Copy number variations (CNVs) are a major source of inter-individual genetic difference, accounting for a greater proportion of the human genome than other forms of variation. Recently, the identification of benign and pathogenic CNVs has improved due to arrays with increased coverage. Nevertheless, most CNVs have not been studied with great precision and questions persist regarding their exact breakpoint, gene content, frequency and functional impact. This is especially true in cancer, in which a role for CNVs as risk factors is under-explored. Li-Fraumeni syndrome (LFS) is a dominantly inherited disorder with an increased risk of early-onset breast cancer, sarcomas, brain tumors and other neoplasms in individuals harboring germline TP53 mutations. Known genetic determinants of LFS do not fully explain its clinical phenotype. In this thesis we describe the association between CNVs and LFS. First, by examining DNA from a healthy population and an LFS cohort using oligonucleotide arrays, we show that the number of CNVs per genome is well conserved in the healthy population, but remarkably enriched in these cancer-prone individuals. We found a significant increase in CNVs among carriers of germline TP53 mutations with a familial cancer history. Second, we find that ii specific CNVs at 17p13.1 are associated with LFS or developmental delay, depending on the exact breakpoint with respect to TP53. Using a purpose built array with 93.75% accuracy, we fine-mapped these microdeletions and find that they arise by Alu-mediated non-allelic homologous recombination, and contain common genes, whose under-expression distinguishes the two phenotypes. Third, we explore somatic CNVs in choroid plexus carcinoma tumor genomes. We show that this tumor is over-represented in LFS, and the number of somatic CNVs is associated with TP53 mutations and disease progression. These studies represent the first genomic analyses of LFS, and suggest a more generalized association between CNVs and cancer.

Introdução: O câncer de mama é a neoplasia mais freqüente e também a principal causa de morte por câncer entre as mulheres. O gene TP53 é polimórfico no códon 72 da proteína que ele codifica, podendo conter arginina (CGC) ou prolina (CCC) nesta posição. Este polimorfismo pode estar envolvido na suscetibilidade e predisposição ao câncer e apresenta uma distribuição étnica e geográfica bastante variável. O genótipo homozigoto para arginina parece ser um fator de risco e prognóstico significativo para o câncer de mama. Métodos: Extraído DNA a partir do sangue periférico de 76 pacientes consecutivas com carcinoma ductal invasor (CDI), tratadas no Serviço de Mastologia do HCPA, em qualquer estágio da doença. 80 amostras de DNA do grupo controle de doadores saudáveis do Banco de Sangue do HCPA foram incluídas de forma aleatória. Foram coletados dados demográficos e dados das características clínicas e histopatológicas e realizada a amplificação do éxon 4 do gene TP53 através da PCR, seguida da identificação do polimorfismo R72P do éxon 4 pela digestão do produto de PCR com a enzima de restrição BstUI, a qual reconhece o sítio de clivagem CG↓CG.Os objetivos foram determinar as freqüências alélicas e genotípicas do polimorfismo R72P nas pacientes com carcinoma de mama ductal invasor, comparando-as com as freqüências no grupo controle e relacionar a presença deste polimorfismo com características clínicopatológicas. Resultados: A distribuição dos genótipos no códon 72 do gene TP53, tanto em pacientes como em controles, encontra-se em equilíbrio de Hardy- Weinberg. A freqüência encontrada para o polimorfismo R72P foi similar entre as pacientes com CDI e os controles, não sendo encontrada diferença significativa na freqüência do genótipo (P = 0,707) e na freqüência alélica (P = 0,469). Conclusões: O polimorfismo R72P no gene TP53 não se associou a maior risco de desenvolvimento de CDI na população estudada. Este achado pode estar relacionado à grande variação inter-racial e étnica em nossa população, decorrente de freqüentes miscigenações e exposição a diferentes fatores ambientais, importantes na evolução do carcinoma de mama. Não houve associação com características clínico-patológicas. / Introduction: Breast cancer is the most frequent neoplasia as well as the main cause of death from cancer among women. The TP53 gene is polymorphic in codon 72 of the protein it encodes, and may contain either arginine (CGC) or proline (CCC) in that position. Such polymorphism may be involved in the susceptibility and predisposition for cancer presenting with a widely variable ethnic and geographic distribution. The arginine homozygous genotype seems to be a significant risk factor and prognostic for breast cancer. Methods: DNA was extracted from peripheral blood of 76 patients suffering from invasive ductal carcinoma (IDC) treated at the HCPA Mastology Service at any stage of the disease. Eigthy healthy controls from the Blood Bank Donors of HCPA were included randomly. Demographic data were collected as well as data from the clinic and histopathological characteristics. Amplification of exon 4 from the TP53 gene was performed through PCR, followed by digestion of the PCR product with the restriction enzyme BstUI, which recognizes the CG↓CG cleavage site, for identification of the R72P polymorphism of exon 4. The objectives were to determine the allele and genotype frequencies of R72P polymorphism in patients suffering from invasive ductal breast carcinoma, comparing with the control group and to corelate the presence of that polymorphism with clinical pathological characteristics. Results: The distribution of genotypes in codon 72 of gene TP53, both for patients and controls was in Hardy-Weinberg equilibrium. The frequency found for R72P polymorphism was similar between IDC patients and controls, with no significant difference being found in the genotype frequency (P = 0.707) and allele frequency (P = 0.469). Conclusions: R72P polymorphism in the TP53 gene was not associated to an increased risk of developing IDC in the population studied. This finding may be related to the great interracial and ethnic variation in our population deriving from frequent miscigenations and exposure to different environmental factors that are important in the evolution of breast cancer. There was also no association with clinical pathological characteristics.

Introdução: As síndromes de Li-Fraumeni (LFS) e Li-Fraumeni Like (LFL) são síndromes hereditárias de predisposição a câncer frequentemente associadas à mutações germinativas no gene TP53. Devido à importância de p53 e diversidade de processos celulares que ela regula, várias vias de sinalização podem ser afetadas pela doença. Nesse estudo discutimos o impacto da mutação p.R337H na proliferação, senescência, autofagia, população e funcionalidade mitocondrial. Métodos: As taxas de proliferação foram avaliadas pelo ensaio de Population Doubling. Os experimentos de senescência, autofagia, massa total e funcionalidade mitocondrial foram realizados por citometria de fluxo. Resultados: As células contendo a mutação proliferaram mais do que as células controle. Além disso, as células mutadas não ativaram autofagia sob tratamento de Rapamicina nem senescência sob tratamento de Doxorubicina ou Cisplatina e exibiram maior população mitocondrial, mas com funcionalidade inalterada após os tratamentos. Conclusão: os dados sugerem que a mutação p.R337H em TP53 afeta a indução de senescência realizada por p53 e suas funções pró-autofágicas, bem como seu controle. As células mutadas proliferam mais do que células sem mutação em TP53 e exibiram maior massa mitocondrial sem perda de funcionalidade após o tratamento com Doxorubicina. / Background: Li-Fraumeni (LFS) and Li-Fraumeni Like (LFL) syndromes are hereditary cancer predisposition syndromes frequently associated with germline mutation in TP53. Due to the importance of the protein p53 and its regulation of several important cellular processes, impairment in some pathways can be implicated. Here we discuss the impact of p.R337H TP53 mutation on proliferation, senescence, autophagy, mitochondrial population and functionality. Methods: Growth rates were assayed with Population Doubling assay. Senescence and autophagy were assessed through flow cytometry and functionality and total population of mitochondria were also analyzed through flow cytometry. Results: mutated cells proliferated more than control cells. TP53 mutated cells didn’t build up autophagy under Rapamycin treatmend nor senescence under Doxorubicin or Cisplatin treatments and showed more mitochondrial mass, but no alterations in mitochondrial functionality after Doxorubicin treatment. Conclusion:data suggests that p.R337H TP53 mutation affect senescence induction by p53 and pro-autophagic actions of p53. Mutated cells proliferate more than control cells and exhibited larger mitochondrial mass without effects in their functionality in response to Doxorubicin treatment.

Introdução: O câncer de mama é a neoplasia mais freqüente e também a principal causa de morte por câncer entre as mulheres. O gene TP53 é polimórfico no códon 72 da proteína que ele codifica, podendo conter arginina (CGC) ou prolina (CCC) nesta posição. Este polimorfismo pode estar envolvido na suscetibilidade e predisposição ao câncer e apresenta uma distribuição étnica e geográfica bastante variável. O genótipo homozigoto para arginina parece ser um fator de risco e prognóstico significativo para o câncer de mama. Métodos: Extraído DNA a partir do sangue periférico de 76 pacientes consecutivas com carcinoma ductal invasor (CDI), tratadas no Serviço de Mastologia do HCPA, em qualquer estágio da doença. 80 amostras de DNA do grupo controle de doadores saudáveis do Banco de Sangue do HCPA foram incluídas de forma aleatória. Foram coletados dados demográficos e dados das características clínicas e histopatológicas e realizada a amplificação do éxon 4 do gene TP53 através da PCR, seguida da identificação do polimorfismo R72P do éxon 4 pela digestão do produto de PCR com a enzima de restrição BstUI, a qual reconhece o sítio de clivagem CG↓CG.Os objetivos foram determinar as freqüências alélicas e genotípicas do polimorfismo R72P nas pacientes com carcinoma de mama ductal invasor, comparando-as com as freqüências no grupo controle e relacionar a presença deste polimorfismo com características clínicopatológicas. Resultados: A distribuição dos genótipos no códon 72 do gene TP53, tanto em pacientes como em controles, encontra-se em equilíbrio de Hardy- Weinberg. A freqüência encontrada para o polimorfismo R72P foi similar entre as pacientes com CDI e os controles, não sendo encontrada diferença significativa na freqüência do genótipo (P = 0,707) e na freqüência alélica (P = 0,469). Conclusões: O polimorfismo R72P no gene TP53 não se associou a maior risco de desenvolvimento de CDI na população estudada. Este achado pode estar relacionado à grande variação inter-racial e étnica em nossa população, decorrente de freqüentes miscigenações e exposição a diferentes fatores ambientais, importantes na evolução do carcinoma de mama. Não houve associação com características clínico-patológicas. / Introduction: Breast cancer is the most frequent neoplasia as well as the main cause of death from cancer among women. The TP53 gene is polymorphic in codon 72 of the protein it encodes, and may contain either arginine (CGC) or proline (CCC) in that position. Such polymorphism may be involved in the susceptibility and predisposition for cancer presenting with a widely variable ethnic and geographic distribution. The arginine homozygous genotype seems to be a significant risk factor and prognostic for breast cancer. Methods: DNA was extracted from peripheral blood of 76 patients suffering from invasive ductal carcinoma (IDC) treated at the HCPA Mastology Service at any stage of the disease. Eigthy healthy controls from the Blood Bank Donors of HCPA were included randomly. Demographic data were collected as well as data from the clinic and histopathological characteristics. Amplification of exon 4 from the TP53 gene was performed through PCR, followed by digestion of the PCR product with the restriction enzyme BstUI, which recognizes the CG↓CG cleavage site, for identification of the R72P polymorphism of exon 4. The objectives were to determine the allele and genotype frequencies of R72P polymorphism in patients suffering from invasive ductal breast carcinoma, comparing with the control group and to corelate the presence of that polymorphism with clinical pathological characteristics. Results: The distribution of genotypes in codon 72 of gene TP53, both for patients and controls was in Hardy-Weinberg equilibrium. The frequency found for R72P polymorphism was similar between IDC patients and controls, with no significant difference being found in the genotype frequency (P = 0.707) and allele frequency (P = 0.469). Conclusions: R72P polymorphism in the TP53 gene was not associated to an increased risk of developing IDC in the population studied. This finding may be related to the great interracial and ethnic variation in our population deriving from frequent miscigenations and exposure to different environmental factors that are important in the evolution of breast cancer. There was also no association with clinical pathological characteristics.

Fundação de Amparo a Pesquisa do Estado de Minas Gerais / The prostate gland can be assaulted by many pathologies. Among them the prostate cancer is the 2nd death cause on men older than 50 years old. Although the etiology of this disease is not well comprehended, the genetic alterations and the presence of infectious agents have been suggested as associated to the development of this cancer. One of the most frequent genetic alterations on the cancers are the ones related to the tumor suppressor gene TP53, responsible for the cell cycle control and apoptosys. In the beginning of the 90s, many works also arose on the attempt to establish a relationship between the human papilloma virus (HPV) infection and the prostate cancer. Within this context, this work had as objectives, to evaluate the HPV prevalence, to analyze the Arg72 Pro polymorphism, to associate this polymorphism to the HPV presence and to track for mutations n the exons 5 to 8 of the PT53 gene in patients presenting prostate cancer. 36 prostatic tissues were analyzed, seeing that these proceeding were from adenocarcinomas, BPH and PIN and peripheral blood of some of these patients, as well as of a group of men randomly chosen on the population. The techniques used for the HPV detection and typing were the PCR and nested PCR. For the Arg72Pro polymorphism analysis and for the tracking of mutations, the PCR and LIS-SSCP techniques were used. There were no differences on the frequencies of the Arg72Pro polymorphism between the BPH and PCa tissues (p=0,36; 95% reliance interval). The frequencies obtained on the blood of some patients with prostatic pathologies also did not differed significantly, whereas the BPH group did not differ from the PCa group (p=0,72, xviii 95% reliance interval), nor this from the frequency found on the population (p=0,08, 95% reliance interval). It was detected Loss of Heterozigosity (LOH) in 9 (34,61%) patients that lost the Pro allele, becoming Arg/Arg. Among these individuals, 5 (35,71%) belonged to the cancer group, 3 (37,5%) to the BPHs and 1 (25%) to the PINs. Among the 36 analyzed patients for the HPV infection, by means of PCR and nested PCR, only 2 (5,55%) presented positivity for HPV types 16 and 39. The t Test, showed that there were no significant differences for the HPV presence among the samples obtained by TUR and radical prostatectomy, nor among the malignant and benignant analyzed tissues. The positive patients for the HPV infection presented an homozygous genotype for arginine, however, the low prevalence of this infection did not allow an association to the Arg 72Pro polymorphism. A possible mutation was detected on the exon 6 in one patient with prostate cancer. In this manner, the low prevalence of the HPV infection, and the nonassociation of this with the Arg72Pro polymorphism as well as the rare frequency of mutations on the analyzed exons suggest that these would not be the essential mechanisms for the prostate cancer development. However, the LOH event could be associated to the progression or development of this tumor, being a precocious or intermediate event, yet not obligatory. More detailed and amplified studies should be done to clear these results, searching for directions to better comprehend the physiological procedures, which result on the genotype-environment association, on this affection. / A glândula próstata pode ser acometida por várias patologias. Dentre elas o câncer de próstata é a 4a causa de morte em homens com idade superior a 50 anos. Apesar da etiologia desta doença não ser bem compreendida, as alterações genéticas e a presença de agentes infecciosos têm sido sugeridas como associadas ao desenvolvimento desse câncer. Uma das alterações genéticas mais freqüentes nos cânceres são as relacionadas ao gene supressor de tumor TP53, responsável pelo controle do ciclo celular e apoptose. No início da década de 90, vários trabalhos também surgiram na tentativa de estabelecer relação entre a infecção pelo vírus do papiloma humano (HPV) e o câncer de próstata. Dentro deste contexto, este trabalho teve como objetivos avaliar a prevalência do HPV, analisar o polimorfismo Arg72Pro, associar este polimorfismo à presença do HPV e rastrear por mutações nos exons de 5 a 8 do gene TP53 em pacientes apresentando câncer de próstata. Foram analisados 36 tecidos prostáticos sendo estes provenientes de adenocarcinoma, HPB e NIP e sangues periféricos de alguns desses pacientes bem como de um grupo de homens escolhidos aleatoriamente na população. As técnicas utilizadas para detecção e tipagem do HPV foram a PCR e a PCR nested. Já para a análise do polimorfismo Arg72Pro e para o rastreamento de mutações foram utilizadas as técnicas de PCR e LIS-SSCP. Não houve diferenças das freqüências do polimorfismo Arg72Pro entre os tecidos com HPB e CaP (p=0,36; intervalo de confiança 95%). As freqüências obtidas nos sangues de alguns dos pacientes com patologias prostáticas também não diferiram significativamente, sendo que o grupo com HPB não diferiu do grupo CaP (p=0,72; xvi intervalo de confiança 95%), nem este da freqüência encontrada na população (p=0,08; intervalo de confiança 95%). Foram detectadas perda de heterozigose (LOH) em 9 (34,61%) pacientes que perderam o alelo Pro, ficando Arg/Arg. Desses indivíduos 5 (35,71%) pertenciam ao grupo do câncer, 3 (37,5%) ao grupo das HPBs e 1 (25%) ao grupo das NIPs. Dentre os 36 pacientes analisados para a infecção pelo HPV, por meio da PCR e PCRnested, apenas 2 (5,55%) apresentaram positividade para HPV do tipo 16 e 39. O Teste t, com nível de significância de 5%, mostrou não haver diferenças significativas para a presença do HPV entre as amostras obtidas por RTU e prostatectomia radical, nem entre os tecidos malignos e benignos analisados. Os pacientes positivos para a infecção do HPV apresentaram o genótipo homozigoto para arginina, entretanto, a baixa prevalência desta infecção não possibilitou associá-la ao polimorfismo Arg72Pro. Foi detectado um perfil eletroforético diferencial no exon 6 em um paciente com câncer de próstata. Desta forma, a baixa prevalência da infecção pelo HPV, a não associação desta com o polimorfismo Arg72Pro bem como a rara freqüência de mutações nos exons analisados sugere que estes não seriam mecanismos essenciais para desenvolvimento do câncer de próstata. Entretanto, o evento de LOH pode estar associado à progressão ou desenvolvimento deste tumor, sendo um evento precoce ou intermediário, porém não obrigatório. Estudos mais detalhados e ampliados devem ser realizados para compreender melhor os processos fisiológicos, que resultam da associação genótipo ambiente, nesta afecção. / Mestre em Genética e Bioquímica

Introdução: As síndromes de Li-Fraumeni (LFS) e Li-Fraumeni Like (LFL) são síndromes hereditárias de predisposição a câncer frequentemente associadas à mutações germinativas no gene TP53. Devido à importância de p53 e diversidade de processos celulares que ela regula, várias vias de sinalização podem ser afetadas pela doença. Nesse estudo discutimos o impacto da mutação p.R337H na proliferação, senescência, autofagia, população e funcionalidade mitocondrial. Métodos: As taxas de proliferação foram avaliadas pelo ensaio de Population Doubling. Os experimentos de senescência, autofagia, massa total e funcionalidade mitocondrial foram realizados por citometria de fluxo. Resultados: As células contendo a mutação proliferaram mais do que as células controle. Além disso, as células mutadas não ativaram autofagia sob tratamento de Rapamicina nem senescência sob tratamento de Doxorubicina ou Cisplatina e exibiram maior população mitocondrial, mas com funcionalidade inalterada após os tratamentos. Conclusão: os dados sugerem que a mutação p.R337H em TP53 afeta a indução de senescência realizada por p53 e suas funções pró-autofágicas, bem como seu controle. As células mutadas proliferam mais do que células sem mutação em TP53 e exibiram maior massa mitocondrial sem perda de funcionalidade após o tratamento com Doxorubicina. / Background: Li-Fraumeni (LFS) and Li-Fraumeni Like (LFL) syndromes are hereditary cancer predisposition syndromes frequently associated with germline mutation in TP53. Due to the importance of the protein p53 and its regulation of several important cellular processes, impairment in some pathways can be implicated. Here we discuss the impact of p.R337H TP53 mutation on proliferation, senescence, autophagy, mitochondrial population and functionality. Methods: Growth rates were assayed with Population Doubling assay. Senescence and autophagy were assessed through flow cytometry and functionality and total population of mitochondria were also analyzed through flow cytometry. Results: mutated cells proliferated more than control cells. TP53 mutated cells didn’t build up autophagy under Rapamycin treatmend nor senescence under Doxorubicin or Cisplatin treatments and showed more mitochondrial mass, but no alterations in mitochondrial functionality after Doxorubicin treatment. Conclusion:data suggests that p.R337H TP53 mutation affect senescence induction by p53 and pro-autophagic actions of p53. Mutated cells proliferate more than control cells and exhibited larger mitochondrial mass without effects in their functionality in response to Doxorubicin treatment.

Introdução: O câncer de mama é a neoplasia mais freqüente e também a principal causa de morte por câncer entre as mulheres. O gene TP53 é polimórfico no códon 72 da proteína que ele codifica, podendo conter arginina (CGC) ou prolina (CCC) nesta posição. Este polimorfismo pode estar envolvido na suscetibilidade e predisposição ao câncer e apresenta uma distribuição étnica e geográfica bastante variável. O genótipo homozigoto para arginina parece ser um fator de risco e prognóstico significativo para o câncer de mama. Métodos: Extraído DNA a partir do sangue periférico de 76 pacientes consecutivas com carcinoma ductal invasor (CDI), tratadas no Serviço de Mastologia do HCPA, em qualquer estágio da doença. 80 amostras de DNA do grupo controle de doadores saudáveis do Banco de Sangue do HCPA foram incluídas de forma aleatória. Foram coletados dados demográficos e dados das características clínicas e histopatológicas e realizada a amplificação do éxon 4 do gene TP53 através da PCR, seguida da identificação do polimorfismo R72P do éxon 4 pela digestão do produto de PCR com a enzima de restrição BstUI, a qual reconhece o sítio de clivagem CG↓CG.Os objetivos foram determinar as freqüências alélicas e genotípicas do polimorfismo R72P nas pacientes com carcinoma de mama ductal invasor, comparando-as com as freqüências no grupo controle e relacionar a presença deste polimorfismo com características clínicopatológicas. Resultados: A distribuição dos genótipos no códon 72 do gene TP53, tanto em pacientes como em controles, encontra-se em equilíbrio de Hardy- Weinberg. A freqüência encontrada para o polimorfismo R72P foi similar entre as pacientes com CDI e os controles, não sendo encontrada diferença significativa na freqüência do genótipo (P = 0,707) e na freqüência alélica (P = 0,469). Conclusões: O polimorfismo R72P no gene TP53 não se associou a maior risco de desenvolvimento de CDI na população estudada. Este achado pode estar relacionado à grande variação inter-racial e étnica em nossa população, decorrente de freqüentes miscigenações e exposição a diferentes fatores ambientais, importantes na evolução do carcinoma de mama. Não houve associação com características clínico-patológicas. / Introduction: Breast cancer is the most frequent neoplasia as well as the main cause of death from cancer among women. The TP53 gene is polymorphic in codon 72 of the protein it encodes, and may contain either arginine (CGC) or proline (CCC) in that position. Such polymorphism may be involved in the susceptibility and predisposition for cancer presenting with a widely variable ethnic and geographic distribution. The arginine homozygous genotype seems to be a significant risk factor and prognostic for breast cancer. Methods: DNA was extracted from peripheral blood of 76 patients suffering from invasive ductal carcinoma (IDC) treated at the HCPA Mastology Service at any stage of the disease. Eigthy healthy controls from the Blood Bank Donors of HCPA were included randomly. Demographic data were collected as well as data from the clinic and histopathological characteristics. Amplification of exon 4 from the TP53 gene was performed through PCR, followed by digestion of the PCR product with the restriction enzyme BstUI, which recognizes the CG↓CG cleavage site, for identification of the R72P polymorphism of exon 4. The objectives were to determine the allele and genotype frequencies of R72P polymorphism in patients suffering from invasive ductal breast carcinoma, comparing with the control group and to corelate the presence of that polymorphism with clinical pathological characteristics. Results: The distribution of genotypes in codon 72 of gene TP53, both for patients and controls was in Hardy-Weinberg equilibrium. The frequency found for R72P polymorphism was similar between IDC patients and controls, with no significant difference being found in the genotype frequency (P = 0.707) and allele frequency (P = 0.469). Conclusions: R72P polymorphism in the TP53 gene was not associated to an increased risk of developing IDC in the population studied. This finding may be related to the great interracial and ethnic variation in our population deriving from frequent miscigenations and exposure to different environmental factors that are important in the evolution of breast cancer. There was also no association with clinical pathological characteristics.

As sÃndromes mielodisplÃsicas (SMD) representam um grupo heterogÃneo de doenÃas clonais que acometem a cÃlula precursora hematopoÃtica pluripotente, caracterizando-se por baixa contagem de cÃlulas no sangue perifÃrico, displasia em uma ou mais linhagens celulares, hematopoese ineficiente, alÃm do risco aumentado de progressÃo para leucemia mielÃide aguda. Embora a doenÃa possa acometer pacientes de outras faixas etÃrias, Ã mais frequente naqueles com idade avanÃada, com mÃdia ao diagnÃstico de 60 a 75 anos. As anormalidades cromossÃmicas sÃo observadas em aproximadamente 50% de todos os casos de SMD, estando, em alguns casos, relacionadas com achados clÃnicos e morfolÃgicos. O objetivo deste trabalho foi determinar, atravÃs da tÃcnica de FISH (hibridizaÃÃo in situ por fluorescÃncia), a frequÃncia de alteraÃÃes envolvendo os genes MLL, RB e TP53 em pacientes com SMD e associar estas alteraÃÃes com os achados citogenÃticos. Os casos inseridos no estudo foram oriundos do ambulatÃrio de SMD do Hospital UniversitÃrio Walter CantÃdio. Dos 33 pacientes selecionados, 17 pertenciam ao grupo com idade acima de 60 anos. 52% dos pacientes foram classificados, segundo a OMS, como citopenia refratÃria com displasia em mÃltiplas linhagens (CRDM) e 61% estratificados, segundo o IPSS, como de risco intermediÃrio 1 (INT-1). Um total de 78% dos pacientes apresentaram alteraÃÃes citogenÃticas, dentre eles 31% possuÃam cariÃtipos complexos (mais de 3 alteraÃÃes por metÃfase). A tÃcnica de FISH permitiu identificar em 18% dos pacientes alteraÃÃes envolvendo um dos trÃs genes avaliados. TrÃs pacientes apresentaram alteraÃÃo do gene TP53, sendo detectada em dois deles (registros 31 e 6) a deleÃÃo de um Ãnico alelo ou de ambos os alelos do gene, respectivamente, e no terceiro (registro 2), detectou-se a amplificaÃÃo do gene TP53, sendo estas alteraÃÃes nÃo visualizadas atravÃs da citogenÃtica clÃssica, por se tratar de um tÃcnica menos sensÃvel. Detectou-se em 6% dos pacientes (registros 7 e 22) rearranjo do gene MLL, no primeiro a FISH descartou a suposta deleÃÃo do gene alegada pela citogenÃtica, provando que o mesmo estava presente no genoma do paciente, porÃm de forma rearranjada e no segundo a citogenÃtica nÃo conseguiu demonstrar o rearranjo do gene. Quanto ao gene RB, a FISH permitiu identificar apenas um paciente (3%) com deleÃÃo de um dos alelos do gene, sendo esta alteraÃÃo tambÃm nÃo detectada pela citogenÃtica clÃssica. A FISH possibilitou identificar, durante a avaliaÃÃo do gene TP53, dois pacientes (registros 5 e 10) apresentando pelo menos 6 cÃpias extras do cromossomo 17, devendo essa alteraÃÃo se tratar de um pequeno clone hiperdiplÃide detectado parcialmente no primeiro paciente e nÃo detectado no segundo. Nos seis pacientes que apresentaram alteraÃÃo dos genes avaliados, a FISH proveu informaÃÃes que adicionaram, confirmaram ou alteraram o resultado previamente emitido pela citogenÃtica clÃssica, sendo estas uma das principais aplicaÃÃes desta tÃcnica devido sua alta sensibilidade quando comparada ao mÃtodo clÃssico. / Myelodysplastic syndromes (MDS) represent a heterogeneous group of clonal disorders affecting the hematopoietic pluripotent cell, characterized by low cell counts in peripheral blood, dysplasia in one or more cell lines, inefficient hematopoiesis and increased risk of progression to acute myeloid leukemia. Although the disease can affect patients of other age groups, they are more frequent in those with advanced age with an average 60 to 75 years at diagnosis. Chromosomal abnormalities are observed in approximately 50% of all cases of MDS and are related with clinical and morphological findings. The aim of this study was to determine, through the technique of FISH (fluorescence in situ hybridization), the frequency of changes involving the MLL, RB, and TP53 genes in patients with MDS and associate these changes with cytogenetic findings. The cases included in the study were selected in the ambulatory of SMD from University Hospital Walter CantÃdio. Thirty three patients were selected, 17 had aged over 60 years. 52% of patients were classified, according to WHO criteria, as refractory cytopenia with dysplasia in multiple lineages (RCDM) and 61% stratified, according to IPSS, as intermediate risk 1 (INT-1). 78% of patients had abnormalities detected by cytogenetics, among them 31% had complex karyotypes (more than 3 changes per metaphase). 18% of patients had changes at least in one of the three genes valued in this study by FISH. Three patients showed alterations of TP53 gene, being detected in two patients (records 31 and 6) the deletion of a single allele or both alleles of the gene, respectively, and in the third (record 2), we detected amplification of TP53 gene, all this changes were not detected by classical cytogenetics, because it is a less sensitive technique. 6% of patients (records 7 and 22) had rearrangement of MLL gene. In the first case, FISH discarded the gene deletion alleged by cytogenetic, proving that it was present in the genome of the patient, but in a rearranged form, and in the second case cytogenetics failed to demonstrate rearrangement of the gene. For the RB gene, FISH identified only one patient (3%) with deletion of one allele of the gene, and this change was also not detected by classical cytogenetics. During evaluating the TP53 gene, FISH allowed identification of two patients (records 5 and 10) presenting at least six extra copies of chromosome 17, probably representing a small hyperdiploid clone partially detected in the first patient and not detected in the second . In the six patients who showed abnormalities of the genes analyzed, FISH has provided information that added, changed or confirmed the result previously given by classical cytogenetics, which are a major application of this technique due to its high sensitivity compared to the traditional method.

abstract: Phenotypic and molecular profiling demonstrates a high degree of heterogeneity in the breast tumors. TP53 tumor suppressor is mutated in 30% of all breast tumors and the mutation frequency in basal-like subtype is as high as 80% and co-exists with several other somatic mutations in different genes. It was hypothesized that tumor heterogeneity is a result of a combination of neo-morphic functions of specific TP53 driver mutations and distinct co-mutations or the co-drivers for each type of TP53 mutation. The 10 most common p53 missense mutant proteins found in breast cancer patients were ectopically expressed in normal-like mammary epithelial cells and phenotypes associated with various hallmarks of cancer examined. Supporting the hypothesis, a wide spectrum of phenotypic changes in cell survival, resistance to apoptosis and anoikis, cell migration, invasion and polarity was observed in the mutants compared to wildtype p53 expressing cells. The missense mutants R248W, R273C and Y220C were most aggressive. Integrated analysis of ChIP and RNA seq showed distinct promoter binding profiles of the p53 mutant proteins different than wildtype p53, implying altered transcriptional activity of mutant p53 proteins and the phenotypic heterogeneity of tumors. Enrichment and model-based pathway analyses revealed dysregulated adherens junction and focal adhesion pathways associated with the aggressive p53 mutants. As several somatic mutations co-appear with mutant TP53, we performed a functional assay to fish out the relevant collaborating driver mutations, the co-drivers. When PTEN was deleted by CRISPR-Cas9 in non-invasive p53-Y234C mutant cell, an increase in cell invasion was observed justifying the concept of co-drivers. A genome wide CRISPR library-based screen on p53-Y234C and R273C cells identified separate candidate co-driver mutations that promoted cell invasion. The top candidates included several mutated genes in breast cancer patients harboring TP53 mutations and were associated with cytoskeletal and apoptosis resistance pathways. Overall, the combined approach of molecular profiling and functional genomics screen highlighted distinct sets of co-driver mutations that can lead to heterogeneous phenotypes and promote aggressiveness in cells with different TP53 mutation background, which can guide development of novel targeted therapies. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2019

Pancreatic ductal adenocarcinoma (PDAC) is a serious oncological disease, which ranks among cancers with the worst prognosis and a three-year life expectancy of 10%. Ex-vivo organoid cultures derived from cancer tissue are popular and reliable research models, which reflect the morphology and histology of the original tissue. Genetic background leading to development PDAC confer typical alterations in genes KRAS, TP53, SMAD4 a CDKN2A. The aim of this thesis was to determine mutations present in organoid cultures derived from human PDAC. We used online genomic databases to estimate specific mutations typical for PDAC. Based on that research we designed protocols for the detection of PDAC genetic alterations and optimized those methods using cultured cells. We applied the approach on primary ex- vivo organoids derived from surgical cancer specimens and detected mutations in KRAS, TP53, SMAD4, or deletion of exons in CDKN2A. Alternatively, we proposed improvements for the analysis of genetic background in PDAC. The data obtained within this thesis will be used for the stratification of metabolomics and biochemical analyses further in the project.