L'objectiu d'aquest tesi és avaluar els diferents passos en el camí que va des de l'exposició a contaminants atmosfèrics/PAHs fins a la malaltia, el càncer de bufeta urinària. Es van mesurar partícules ultrafines a Barcelona. S'ha avaluat l'exposició a contaminació atmosfèrica en un estudi cas-control, recollint informació sobre la història residencial incloent diversos indicadors de l'exposició a contaminació atmosfèrica i altres factors de risc potencials. Es va dur a terme una revisió sistemàtica de la literatura per avaluar si els nivells de metabòlits del pirè i els aductes d'ADN i de proteïnes es correlacionaven amb nivells baixos d'exposició a PAHs. Vam mesurar els nivells d'aductes d'ADN en un subgrup d'individus de l'estudi cas-control amb la tècnica del radioetiquetatge amb fòsfor-32, tractament de la nucleasa P1. Vam analitzar 22 SNPs en set gens de la via de reparació de l'ADN per excisió de nucleòtids. / The aim of this thesis is to evaluate the different steps in the pathway from exposure (air-contaminants/PAHs) to disease (bladder cancer). We measured ultrafine particles in Barcelona. We evaluated the exposure to air pollutants in a case-control study, collecting information on the residential history with proxies for exposure to air pollution and other potential risk factors. We did a systematic review of the literature to evaluate if pyrene metabolites and DNA and protein adducts are correlated with low level exposure to PAHs. We measured bulky DNA adducts in a subgroup of subjects of the case-control study using 32P-Postlabeling, nuclease P1 treatment. We analyzed 22 SNPs in 7 genes of the nucleotide excision repair pathway.

Methylmercury (MeHg) is a pervasive environmental contaminant with potent neurotoxic, teratogenic and likely carcinogenic activity, for which the underlying molecular mechanisms remain largely unclear. Base excision repair (BER) is important in mitigating the pathogenic effects of oxidative stress, which has also been implicated in the mechanism of MeHg toxicity, however the importance of BER in MeHg toxicity is currently unknown. Accordingly, we addressed this question using: (1) spontaneously- and Simian virus 40 (SV40) large T antigen-immortalized oxoguanine glycosylase 1-null (Ogg1-/-) murine embryonic fibroblasts (MEFs); and, (2) human Ogg1 (hOgg1)- or formamidopyrimidine glycosylase (Fpg)-expressing human embryonic kidney (HEK) cells; reciprocal in vitro cellular models with deficient and enhanced ability to repair oxidatively damaged DNA respectively. When spontaneously-immortalized wild-type and Ogg1-/- MEFs were exposed to environmentally relevant, low micromolar concentrations of MeHg, both underwent cell cycle arrest but Ogg1-/- cells exhibited a greater sensitivity to MeHg than wild-type controls with reduced clonogenic survival and increased apoptosis, DNA damage and DNA damage response activation. Antioxidative catalase alleviated the MeHg-initiated DNA damage in both wild-type and Ogg1-/- cells, but failed to block MeHg-mediated apoptosis at micromolar concentrations. As in spontaneously immortalized MEFs, MeHg induced cell cycle arrest in SV40 large T antigen-immortalized MEFs, with increased sensitivity to MeHg persisting in the Ogg1-/- MEFs. Importantly, cells seeded at a higher density exhibited compromised proliferation, which protected against MeHg-mediated cell cycle arrest and DNA damage. In the reciprocal model of enhanced DNA repair, hOgg1- and Fpg-expressing cells appeared paradoxically more sensitive than wild-type controls to acute MeHg exposure for all cellular and biochemical parameters, potentially due to the accumulation of toxic intermediary abasic sites. Accordingly, our results provide the first evidence that Ogg1 status represents a critical determinant of risk for MeHg toxicity independent of cellular immortalization method, with variations in cellular proliferation and interindividual variability in antioxidative and DNA repair capacities constituting important determinants of risk for environmentally-initiated oxidatively damaged DNA and its pathological consequences.

Methylmercury (MeHg) is a pervasive environmental contaminant with potent neurotoxic, teratogenic and likely carcinogenic activity, for which the underlying molecular mechanisms remain largely unclear. Base excision repair (BER) is important in mitigating the pathogenic effects of oxidative stress, which has also been implicated in the mechanism of MeHg toxicity, however the importance of BER in MeHg toxicity is currently unknown. Accordingly, we addressed this question using: (1) spontaneously- and Simian virus 40 (SV40) large T antigen-immortalized oxoguanine glycosylase 1-null (Ogg1-/-) murine embryonic fibroblasts (MEFs); and, (2) human Ogg1 (hOgg1)- or formamidopyrimidine glycosylase (Fpg)-expressing human embryonic kidney (HEK) cells; reciprocal in vitro cellular models with deficient and enhanced ability to repair oxidatively damaged DNA respectively. When spontaneously-immortalized wild-type and Ogg1-/- MEFs were exposed to environmentally relevant, low micromolar concentrations of MeHg, both underwent cell cycle arrest but Ogg1-/- cells exhibited a greater sensitivity to MeHg than wild-type controls with reduced clonogenic survival and increased apoptosis, DNA damage and DNA damage response activation. Antioxidative catalase alleviated the MeHg-initiated DNA damage in both wild-type and Ogg1-/- cells, but failed to block MeHg-mediated apoptosis at micromolar concentrations. As in spontaneously immortalized MEFs, MeHg induced cell cycle arrest in SV40 large T antigen-immortalized MEFs, with increased sensitivity to MeHg persisting in the Ogg1-/- MEFs. Importantly, cells seeded at a higher density exhibited compromised proliferation, which protected against MeHg-mediated cell cycle arrest and DNA damage. In the reciprocal model of enhanced DNA repair, hOgg1- and Fpg-expressing cells appeared paradoxically more sensitive than wild-type controls to acute MeHg exposure for all cellular and biochemical parameters, potentially due to the accumulation of toxic intermediary abasic sites. Accordingly, our results provide the first evidence that Ogg1 status represents a critical determinant of risk for MeHg toxicity independent of cellular immortalization method, with variations in cellular proliferation and interindividual variability in antioxidative and DNA repair capacities constituting important determinants of risk for environmentally-initiated oxidatively damaged DNA and its pathological consequences.

Neurodegenerative disorders are heterogenous in nature and include a range of ataxias with oculomotor apraxia, which are characterised by a wide variety of neurological and ophthalmological features. This family includes recessive and dominant disorders. A subfamily of autosomal recessive cerebellar ataxias are characterised by defects in the cellular response to DNA damage. These include the well characterised disorders Ataxia-Telangiectasia (A-T) and Ataxia-Telangiectasia Like Disorder (A-TLD) as well as the recently identified diseases Spinocerebellar ataxia with axonal neuropathy Type 1 (SCAN1), Ataxia with Oculomotor Apraxia Type 2 (AOA2), as well as the subject of this thesis, Ataxia with Oculomotor Apraxia Type 1 (AOA1). AOA1 is caused by mutations in the APTX gene, which is located at chromosomal locus 9p13. This gene codes for the 342 amino acid protein Aprataxin. Mutations in APTX cause destabilization of Aprataxin, thus AOA1 is a result of Aprataxin deficiency. Aprataxin has three functional domains, an N-terminal Forkhead Associated (FHA) phosphoprotein interaction domain, a central Histidine Triad (HIT) nucleotide hydrolase domain and a C-terminal C2H2 zinc finger. Aprataxins FHA domain has homology to FHA domain of the DNA repair protein 5’ polynucleotide kinase 3’ phosphatase (PNKP). PNKP interacts with a range of DNA repair proteins via its FHA domain and plays a critical role in processing damaged DNA termini. The presence of this domain with a nucleotide hydrolase domain and a DNA binding motif implicated that Aprataxin may be involved in DNA repair and that AOA1 may be caused by a DNA repair deficit. This was substantiated by the interaction of Aprataxin with proteins involved in the repair of both single and double strand DNA breaks (XRay Cross-Complementing 1, XRCC4 and Poly-ADP Ribose Polymerase-1) and the hypersensitivity of AOA1 patient cell lines to single and double strand break inducing agents. At the commencement of this study little was known about the in vitro and in vivo properties of Aprataxin. Initially this study focused on generation of recombinant Aprataxin proteins to facilitate examination of the in vitro properties of Aprataxin. Using recombinant Aprataxin proteins I found that Aprataxin binds to double stranded DNA. Consistent with a role for Aprataxin as a DNA repair enzyme, this binding is not sequence specific. I also report that the HIT domain of Aprataxin hydrolyses adenosine derivatives and interestingly found that this activity is competitively inhibited by DNA. This provided initial evidence that DNA binds to the HIT domain of Aprataxin. The interaction of DNA with the nucleotide hydrolase domain of Aprataxin provided initial evidence that Aprataxin may be a DNA-processing factor. Following these studies, Aprataxin was found to hydrolyse 5’adenylated DNA, which can be generated by unscheduled ligation at DNA breaks with non-standard termini. I found that cell extracts from AOA1 patients do not have DNA-adenylate hydrolase activity indicating that Aprataxin is the only DNA-adenylate hydrolase in mammalian cells. I further characterised this activity by examining the contribution of the zinc finger and FHA domains to DNA-adenylate hydrolysis by the HIT domain. I found that deletion of the zinc finger ablated the activity of the HIT domain against adenylated DNA, indicating that the zinc finger may be required for the formation of a stable enzyme-substrate complex. Deletion of the FHA domain stimulated DNA-adenylate hydrolysis, which indicated that the activity of the HIT domain may be regulated by the FHA domain. Given that the FHA domain is involved in protein-protein interactions I propose that the activity of Aprataxins HIT domain may be regulated by proteins which interact with its FHA domain. We examined this possibility by measuring the DNA-adenylate hydrolase activity of extracts from cells deficient for the Aprataxin-interacting DNA repair proteins XRCC1 and PARP-1. XRCC1 deficiency did not affect Aprataxin activity but I found that Aprataxin is destabilized in the absence of PARP-1, resulting in a deficiency of DNA-adenylate hydrolase activity in PARP-1 knockout cells. This implies a critical role for PARP-1 in the stabilization of Aprataxin. Conversely I found that PARP-1 is destabilized in the absence of Aprataxin. PARP-1 is a central player in a number of DNA repair mechanisms and this implies that not only do AOA1 cells lack Aprataxin, they may also have defects in PARP-1 dependant cellular functions. Based on this I identified a defect in a PARP-1 dependant DNA repair mechanism in AOA1 cells. Additionally, I identified elevated levels of oxidized DNA in AOA1 cells, which is indicative of a defect in Base Excision Repair (BER). I attribute this to the reduced level of the BER protein Apurinic Endonuclease 1 (APE1) I identified in Aprataxin deficient cells. This study has identified and characterised multiple DNA repair defects in AOA1 cells, indicating that Aprataxin deficiency has far-reaching cellular consequences. Consistent with the literature, I show that Aprataxin is a nuclear protein with nucleoplasmic and nucleolar distribution. Previous studies have shown that Aprataxin interacts with the nucleolar rRNA processing factor nucleolin and that AOA1 cells appear to have a mild defect in rRNA synthesis. Given the nucleolar localization of Aprataxin I examined the protein-protein interactions of Aprataxin and found that Aprataxin interacts with a number of rRNA transcription and processing factors. Based on this and the nucleolar localization of Aprataxin I proposed that Aprataxin may have an alternative role in the nucleolus. I therefore examined the transcriptional activity of Aprataxin deficient cells using nucleotide analogue incorporation. I found that AOA1 cells do not display a defect in basal levels of RNA synthesis, however they display defective transcriptional responses to DNA damage. In summary, this thesis demonstrates that Aprataxin is a DNA repair enzyme responsible for the repair of adenylated DNA termini and that it is required for stabilization of at least two other DNA repair proteins. Thus not only do AOA1 cells have no Aprataxin protein or activity, they have additional deficiencies in PolyADP Ribose Polymerase-1 and Apurinic Endonuclease 1 dependant DNA repair mechanisms. I additionally demonstrate DNA-damage inducible transcriptional defects in AOA1 cells, indicating that Aprataxin deficiency confers a broad range of cellular defects and highlighting the complexity of the cellular response to DNA damage and the multiple defects which result from Aprataxin deficiency. My detailed characterization of the cellular consequences of Aprataxin deficiency provides an important contribution to our understanding of interlinking DNA repair processes.

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / A célula epitelial é o primeiro contato entre os micro-organismos e o hospedeiro. Essa interação pode levar a produção de diversas citocinas, quimiocinas, moléculas inflamatórias e também estimular a geração de espécies reativas de oxigênio (ERO). Neste trabalho avaliamos se a interação com as células HEp-2 poderia ser genotóxica para os mutantes derivados de Escherichia coli K-12 deficientes em algumas enzimas que fazem parte do sistema de reparo por excisão de base (BER). Além disto, avaliamos a expressão do sistema SOS, que é induzido pela presença de danos no genoma bacteriano. Os resultados obtidos mostraram a presença de filamentos, na interação com células HEp-2, principalmente, no mutante xthA (BW9091) e no triplo mutante xthA nfo nth (BW535). Quando a interação foi quantificada na ausência da D-manose, observamos um aumento das bactérias aderidas. Além disto, a quantidade e o tamanho dos filamentos também aumentaram, mostrando que as adesinas manose-sensíveis estavam envolvidas na filamentação bacteriana. Para comprovar se o aumento da filamentação observada neste ensaio foram uma consequência da indução do sistema SOS, desencadeada pela interação com as células HEp-2, quantificamos a expressão do SOS, na presença e na ausência da D-manose. De fato, observamos que a indução do SOS na ausência da D-manose foi maior, quando comparada, com o ensaio realizado na presença de D-manose. Além disto, observamos que a ausência de xthA foi importante para o aumento da filamentação observada na ausência de D-manose. Diante destes resultados, verificamos se a resposta de filamentação ocorreria quando as bactérias interagiam com uma superfície abiótica como o vidro. Observamos também inúmeros filamentos nos mutantes BER, BW9091 e BW535, quando comparados a cepa selvagem AB1157. Essa filamentação foi associada à indução do SOS, em resposta a interação das bactérias com o vidro. Em parte a filamentação e a indução do SOS observadas na interação ao vidro, foram associadas à produção de ERO. Quantificamos também o número de bactérias aderidas e observamos que as nossas cepas formavam biofilmes moderados. Contudo, a formação de biofilme dependia da capacidade da bactéria induzir o sistema SOS, tanto em aerobiose como em anaerobiose. A tensão do oxigênio foi importante para interação dos mutantes BER, uma vez que os mutantes BW9091 e BW535 apresentaram uma quantidade de bactérias aderidas menor em anaerobiose. Contudo, a diminuição observada não estava vinculada a morte dos mutantes BER. Também realizamos microscopia de varredura na cepa selvagem e nos mutantes, BW9091 e BW535 e confirmamos que as três cepas formavam biofilmes tanto em aerobiose como em anaerobiose. Observamos uma estrutura sugestiva de matriz extracelular envolvendo os biofilmes da cepa selvagem AB1157 e do mutante BW9091. No entanto, a formação desta estrutura por ambas as cepas dependia da tensão de oxigênio, pois nos biofilmes formados em anaerobiose essa estrutura estava ausente. Em conclusão, mostramos que na interação das bactérias com a superfície biótica e abiótica, ocorreu lesão no genoma, com indução do SOS e a resposta de filamentação associada. / The epithelial cell is the first contact between microorganisms and host. This interaction results in production of several cytokines, chemokines, and inflammatory molecules by epithelial cells and also stimulate the generation of reactive oxygen species (ROS). In the present study, we have evaluated whether the interaction to HEp-2 cells causes genotoxicity to mutants derived from Escherichia coli K-12 deficient in some enzymes that are part of the system of base excision repair (BER). Moreover, we measured the expression of SOS system, which is induced by the presence of damage to the bacterial genome. Our results showed mainly presence of filamentous bacterial growth in xthA mutant (BW9091) and triple xthA nfo nth mutant (BW535) when submitted to HEp-2 cells interaction assays. When experiments were performed in the absence of mannose, data showed enhanced interaction of viable bacteria to HEp-2 cells for all strains tested. Furthermore, the removal of D-mannose resulted in an increase in both number and size of bacterial filamentous forms, indicating the involvement of mannose-sensitive adhesins in the filamentation of these strains. In order to verify whether the increased filamentation growth in this assay was a consequence of SOS induction, triggered by interaction to HEp-2 cells, we measured expression of SOS in the presence and absence of D-mannose. Indeed, we observed higher expression of SOS response in the absence of mannose than in experiments performed in the presence of D-mannose. Moreover, we observed that the absence of xthA was important to filamentation increasing in absence of D-mannose. Based on these results, we verified if interaction to abiotic surfaces, like glass, could lead to filamentation of these strains. We also observed numerous filaments in BER mutants, BW9091 and BW535, when compared to wild-type strain AB1157. The filamentation observed was a consequence of SOS induction, triggered by attachment to the glass surface. In part, the filamentation and SOS induction observed in these experiments were related to ROS production. We also quantified interacted bacterial cells and it was observed moderated biofilm formation in all strains tested. However, biofilm formation depended on the ability of the bacteria to induce the SOS response, under both aerobic and anaerobic conditions. The oxygen tension was important factor for interaction of the BER mutants, since these mutants exhibited decreased quantitative adherence under anaerobic conditions. However, this decrease was not related to BER mutants death. Scanning electron microscopy was also performed in the wild-type strain and BER mutants (BW9091 e BW535) and biofilm formation was confirmed under both aerobic and anaerobic conditions. We observed a structure similar to a extracellular matrix which involved biofilms of wild type strain (AB1157) and xthA mutant (BW9091). However, the formation of this structure by both strains depended on the oxygen tension, since biofilm formation, under anaerobiosis condition, did not presented this structure. In conclusion, was provided that bacterial interaction to biotic and abiotic surfaces can lead to damage of bacterial genome, resulting in SOS induction and associated filamentation.

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / A célula epitelial é o primeiro contato entre os micro-organismos e o hospedeiro. Essa interação pode levar a produção de diversas citocinas, quimiocinas, moléculas inflamatórias e também estimular a geração de espécies reativas de oxigênio (ERO). Neste trabalho avaliamos se a interação com as células HEp-2 poderia ser genotóxica para os mutantes derivados de Escherichia coli K-12 deficientes em algumas enzimas que fazem parte do sistema de reparo por excisão de base (BER). Além disto, avaliamos a expressão do sistema SOS, que é induzido pela presença de danos no genoma bacteriano. Os resultados obtidos mostraram a presença de filamentos, na interação com células HEp-2, principalmente, no mutante xthA (BW9091) e no triplo mutante xthA nfo nth (BW535). Quando a interação foi quantificada na ausência da D-manose, observamos um aumento das bactérias aderidas. Além disto, a quantidade e o tamanho dos filamentos também aumentaram, mostrando que as adesinas manose-sensíveis estavam envolvidas na filamentação bacteriana. Para comprovar se o aumento da filamentação observada neste ensaio foram uma consequência da indução do sistema SOS, desencadeada pela interação com as células HEp-2, quantificamos a expressão do SOS, na presença e na ausência da D-manose. De fato, observamos que a indução do SOS na ausência da D-manose foi maior, quando comparada, com o ensaio realizado na presença de D-manose. Além disto, observamos que a ausência de xthA foi importante para o aumento da filamentação observada na ausência de D-manose. Diante destes resultados, verificamos se a resposta de filamentação ocorreria quando as bactérias interagiam com uma superfície abiótica como o vidro. Observamos também inúmeros filamentos nos mutantes BER, BW9091 e BW535, quando comparados a cepa selvagem AB1157. Essa filamentação foi associada à indução do SOS, em resposta a interação das bactérias com o vidro. Em parte a filamentação e a indução do SOS observadas na interação ao vidro, foram associadas à produção de ERO. Quantificamos também o número de bactérias aderidas e observamos que as nossas cepas formavam biofilmes moderados. Contudo, a formação de biofilme dependia da capacidade da bactéria induzir o sistema SOS, tanto em aerobiose como em anaerobiose. A tensão do oxigênio foi importante para interação dos mutantes BER, uma vez que os mutantes BW9091 e BW535 apresentaram uma quantidade de bactérias aderidas menor em anaerobiose. Contudo, a diminuição observada não estava vinculada a morte dos mutantes BER. Também realizamos microscopia de varredura na cepa selvagem e nos mutantes, BW9091 e BW535 e confirmamos que as três cepas formavam biofilmes tanto em aerobiose como em anaerobiose. Observamos uma estrutura sugestiva de matriz extracelular envolvendo os biofilmes da cepa selvagem AB1157 e do mutante BW9091. No entanto, a formação desta estrutura por ambas as cepas dependia da tensão de oxigênio, pois nos biofilmes formados em anaerobiose essa estrutura estava ausente. Em conclusão, mostramos que na interação das bactérias com a superfície biótica e abiótica, ocorreu lesão no genoma, com indução do SOS e a resposta de filamentação associada. / The epithelial cell is the first contact between microorganisms and host. This interaction results in production of several cytokines, chemokines, and inflammatory molecules by epithelial cells and also stimulate the generation of reactive oxygen species (ROS). In the present study, we have evaluated whether the interaction to HEp-2 cells causes genotoxicity to mutants derived from Escherichia coli K-12 deficient in some enzymes that are part of the system of base excision repair (BER). Moreover, we measured the expression of SOS system, which is induced by the presence of damage to the bacterial genome. Our results showed mainly presence of filamentous bacterial growth in xthA mutant (BW9091) and triple xthA nfo nth mutant (BW535) when submitted to HEp-2 cells interaction assays. When experiments were performed in the absence of mannose, data showed enhanced interaction of viable bacteria to HEp-2 cells for all strains tested. Furthermore, the removal of D-mannose resulted in an increase in both number and size of bacterial filamentous forms, indicating the involvement of mannose-sensitive adhesins in the filamentation of these strains. In order to verify whether the increased filamentation growth in this assay was a consequence of SOS induction, triggered by interaction to HEp-2 cells, we measured expression of SOS in the presence and absence of D-mannose. Indeed, we observed higher expression of SOS response in the absence of mannose than in experiments performed in the presence of D-mannose. Moreover, we observed that the absence of xthA was important to filamentation increasing in absence of D-mannose. Based on these results, we verified if interaction to abiotic surfaces, like glass, could lead to filamentation of these strains. We also observed numerous filaments in BER mutants, BW9091 and BW535, when compared to wild-type strain AB1157. The filamentation observed was a consequence of SOS induction, triggered by attachment to the glass surface. In part, the filamentation and SOS induction observed in these experiments were related to ROS production. We also quantified interacted bacterial cells and it was observed moderated biofilm formation in all strains tested. However, biofilm formation depended on the ability of the bacteria to induce the SOS response, under both aerobic and anaerobic conditions. The oxygen tension was important factor for interaction of the BER mutants, since these mutants exhibited decreased quantitative adherence under anaerobic conditions. However, this decrease was not related to BER mutants death. Scanning electron microscopy was also performed in the wild-type strain and BER mutants (BW9091 e BW535) and biofilm formation was confirmed under both aerobic and anaerobic conditions. We observed a structure similar to a extracellular matrix which involved biofilms of wild type strain (AB1157) and xthA mutant (BW9091). However, the formation of this structure by both strains depended on the oxygen tension, since biofilm formation, under anaerobiosis condition, did not presented this structure. In conclusion, was provided that bacterial interaction to biotic and abiotic surfaces can lead to damage of bacterial genome, resulting in SOS induction and associated filamentation.

Introdução: O adenocarcinoma gástrico é uma doença de elevada incidência e alta mortalidade. A gastrectomia com linfadenectomia é tratamento potencialmente curativo, promovendo controle loco-regional da doença e fornecendo material para análise histopatológica. Para o adequado estadiamento dos pacientes é recomendado que pelo menos 16 linfonodos sejam examinados pela patologia, entretanto, espera-se maior sobrevida quando >= 30 linfonodos são avaliados, mesmo em pacientes com tumores precoces. A justificativa para este achado é o sub-estadiamento de pacientes com poucos linfonodos examinados. Linfonodos pequenos são particularmente difíceis de serem encontrados, mas podem conter metástases e impactar negativamente na sobrevida. Visando facilitar sua identificação, soluções clareadoras de gordura foram propostas, entretanto não há evidência clara de seu benefício clínico. Objetivos: Comparar as soluções de Carnoy e de formalina neutra tamponada em relação ao número absoluto de linfonodos encontrados na peça cirúrgica de pacientes submetidos a gastrectomia. Averiguar se linfonodos retirados cirurgicamente são perdidos com a fixação em formalina e, caso isso ocorra, se este fato é relevante para o estadiamento. Observar se o protocolo de pesquisa influenciou o número de linfonodos encontrados. Métodos: Cinquenta produtos de gastrectomia subtotal com linfadenectomia D2 por adenocarcinoma gástrico foram randomizados para fixação em Carnoy ou formalina com posterior dissecção da peça em busca de linfonodos. Após a dissecção do grupo Formalina, a gordura residual a ser desprezada foi imersa em Carnoy e reavaliada posteriormente. Os dados de 25 gastrectomias D2 operadas previamente ao estudo também foram avaliados. Resultados: A média de linfonodos encontrados nos grupos Carnoy e Formalina foi de 50,4 e 34,8; respectivamente (p < 0,001). Na gordura residual foram encontrados linfonodos em todos os casos (média 16,9 linfonodos), elevando a média do grupo Formalina para 51,7 (valor similar ao do grupo Carnoy, p=0,809). Com exceção de 1 linfonodo de 7mm, todos os demais encontrados na gordura residual mediram <= 3mm. Treze linfonodos metastáticos passaram despercebidos com a fixação em formalina e a revisão da gordura residual determinou a mudança de estadiamento de 2 (8%) pacientes. Os linfonodos encontrados no Carnoy possuíam tamanho significativamente menor quando comparados aos do grupo Formalina (p=0,01). A média de linfonodos encontrados no grupo retrospectivo foi similar ao do grupo Formalina prospectivo (p=0,802). Conclusões: Quando comparada à formalina, a solução de Carnoy permite encontrar número maior de linfonodos no espécime cirúrgico de gastrectomias com linfadenectomia. Linfonodos milimétricos foram perdidos após a fixação em formalina, estes foram identificados com o Carnoy e são clinicamente relevantes, pois podem conter metástases modificando assim, o estádio clínico e prognóstico do paciente. A implementação de protocolo de pesquisa não influenciou o número de linfonodos encontrados neste estudo / Background: Gastric adenocarcinoma is a frequent disease with high mortality ratio. Gastrectomy with lymphadenectomy is potentially curative, allows local control of the disease and provides material for TNM classification. While pathology examination of at least 16 lymph nodes is recommended following surgery, longer survival rates are expected when >=30 lymph nodes are examined, even for early gastric cancer. The understaging of patients with less examined lymph nodes justifies this findings. Small lymph nodes are particularly difficult to identify and fat clearing solutions have been proposed to improve this, but there is no evidence of their clinical benefit. Objectives: Compare Carnoy\'s solution (CS) and formalin in terms of the total number of examined lymph nodes following gastrectomy. Verify if surgically retrieved lymph nodes are lost with the formalin fixation and if this fact is clinically significant. Observe if a research protocol influences the number of examined lymph nodes. Methods: Fifty specimens of gastrectomy with D2 lymphadenectomy were randomized for fixation in CS or formalin with posterior dissection in search for lymph nodes. In the Formalin group, the residual fat to be discarded was immersed in CS and dissected again. Data from 25 D2 gastrectomies performed previously the present study were retrospectively analyzed. Results: The medium number of examined lymph nodes was 50.4 and 34.8 for CS and formalin, respectively (p < 0.001). Lost lymph nodes were found in all cases in the Residual Fat group (medium 16.9), this increased the Formalin group average to 51.7 (which is similar to the CS group, p=0.809). With one exception (7mm), all other examined lymph nodes in the Residual Fat group measured <= 3mm. Thirteen lymph nodes from this group were metastatic, this determined the upstaging of 2 (8%) patients. Lymph nodes from the CS group were smaller than those found in the formalin group (p=0.01). The medium number of retrieved lymph nodes in the retrospective group was similar to the formalin group (p=0.802). Conclusions: When compared to formalin, Carnoy\'s solution increases lymph node detection following gastrectomy with lymphadenectomy. CS identifies small lymph nodes lost with formalin fixation and that are clinically significant, since they may contain metastasis, modifying the TNM classification. No influence of the research protocol over the number of examined lymph nodes was observed in the present study.

L'objectif de cette thèse était de mettre en oeuvre le développement d'une thérapie des plaies cutanées profondes basée sur l'utilisation de nanoparticules (NP) biodégradables de poly(acide lactique) (NP-PLA) vectrices de médiateurs de la cicatrisation. Le but était d'accélérer la cicatrisation cutanée et de favoriser la reconstruction d'un derme fonctionnel. La méthode a été de (i) réduire la réaction inflammatoire pour en contenir les effets délétères et (ii) stimuler la réépithélialisation pour accélérer la cicatrisation et réduire le risque infectieux. Les moyens ont été l'utilisation d'un antioxydant, la vitamine E (VE) et d'un facteur de croissance des fibroblastes (le FGF2) vectorisés par des nanoparticules biocompatibles et biodégradables de poly(acide lactique) (PLA). Nos NP-PLA contiennent l'antioxydant (VE) dans leur coeur hydrophobe, et portent le facteur de croissance fibroblastique (FGF2) à leur surface. Ces formulations ont été (i) caractérisées par des méthodes physico-chimiques et (ii) testées par des méthodes in vitro pour évaluer leurs effets potentiels, en tant que système de délivrance de VE et de FGF2, sur la cicatrisation des plaies. Des modèles expérimentaux in vivo ont été développés et caractérisés pour mettre en évidence l'efficacité des NP-PLA fonctionnalisées pour la cicatrisation cutanée et la reconstruction dermique fonctionnelle. Nos résultats montrent que l'activité antioxydante de la VE n'est pas perturbée par l'encapsulation dans des NP-PLA et qu'elle est légèrement supérieure à celle de la VE libre dans un système in vitro. De même, l'activité biologique du FGF2 sur la prolifération et la migration des fibroblastes dans un système in vitro n'est pas altérée par son adsorption sur des NP-PLA. Aucune de ces deux NP-PLA fonctionnalisées n'a de cytotoxicité avérée in vitro. Deux modèles expérimentaux de plaies cutanées profondes ont été développés sur souris sans poils SKH1 saines : (i) Un modèle robuste de brûlure cutanée thermique de 3ème degré qui se caractérise par une inflammation massive de la plaie et par un stade de granulation tardif après 16 jours de cicatrisation. (ii) Un modèle de plaie d'excision cutanée a également été utilisé. Un modèle de cicatrisation retardée a été obtenu par induction chimique d'un diabète de type I stable avant réalisation des plaies d'excision ou de brûlure. Ces modèles de plaies cutanées ont été caractérisés tout au long du processus de cicatrisation par des études (i) macroscopiques de cinétique de fermeture des plaies, (ii) histologiques d'inflammation, de nécrose et de réépithélialisation, (iii) physiologiques de perfusion sanguine cutanée. L'expression de 84 gènes impliqués dans le processus de cicatrisation a été étudiée sur le tissu cicatriciel 14 jours après formation de la plaie. Pour conclure, nos résultats mettent en évidence le potentiel de vectorisation de molécules thérapeutiques des NP de PLA pour le développement de futures stratégies de délivrance ciblée de VE et de FGF2 dans les plaies cutanées profondes. Les modèles expérimentaux in vivo développés et caractérisés, ouvrent la voie aux études précliniques d'efficacité des NP-PLA fonctionnalisées dans le processus de cicatrisation des plaies profondes / The objective of this thesis was to develop a therapy of cutaneous deep wounds based on biodegradable poly (lactic-acid) nanoparticles (PLA-NP) releasing wound healing mediators. The goal was to accelerate wound healing and to promote the reconstruction of a functional dermis. Our method was (i) to reduce the inflammatory reaction in the aim of limiting its deleterious effects, (ii) to stimulate reepithelialization to accelerate wound healing and to reduce the risk of infections. The implementation of means was based on the use of an antioxidant (vitamin E, VE) and a fibroblast growth factor (FGF2) carried by biocompatible and biodegradable poly(lactic-acid) based nanoparticles. Our PLA-NP contained the antioxidant (VE), in their hydrophobic core and carried the fibroblastic growth factor (FGF2) on their surface. These formulations were (i) characterized by physico-chemical methods and (ii) tested by in vitro methods to evaluate their effects as a delivery system of VE and FGF2 on wound healing. Experimental in vivo models have been developed and characterized in the aim of studying the potential beneficial effect of functionalized PLA-NP on wound healing and functional reconstruction of dermis. Our results show that the antioxidant activity of VE was not inhibited by encapsulation into PLA-NP and was lightly increased compared with free VE in an in vitro system. The biological activity of FGF2 on proliferation and migration of fibroblasts in an in vitro system was not altered by adsorption onto PLA-NP as well. No cytotoxicity of these functionalized PLA-NP was detected in vitro. Two experimental models of deep cutaneous wounds were developed on the healthy SKH1 hairless mouse: (i) A robust third degree thermal burn model that was characterized by massive inflammation of the wound and a late granulation stage after 16 days of healing. (ii) A model of excisional skin wound was also used. A model of delayed wound healing was established by chemical induction of stable type I diabetes prior to excision and burn injuries. The healing process of these models of cutaneous wounds was characterized by (i) macroscopic studies of wound closure, (ii) histological studies of inflammation, necrosis and reepithelialization, and (iii) by physiological studies of cutaneous blood perfusion. A study of the expression of 84 genes involved in the healing process was carried out on the scar tissue 14 days post-wound. In conclusion, our results highlight the potential efficacy of PLA-NP as a vector of therapeutic molecules for the development of future strategies for targeted delivery of VE and FGF2 in deep skin wounds. The developed and characterized in vivo experimental models open the way to preclinical studies of efficacy of functionalized PLA-NP on the healing process of deep wounds

Genomic integrity is important for living cells' correct functioning and propagation. Deoxyribonucleic acid as a molecule is a subject to chemical reactions with agents that can come from environment as well as from internal metabolism processes. These reactions can induce damage to DNA and thus compromise the genetic information, and result in disease and death of an organism. To mitigate the damage to DNA, cells have evolved to have multiple DNA repair pathways. Presented here is a computational study of DNA repair genes. The structure of the Homo sapiens direct DNA repair gene ALKBH1 is predicted utilizing homology modeling methods and using AlkB and DBL proteins as templates. Analysis of the obtained structure and molecular dynamics simulations give insights into potentially functionally important residues of the protein. In particular, zinc finger domains are predicted, and lysines that could perform catalytic activities are investigated. Subsequent mutagenesis experiments revealed the effect of the residues predicted to form zinc fingers on activity of ALKBH1. Structure and dynamics of AlkD, a Bascillus cereus base excision DNA repair protein is also studied. This protein has been shown to bind DNA with large alkyl adducts and perform excision catalysis without base flipping which is characteristic to other enzymes in the same family. MD simulations of AlkD revealed that B helix, which interacts with DNA, has higher fluctuations when AlkD is not bound to DNA, and thus could have a role in binding and recognition of DNA. For the purpose of finding biomarkers and to further our understanding of a mode of action of DNA repair genes, statistical methods were applied to identify mutations that are linked to cancer phenotypes. Analysis was based on case-control studies of patients with cancers of prostate, breast, pancreas, lung as well as chronic lymphocytic leukemia from NCBI dbGAP database. Those mutations that result in missense mutations were further investigated. In particular, extensive MD simulations and experimental investigations were performed on the mutation in the ALKBH7 gene that was found to be linked to prostate cancer.

The sensitivity of Xeroderma pigmentosa (XP) patients to sunlight has spurred the discovery and genetic and biochemical analysis of the eight XP gene products (XPA-XPG plus XPV) responsible for this disorder. These studies also have served to elucidate the nucleotide excision repair (NER) process, especially the critical role played by the XPA protein. More recent studies have shown that NER also involves numerous other proteins normally employed in DNA metabolism and cell cycle regulation. Central among these is ataxia telangiectasia and Rad3-related (ATR), a protein kinase involved in intracellular signaling in response to DNA damage, especially DNA damage-induced replicative stresses. This review summarizes recent findings on the interplay between ATR as a DNA damage signaling kinase and as a novel ligand for intrinsic cell death proteins to delay damage-induced apoptosis, and on ATR’s regulation of XPA and the NER process for repair of UV-induced DNA adducts. ATR’s regulatory role in the cytosolic-to-nuclear translocation of XPA will be discussed. In addition, recent findings elucidating a non-NER role for XPA in DNA metabolism and genome stabilization at ds-ssDNA junctions, as exemplified in prematurely aging progeroid cells, also will be reviewed.