function and try to elucidate if, and how, this function could participates to the BRCA1’s tumor suppressive activity. I first showed that BRCA1 is associated with the ribosomal fraction of the cell, and more precisely, with the subpolysomal fraction, which could indicate that BRCA1 participates to the initiation step of translation. Moreover, our results suggest that BRCA1 could participate to a non canonical initiation complex. Given that BRCA1 is not a canonical translation initiation factor, it is unlikely that BRCA1 regulates the translation of all mRNAs. Our hypothesis is that BRCA1 could regulate the translation of specific mRNAs involved in its various cell surveillance functions. In an attempt to identify the BRCA1 translational targets, we performed a microarray analysis of polysomes-bound mRNAs in MCF7 cells transiently expressing siRNA directed against BRCA1 or control siRNA. We found that, among the translational targets of BRCA1, many indeed encode proteins involved in the same main functions as BRCA1’s. Altogether, our results suggest that the involvement of BRCA1 in translation regulation could be another way by which BRCA1 exerts its tumor suppressor role. Moreover, the analysis of the BRCA1’s translational targets could lead to the identification of new functions for BRCA1 as well as to the discovery of new tumoral markers and therapeutic targets for the BRCA1 mutated patients

Le macrosatellite RNU2 est constitué de répétitions en tandem d'une unité de 6,1 kb. Largement étudié pendant les années 1980 et 1990, il est maintenant oublié des études pan-génomiques du fait de son absence du génome de référence. J'ai dans un premier temps finement caractérisé ce macrosatellite, en réalisant un assemblage in silico de la région génomique, en développant un code-barres pour la technique de peignage moléculaire et en analysant les données du projet 1000 Génomes. J'ai ainsi validé la localisation du locus RNU2 124 kb en amont de BRCA1, et affiné les données de polymorphisme en montrant que le nombre allélique de copies pouvait varier entre 5 et 82 chez 42 individus. J'ai tiré profit de sa localisation au sein d'un large bloc de déséquilibre de liaison pour définir le taux de mutation de ce macrosatellite à l'origine du nombre important d'allèles identifiables au sein de la population générale. Compte tenu de sa proximité avec BRCA1 et de son fort taux de polymorphisme, j'ai étudié le nombre global de copies du CNV dans 2 cohortes de cas de cancer du sein et témoins associés. J'ai montré que le nombre global de copies est significativement plus élevé chez les cas que chez les témoins. Ce travail suggère que le nombre de copies du macrosatellite RNU2 pourrait être impliqué dans la prédisposition génétique au cancer du sein, impliquant ainsi pour la première fois un CNV dans un mécanisme d'inactivation d'un gène de prédisposition au cancer / The RNU2 macrosatellite is composed by tandem repeats of a 6.1 kb-long unit. Extensively studied during the 1980’s and the 1990’s, this locus is now omitted from genome-wide analysis as a result of its absence from the human reference genome. Firstly, I finely characterized this macrosatellite by performing an in silico assembly of this genomic region, by designing a barcode for the molecular combing technique and by analyzing the 1,000 Genomes data. I thus validated the localization of the RNU2 locus 124 kb upstream of BRCA1, and refined the polymorphism data by showing that the allelic copy number ranged from 5 to 82 in 42 individuals. I took advantage of its localization in a large disequilibrium block to determine the mutation rate of this macrosatellite, responsible for the high number of alleles found in the general population. Considering its close proximity to BRCA1 and its high level of polymorphism, I studied the global copy number in 2 cohorts of breast cancer cases and controls. I thus showed that the RNU2 global copy number is significantly higher in breast cancer cases than in controls. My work suggests that the RNU2 macrosatellite copy number could be involved in breast cancer genetic predisposition. This would provide the first example of one inactivating mechanism of a cancer predisposing gene by a macrosatellite

Cerca de 10% dos casos de câncer de mama e/ou ovário são caracterizados como hereditários, onde a presença de mutações germinativas no gene de suscetibilidade BRCA1 aumenta o risco de desenvolver esses cânceres durante a vida da mulher. O BRCA1 é um gene supressor tumoral envolvido na resposta de danos ao DNA, controle do ciclo celular, na remodelação da cromatina, ubiquitinação e regulação da transcrição. O presente estudo tem como objetivo central caracterizar as mutações do gene BRCA1 associadas a Síndrome Hereditária do Câncer de Mama e/ou Ovário (HBOC) em pacientes atendidos no Serviço de Aconselhamento Genético do Câncer do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (HCFMRP/USP). Os vinte e dois éxons codificantes do BRCA1 foram analisados utilizando o método de High Resolution Melting (HRM) para triagem de mutações pontuais, seguido pelo sequenciamento de DNA dos casos selecionados para validação. A técnica de MLPA (Multiplex Ligation-dependent Probe Amplification) também foi usada para detectar grandes deleções e duplicações. Uma vez confirmada a mutação, membros da família considerados de alto risco, serão investigados para a mutação específica, a fim de proporcionar-lhes um aconselhamento genético apropriado para a detecção precoce do câncer. No presente estudo, foram investigados 41 pacientes que preencheram os critérios para o teste genético de acordo com NCCN Clinical Practice Guidelines in Oncology v.1.2010. Um total de 21 mutações foram identificadas, duas das quais são patogênicas: a deleção dos éxons 17-18 e a deleção dos éxon 19. Ambas estão localizadas no domínio BRCT do gene BRCA1, essencial para a ligação de fosfoproteínas críticas para a ativação do complexo de reparo do DNA. Outra mutação, a S616del, foi tratada como patogênica, mas apresenta informações controversas em diferentes estudos. O trabalho também identificou uma nova mutação, Val1117Ile. Um estudo de haplótipos das mutações identificadas nos pacientes foi realizado e revelou que um dos haplótipos, denominado de 6, contendo quatro resíduos mutados (871Leu, 1038Gly, 1183Arg e 1613Gly) estava presente em 50% das pacientes. O estudo de associação com 82 indivíduos saudáveis, mostrou diferença significativa (p=0,026) nos pacientes, sugerindo assim um risco aumentado de HBOC. Adicionalmente, foi analisada a mutação germinativa R337H no gene p53 para os casos suspeitos de Síndrome de Li-Fraumeni. Em síntese, o presente estudo contribui com a identificação de uma nova mutação não-sinônina no gene BRCA1 e sugere que o haplótipo 871Leu-1038Gly-1183Arg-1613Gly possa conferir risco aumentado do câncer de mama e/ou ovário em pacientes diagnosticados com HBOC. / About 10% of cases of breast and/or ovary cancer are characterized as hereditary, where the presence of germline mutations in susceptibility BRCA1 gene increases the risk of developing these cancers during womans lifetime. BRCA1 is a tumor suppressor gene involved in DNA damage response, cell cycle control, chromatin remodeling, ubiquitination and transcriptional regulation. The present study aims to characterize BRCA1 gene mutations associated with Hereditary Breast/Ovary Cancer Syndrome (HBOC) in patients from the Cancer Genetic Counseling Service of the General Hospital of the Medical School of Ribeirão Preto, University of São Paulo (HCFMRP-USP). The twenty two coding exons of BRCA1 were analyzed using High Resolution Melting (HRM) method for the screening of point mutations, followed by DNA sequencing of the cases selected to validation. MLPA (Multiplex Ligation-dependent Probe Amplification) technique was also used to detect gross deletions and duplications. Once confirmed the mutation, family members most at risk will be analyzed for the specific mutation in order to provide them with an appropriate genetic counseling for early detection of cancer. In the present study, we investigated 41 patients that fulfilled the criteria for genetic testing according to NCCN Clinical Practice Guidelines in Oncology v.1.2010. A total of 21 mutations were identified, two of them are pathogenic: a deletion of exons 17-18 and a deletion of exon 19. Both of them are located in the BRCT domain of BRCA1 gene, impairing the binding of essential phosphoproteins critical to the activation of DNA repair complex. Another mutation, S616del, shows controversial information about its pathogenesis in different studies.The present study also describes a new mutation, Val1117Ile. A study of haplotypes of the mutations identified in patients was performed and revealed that one of the haplotypes, called 6, containing four mutated residues (871Leu, 1038Gly, and 1183Arg 1613Gly) was present in 50% of patients. The association study with 82 healthy subjects showed a significant difference (p = 0.026) in patients, thus suggesting an increased risk for HBOC. Additionally, the germline mutation R337H on p53 gene was also analyzed in the present study for suspected cases of Li-Fraumeni Syndrome. In summary, this study contributes to the identification of a new missense mutation in the BRCA1 gene and suggests that the haplotype-871Leu-1038Gly 1183Arg-1613Gly may confer increased risk of breast cancer and / or ovarian cancer in patients diagnosed with HBOC.