A Síndrome de Marfan (SMF) (OMIM# 154700) é a mais comum das doenças genéticas do tecido conjuntivo Herdada de forma autossômica dominante, ela apresenta incidência de 1 em cada 5.000 indivíduos. Apesar de apresentar grande variabilidade clínica inter e intrafamiliar, o fenótipo da SMF possui penetrância completa, e suas manifestações clínicas afetam primariamente os sistemas esquelético, ocular e cardiovascular. Afim de estudar os mecanismos patogênicos da SMF foi desenvolvido um modelo murino, mgΔneoLoxP, que reproduz as manifestações ósseas, cardiovasculares e pulmonares da síndrome. O modelo foi estabelecido nas linhagens isogênicas 129/Sv e C57BL/6, que apresentam diferenças tanto quanto a idade de acometimento quanto a gravidade das alterações, é possível que as diferenças alélicas existentes entre essas linhagens alterem a manifestação fenotípica, ou seja, que existam genes modificadores para a SMF. Assim, objetivo deste projeto é utilizar este modelo experimental para identificar genes modificadores do fenótipo da SMF e tentar entender melhor a arquitetura genética da síndrome. Ao todo foram gerados 82 animais 129xB6 F2 heterozigotos para o alelo mgΔneoLoxP, a analise de ligação utilizando microssatélites e SNPs nos animais com fenótipos mais extremos mostraram ligação sugestiva do fenótipo ósseo com as regiões compreendidas entre as posições 56 cM e 68 cM do cromossomo 3; e 2 cM e 20 cM do cromossomo X; ligação significativa entre as posições 41cM e 49 cM do cromossomo 6; além de mostrar ligação sugestiva do fenótipo cardiovascular do 66 cM ao 70 cM do cromossomo 4; e do 44 cM ao 52 cM do cromossomo 13. Além da variabilidade entre linhagens, os animais 129 apresentam uma grande variabilidade fenotípica interna, o que por se tratar de animais isogênicos causada por fatores aleatórios ou devido a modificações epigenéticas que alterem o nível de expressão de alguns genes e assim o fenótipo. A comparação entre animais 129 leves e graves levou a identificação de 25 genes diferencialmente expressos dos quais 11 apresentavam funções relevantes para a SMF, entretanto foram aferidos os níveis de expressão de 2 destes que não validaram os resultados obtidos devido a uma grande variação observada entre os animais de todos as classes fenotípicas. Também foram identificadas 46 vias que se apresentavam mais frequentes nos conjuntos de genes obtidos entre as duas classes fenotípica de animais heterozigotos contra os animais selvagens. Tanto as vias, quanto os genes identificados através de ligação quanto diferença de expressão mostram uma convergência para as funções dos genes de interesse, sendo que entre eles existem genes já associados com a SMF, controle de ativação de TGF-B e da biogênese das microfibras da matriz extracelular, quanto genes que ainda não foram associados mas são possíveis modificadores do fenótipo, tais como genes envolvidos nos processos de enovelamento e degradação protéico e nos processos de endocitose e exocitose de vesículas, que podem alterar a quantidade de fibrilina-1 truncada disponível e assim o fenótipo / The Marfan syndrome (MFS) (OMIM # 154700) is the most common genetic disorder of the connective tissue and is inherited in a autosomal dominant fashion, it has an incidence of 1 in 5,000 individuals. Despite a great clinical variability being one of the \"trademarks\" of the syndrome, the phenotype of the MFS has complete penetrance and its clinical manifestations primarily affect the skeletal, ocular and cardiovascular systems. In order to study the pathogenic mechanisms of MFS was developed a mouse model, named mgΔneoLoxP, which reproduces the skeletal, cardiovascular and pulmonary manifestations of the syndrome. The model was established in inbred mouse strains 129/Sv and C57BL / 6, which phenotypes differ as to age of onset and severity of manifestation. It is possible that allelic differences between these inbred strains alter the phenotyic manifestation of disease, leading to the conclusion that may exist modifier genes involved in the for MFS. This study inteds to use this experimental model to identify phenotype modifier genes of MFS so a better understand the genetic architecture of the syndrome. Altogether, 82 129xB6 F2 heterozygous animals were generated so that a linkage analysis using microsatellite and SNP could be conducted. The linkage analysis using a selective genotyping procedure showed a suggestive linkage of the skeletal phenotype with regions included between positions 56 cM and 68 cM on chromosome 3, and 2 cM and 20 cM on chromosome X; and a significant linkage between positions 41cM and 49 cM on chromosome 6; also showing suggestive linkage of the cardiovascular phenotype from 66 cM to 70 cM on chromosome 4, and 44 cM to 52 cM on chromosome 13. Besides the variability between strains, 129 animals have a wide inner strain phenotypic variability, which in the case of isogenic animals should be caused by random factors or due to epigenetic modifications that may alter the expression level some genes and thus the phenotype. The comparison between animals of the 129 strain with mild and severe alterations led to the identification of 25 differentially expressed genes of which 11 showed relevant functions to the MFS, however it was only possible to measure the expression levels of two genes using real-time PCR, although those did not validate the results obtained from the expression microarray due to a large expression variation in all phenotypic classes. It was also identified 46 pathways that were more frequent in the gene lists obtained from the comparison between the two phenotypic classes of heterozygous animals against 129 wildtype animals. There is a similarity in the function of genes or pathways of interest found in pathways analysis and genes identified, either by differential expression or linkage analisys, and among them there genes already associated with the MFS, such as in the control activity of TGF-B and biogenesis of microfibers in the extracellular matrix, as also genes that were not associated with MFS but are possible phenotype modifier genes, such as genes involved in protein folding and degradation processes and of endocytosis and exocytosis processes of vesicle, which can change the amount of truncated fibrillin-1 available and thus the phenotype

A Síndrome de Marfan (SMF) (OMIM# 154700) é a mais comum das doenças genéticas do tecido conjuntivo Herdada de forma autossômica dominante, ela apresenta incidência de 1 em cada 5.000 indivíduos. Apesar de apresentar grande variabilidade clínica inter e intrafamiliar, o fenótipo da SMF possui penetrância completa, e suas manifestações clínicas afetam primariamente os sistemas esquelético, ocular e cardiovascular. Afim de estudar os mecanismos patogênicos da SMF foi desenvolvido um modelo murino, mgΔneoLoxP, que reproduz as manifestações ósseas, cardiovasculares e pulmonares da síndrome. O modelo foi estabelecido nas linhagens isogênicas 129/Sv e C57BL/6, que apresentam diferenças tanto quanto a idade de acometimento quanto a gravidade das alterações, é possível que as diferenças alélicas existentes entre essas linhagens alterem a manifestação fenotípica, ou seja, que existam genes modificadores para a SMF. Assim, objetivo deste projeto é utilizar este modelo experimental para identificar genes modificadores do fenótipo da SMF e tentar entender melhor a arquitetura genética da síndrome. Ao todo foram gerados 82 animais 129xB6 F2 heterozigotos para o alelo mgΔneoLoxP, a analise de ligação utilizando microssatélites e SNPs nos animais com fenótipos mais extremos mostraram ligação sugestiva do fenótipo ósseo com as regiões compreendidas entre as posições 56 cM e 68 cM do cromossomo 3; e 2 cM e 20 cM do cromossomo X; ligação significativa entre as posições 41cM e 49 cM do cromossomo 6; além de mostrar ligação sugestiva do fenótipo cardiovascular do 66 cM ao 70 cM do cromossomo 4; e do 44 cM ao 52 cM do cromossomo 13. Além da variabilidade entre linhagens, os animais 129 apresentam uma grande variabilidade fenotípica interna, o que por se tratar de animais isogênicos causada por fatores aleatórios ou devido a modificações epigenéticas que alterem o nível de expressão de alguns genes e assim o fenótipo. A comparação entre animais 129 leves e graves levou a identificação de 25 genes diferencialmente expressos dos quais 11 apresentavam funções relevantes para a SMF, entretanto foram aferidos os níveis de expressão de 2 destes que não validaram os resultados obtidos devido a uma grande variação observada entre os animais de todos as classes fenotípicas. Também foram identificadas 46 vias que se apresentavam mais frequentes nos conjuntos de genes obtidos entre as duas classes fenotípica de animais heterozigotos contra os animais selvagens. Tanto as vias, quanto os genes identificados através de ligação quanto diferença de expressão mostram uma convergência para as funções dos genes de interesse, sendo que entre eles existem genes já associados com a SMF, controle de ativação de TGF-B e da biogênese das microfibras da matriz extracelular, quanto genes que ainda não foram associados mas são possíveis modificadores do fenótipo, tais como genes envolvidos nos processos de enovelamento e degradação protéico e nos processos de endocitose e exocitose de vesículas, que podem alterar a quantidade de fibrilina-1 truncada disponível e assim o fenótipo / The Marfan syndrome (MFS) (OMIM # 154700) is the most common genetic disorder of the connective tissue and is inherited in a autosomal dominant fashion, it has an incidence of 1 in 5,000 individuals. Despite a great clinical variability being one of the \"trademarks\" of the syndrome, the phenotype of the MFS has complete penetrance and its clinical manifestations primarily affect the skeletal, ocular and cardiovascular systems. In order to study the pathogenic mechanisms of MFS was developed a mouse model, named mgΔneoLoxP, which reproduces the skeletal, cardiovascular and pulmonary manifestations of the syndrome. The model was established in inbred mouse strains 129/Sv and C57BL / 6, which phenotypes differ as to age of onset and severity of manifestation. It is possible that allelic differences between these inbred strains alter the phenotyic manifestation of disease, leading to the conclusion that may exist modifier genes involved in the for MFS. This study inteds to use this experimental model to identify phenotype modifier genes of MFS so a better understand the genetic architecture of the syndrome. Altogether, 82 129xB6 F2 heterozygous animals were generated so that a linkage analysis using microsatellite and SNP could be conducted. The linkage analysis using a selective genotyping procedure showed a suggestive linkage of the skeletal phenotype with regions included between positions 56 cM and 68 cM on chromosome 3, and 2 cM and 20 cM on chromosome X; and a significant linkage between positions 41cM and 49 cM on chromosome 6; also showing suggestive linkage of the cardiovascular phenotype from 66 cM to 70 cM on chromosome 4, and 44 cM to 52 cM on chromosome 13. Besides the variability between strains, 129 animals have a wide inner strain phenotypic variability, which in the case of isogenic animals should be caused by random factors or due to epigenetic modifications that may alter the expression level some genes and thus the phenotype. The comparison between animals of the 129 strain with mild and severe alterations led to the identification of 25 differentially expressed genes of which 11 showed relevant functions to the MFS, however it was only possible to measure the expression levels of two genes using real-time PCR, although those did not validate the results obtained from the expression microarray due to a large expression variation in all phenotypic classes. It was also identified 46 pathways that were more frequent in the gene lists obtained from the comparison between the two phenotypic classes of heterozygous animals against 129 wildtype animals. There is a similarity in the function of genes or pathways of interest found in pathways analysis and genes identified, either by differential expression or linkage analisys, and among them there genes already associated with the MFS, such as in the control activity of TGF-B and biogenesis of microfibers in the extracellular matrix, as also genes that were not associated with MFS but are possible phenotype modifier genes, such as genes involved in protein folding and degradation processes and of endocytosis and exocytosis processes of vesicle, which can change the amount of truncated fibrillin-1 available and thus the phenotype

Orientador: Carmen Sílvia Bertuzzo / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-27T06:53:07Z (GMT). No. of bitstreams: 1 Rezende_LucianaMontes_M.pdf: 2160530 bytes, checksum: b9f9b53af213aa35b20cf6a49d746a91 (MD5) Previous issue date: 2015 / Resumo: O Câncer de Mama (CM) é a forma de neoplasia mais diagnosticada e a principal causa de morte por câncer em várias regiões do mundo, sendo a maior parte CM esporádico. O estilo de vida reprodutivo representa importante fator de risco relacionado à exposição ao estrógeno durante a vida, visto que o hormônio é responsável por estimular a proliferação celular mamária. Por outro lado, a enzima metilenotetrahidrofolato redutase (MTHFR) regula o balanço celular entre a metilação e a síntese de ácidos nucléicos. Polimorfismos nos genes dos receptores de estrógeno (ESR1 e ESR2) e do metabolismo do folato (MTHFR) têm sido associados ao risco de CM em diferentes populações. Objetivos: Avaliar a associação entre CM esporádico e os polimorfismos c.2014G>A (ESR1), c.1730G>A (ESR2), c.677C>T e c.1298A>C (MTHFR), incluindo as variáveis clínicas. Material e Métodos: Foram selecionadas 253 amostras de DNA de mulheres com CM esporádico do Laboratório de Genética Molecular do Câncer (FCM-Unicamp) e 257 controles femininos com idade superior a 50 anos e sem história familiar para CM ou câncer de ovário. As amostras foram genotipadas por RFLP-PCR. Foram incluídas variáveis clínicas relacionadas ao indivíduo, aos tumores e ao estilo de vida reprodutivo. Para a análise estatística, foi utilizado o software SPSS vs21.0, empregado o teste ?2 para a distribuição dos polimorfismos e, quando observada diferença no percentual destes, foi calculado a Razão de Prevalência. Resultados: Não foi observada diferença significativa entre os grupos em relação à ocorrência de CM para os polimorfismos: c.2014G>A (p=0,281), c.1730G>A (p=0,241), c.677C>T (p=0,443) e c.1298A>C (p=0,805). Ao associar os genótipos às variáveis clínicas, o alelo A (c.2014G>A) foi menos prevalente em tumores com expressão do receptor de estrógeno (RE positivos) (OR=0,469; 95% IC=0,262 ¿ 0,841) e mais prevalente no estadio 0 em relação aos demais (OR=3,911; 95% IC=1,394 ¿ 10,97), enquanto no genótipo GA teve expressão diminuída de RE e no GG, maior expressão de receptor de estrógeno (RP). Para o c.1730G>A, o genótipo GA foi mais prevalente entre as mulheres que amamentaram (OR=2,257; 95% IC=1,254 ¿ 4,061), menos prevalente em hipertensão arterial sistêmica (HAS) (OR=0,578; 95% IC=0,339 ¿ 0,987) e conferiu proteção do estadio 0 em relação aos demais (OR=4,383; 95% IC=1,606 ¿ 11,96). Na análise do haplótipo c.2014G>A/c.1730G>A, GG/GG foi menos prevalente entre as mulheres que amamentaram (OR=0,525; 95% IC=0,298 ¿ 0,924) e teve maior expressão de RP. Para os polimorfismos no MTHFR, o genótipo CC (c.677C>T) representou um fator de risco para metástases a distância (OR=5,311; 95% IC=1,124 ¿ 25,09) e teve menor expressão de RE, enquanto o genótipo AA (c.1298A>C) foi menos prevalente no estadio 0 em relação aos demais (OR=0,034; 95% IC=0,067 ¿ 0,669) e apresentou maior expressão de RE. Na análise do haplótipo c.677C>T/c.1298A>C, o CC/AA foi associado ao uso de contraceptivo hormonal (OR=3,671; 95% IC=1,344 ¿ 10,03) e HAS (OR=1,979; 95% IC=1,036 ¿ 3,782); e o CT/AC foi menos prevalente no carcinoma invasivo de tipo não especial (NST) (OR=0,032; 95% IC=0,243 ¿ 0,918) e conferiu proteção do estadio 0 em relação aos demais (OR=3,476; 95% IC=1,341 ¿ 10,47). Conclusões: Os polimorfismos parecem não alterar o risco para o desenvolvimento de CM esporádico, no entanto, podem estar associados à sua gravidade / Abstract: The Breast Cancer (BC) is the most frequently diagnosed form of cancer and the main cause of cancer death in worldwide. The reproductive lifestyle is an important risk factor related to exposure to estrogen during the life, being the hormone is responsible for stimulating cell proliferation in the breast. On the other hand, the enzyme methylenetetrahydrofolate reductase (MTHFR) regulates cell balance between synthesis and methylation of nucleic acids. Polymorphisms in the genes of the estrogen receptor (ESR1 and ESR2) and folate metabolism (MTHFR) have been associated with risk of breast cancer in different populations. Objectives: To evaluate the association between sporadic BC and c.2014G>A (ESR1), c.1730G>A (ESR2), c.677C>T and c.1298A>C (MTHFR) polymorphisms, including the risk factor and the association with clinical variables. Material and methods: We enrolled 253 DNA samples from women with sporadic BC from Molecular Genetics of Cancer Laboratory (FCM/Unicamp) and 257 female controls over the age of 50 and without family history of BC or ovarian cancer. The samples were genotyped by PCR-RFLP. Clinical variables were included related to the individual, to tumors and reproductive lifestyle. For statistical analysis, SPSS software vs21.0 was used, the ?2 test was applied for the distribution of polymorphisms and when significant differences was observed, we calculated the odds ratio. Results: There was no significant difference between the groups in the occurrence of BC for the polymorphisms: c.2014G>A (p=0.281), c.1730G>A (p=0.241), c.677C>T (p=0.043) and c.1298A>C (p=0.805). By associating genotypes to clinical variables, the A allele (c.2014G>A) was less prevalent in tumors with positive ER (OR=0.469; 95% CI=0.262 to 0.841) and more prevalent in stage 0 compared to the other (OR=3.911; 95% CI=1.394 to 10.97), while the GA genotype had lower expression of ER and GG, most PR expression. For c.1730G>A, the GA genotype was more prevalent among women who breastfed (OR=2.257; 95% CI=1.254 to 4.061), less prevalent in hypertension (OR=0.578; 95% CI=0.339 to 0.987) and conferred protection to stage 0 in relation to others (OR=4.383; 95% CI=1.606 to 11.96). In the haplotype analysis c.2014G>A/c.1730G>A, GG/GG was less prevalent among those who breastfed (OR=0.525; 95% CI=0.298 to 0.924) and had higher PR expression. For polymorphisms in MTHFR, the CC genotype (c.677C>T) was a risk factor for distant metastasis (OR=5.311; 95% CI=1.124 to 25.09) and had lower expression of SR, while the genotype AA (c.1298A>C) was less prevalent in stage 0 in relation to others (OR=0.034; 95% CI=0.067 to 0.669) and showed a higher expression of ER. In the haplotype analysis for c.677C>T and c.1298A>C, the CC/AA combination was associated with hormonal contraceptive use (OR=3.671, 95% CI=1.344 to 10.03) and hypertension (OR=1.979; 95 % CI=1.036 to 3.782). The CT/AC was less prevalent in invasive carcinoma NST (OR=0.032; 95% CI=0.243 to 0.918) and conferred protection to stage 0 in relation to others (OR=3.476; 95% CI=1.341 to 10.47). Conclusions: The polymorphisms analyzed do not appear to alter the risk for developing sporadic BC, however, may be associated with its severity / Mestrado / Ciencias Biomedicas / Mestra em Ciências Médicas

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Cystic fibrosis (CF) is a single gene Mendelian disorder characterized by pulmonary disease and pancreatic insufficiency. Pulmonary disease is the major cause of death in CF patients. Although some cystic fibrosis transmembrane conductance regulator (CFTR) genotypes are associated with less severe disease, patients possessing the same genotype show great variation in pulmonary disease severity and progression. Genes involved in modulating the inflammatory response and genes increasing susceptibility to infection are proposed as modifiers of pulmonary disease severity. Polymorphisms selected for based on evidence that they affect the function of the gene and prevalence of the putative risk allele: 1) antiprotease gene alpha-1-antitrypsin (alpha-1-AT), 2) innate immunity genes: mannose binding lectin (MBL2) (promoter [G→C] at -221 and codon 52 (Arg52Cys, D allele), 54 (Gly54Asp, B allele), and 57 (Gly57Glu, C allele), and pulmonary surfactant genes SPA-1 (Arg219Trp), SPA-2 (Thr9Asn, Lys223Gln) and SPD (Thr11Met), 3) antioxidant genes GSTM1 and T1 (gene deletion polymorphisms), GSTP1 (Ile105Val) and GCLC repeats, 4) mucin genes (MUC2 and MUC5B). Pulmonary disease progression and survival in patients with chronic Burkholderia cepacia complex (BCC) infection were also investigated controlling for genomovar and RAPD type of the organism. BCC infection was associated with more severe pulmonary disease progression and worse survival. Alpha-1-AT genotype was not a major contributor to variability of pulmonary disease severity, but the results suggest that alpha-1-AT plasma levels during pulmonary infections may be affected by poor nutritional status. We showed similar pulmonary disease progression and MBL2 genotype. Contrary to the previous literature, wild-type MBL2 genotype was associated with steeper decline in pulmonary disease over time following chronic infection with BCC, but genotype was not associated with increased susceptibility to BCC infection. We showed inconsistant results for the pulmonary surfactant gene polymorphisms, GSTM1, T1 and GSTP1 polymorphisms, and number of repeats for GCLC and MUC5B depending on the phenotype investigated. We conclude that some of the variability in pulmonary disease severity and progression in CF is explained by polymorphisms in secondary genes.

Cystic fibrosis (CF) is a single gene Mendelian disorder characterized by pulmonary disease and pancreatic insufficiency. Pulmonary disease is the major cause of death in CF patients. Although some cystic fibrosis transmembrane conductance regulator (CFTR) genotypes are associated with less severe disease, patients possessing the same genotype show great variation in pulmonary disease severity and progression. Genes involved in modulating the inflammatory response and genes increasing susceptibility to infection are proposed as modifiers of pulmonary disease severity. Polymorphisms selected for based on evidence that they affect the function of the gene and prevalence of the putative risk allele: 1) antiprotease gene alpha-1-antitrypsin (alpha-1-AT), 2) innate immunity genes: mannose binding lectin (MBL2) (promoter [G→C] at -221 and codon 52 (Arg52Cys, D allele), 54 (Gly54Asp, B allele), and 57 (Gly57Glu, C allele), and pulmonary surfactant genes SPA-1 (Arg219Trp), SPA-2 (Thr9Asn, Lys223Gln) and SPD (Thr11Met), 3) antioxidant genes GSTM1 and T1 (gene deletion polymorphisms), GSTP1 (Ile105Val) and GCLC repeats, 4) mucin genes (MUC2 and MUC5B). Pulmonary disease progression and survival in patients with chronic Burkholderia cepacia complex (BCC) infection were also investigated controlling for genomovar and RAPD type of the organism. BCC infection was associated with more severe pulmonary disease progression and worse survival. Alpha-1-AT genotype was not a major contributor to variability of pulmonary disease severity, but the results suggest that alpha-1-AT plasma levels during pulmonary infections may be affected by poor nutritional status. We showed similar pulmonary disease progression and MBL2 genotype. Contrary to the previous literature, wild-type MBL2 genotype was associated with steeper decline in pulmonary disease over time following chronic infection with BCC, but genotype was not associated with increased susceptibility to BCC infection. We showed inconsistant results for the pulmonary surfactant gene polymorphisms, GSTM1, T1 and GSTP1 polymorphisms, and number of repeats for GCLC and MUC5B depending on the phenotype investigated. We conclude that some of the variability in pulmonary disease severity and progression in CF is explained by polymorphisms in secondary genes.

La mucoviscidose (CF) est la maladie génétique récessive létale la plus fréquente dans la population caucasienne. Elle est caractérisée par une obstruction et des infections des voies respiratoires et une inflammation chronique. La morbidité et la mortalité sont principalement dues à l'atteinte pulmonaire, qui est variable chez les patients, même lorsqu’ils sont porteurs du même génotype. Les facteurs responsables sont multiples : les mutations dans CFTR (le gène responsable de la maladie), les gènes modificateurs, mais aussi les facteurs environnementaux et les modifications épigénétiques. L'objectif principal de ce projet était de déterminer s'il y avait une corrélation entre la méthylation de l'ADN et la sévérité de l'atteinte pulmonaire chez les patients CF. Nous avons obtenu la cohorte METHYLCF (49 patients CF p.Phe508del homozygotes et 24 témoins sains) ainsi qu’une biobanque d'ADN à partir de sang total et de cellules épithéliales nasales (NEC). Les patients CF ont été stratifiés en fonction de leur VEMS, ajusté à l’âge. D’une part, nous avons analysé la méthylation de l'ADN dans CFTR plus 13 gènes modificateurs en utilisant la méthode de conversion au bisulfite et séquençage de nouvelle génération (plateforme 454 Roche). D’autre part, nous avons réalisé une analyse pan-génomique de la méthylation de l'ADN avec la plateforme 450k BeadChip (Illumina). Les sites différentiellement méthylés (DMS) sélectionnés ont été validés par pyroséquençage (PyroMark Q24, Qiagen). Deux gènes modificateurs ont été identifiés comme différentiellement méthylés chez les patients CF par rapport aux témoins: EDNRA dans le sang et HMOX1 dans le sang et dans les NEC. De façon intéressante, dans les NEC, la méthylation de EDNRA, HMOX1 et GSTM3 a été corrélée avec la sévérité de l’atteinte pulmonaire. De plus, de faibles niveaux de méthylation d'ADN dans GSTM3 ont été associés à la présence de l'allèle GSTM3*B, un polymorphisme de séquence qui a un effet protecteur chez les patients CF. Grâce à l'analyse tout-génome, nous avons identifié 1267 DMS, associés à 638 gènes, chez les patients CF par rapport aux témoins, et 187 DMS, associés à 116 gènes, chez les patients CF sévères par rapport aux modérés. Parmi ces gènes, il y a de nombreux gènes importants pour l’adhésion cellulaire et les réponses immunitaire et inflammatoire. Les DMS identifiés sont enrichis dans des régions prédites comme enhancers, pouvant représenter des séquences régulatrices, mais également en régions intergéniques. De façon intéressante, 80 gènes différentiellement méthylés sur 638 étaient différentiellement exprimés (méta-analyse de données transcriptomiques disponibles). Six sur neuf DMS sélectionnés ont été validés et cinq DMS sur six ont été répliqués dans une population indépendante. De plus, 23 DMS, dont 10 intergéniques, étaient corrélés avec le VEMS. Notre étude a montré que la méthylation de l'ADN est profondément modifiée dans le sang et dans les NEC des patients CF. Des faibles changements de méthylation de l'ADN ont été observés dans des gènes modificateurs connus ; des changements de méthylation plus importants ont été observés dans d'autres gènes qui pourraient représenter de nouveaux modificateurs de la fonction pulmonaire. Ensemble, ces gènes pourraient moduler la sévérité de l’atteinte pulmonaire chez les patients CF. / Cystic fibrosis (CF) is the most common life-threatening recessive genetic disease in the Caucasian population. It is characterized by airway obstruction, respiratory infection and inflammation. Morbidity and mortality are mainly due to lung disease, which is variable among CF patients, even for those having the same genotype. Contributing factors are mutations in CFTR (the disease-causing gene), modifier genes, but also environmental factors and epigenetics. The main goal of this project was to determine whether there was a correlation between DNA methylation and the severity of CF lung disease. We built the METHYLCF cohort (49 p.Phe508del homozygous CF patients and 24 healthy controls) and a DNA biobank from whole blood and nasal epithelial cells (NEC). CF patients were stratified accordion to their FEV1% predicted, adjusted to age. We profiled DNA methylation at 14 modifier genes using bisulfite conversion and next-generation sequencing (454 Roche). Genome-wide DNA methylation was analyzed with the 450K Beadchip (Illumina). Selected differentially methylated sites (DMS) were validated by pyrosequencing. Using the candidate modifier gene approach, we showed that two CF modifier genes were differentially methylated in CF patients compared to controls: EDNRA in blood and HMOX1 in blood and NEC. Methylation of EDNRA, HMOX1 and GSTM3 was associated with lung disease severity in NEC. Interestingly, low DNA methylation levels at GSTM3 were associated with the GSTM3*B allele, a polymorphic 3-bp deletion that has a protective effect on CF patients. In addition, through the genome-wide analysis, we identified 1267 DMS, associated with 638 genes, between CF patients and controls and 187 DMS, associated with 116 genes, between severe CF and mild CF patients. DMS were enriched at predicted enhancers, which may represent regulatory sequences, and also at intergenic regions. Gene ontology analyses highlighted cellular processes relevant to CF, i.e. cell adhesion and inflammatory and immune response. Interestingly, 80 out of 638 differentially methylated genes were differentially expressed in publicly available NEC transcriptomic data. Six out of 9 selected DMS were validated and five out of six DMS were replicated in an independent set of patients. Additionally, 23 DMS, 10 of which were intergenic, correlated with FEV1% predicted. Our study has shown that DNA methylation is altered in blood and NEC of CF patients. Small DNA methylation changes were observed at known CF modifier genes; more dramatic DNA methylation changes were found at other genes that may impact lung function. Collectively, these epigenomic variations may lead to different degrees of lung disease severity in CF patients.

Cystic fibrosis (CF) is a single gene Mendelian disorder characterized by pulmonary disease and pancreatic insufficiency. Pulmonary disease is the major cause of death in CF patients. Although some cystic fibrosis transmembrane conductance regulator (CFTR) genotypes are associated with less severe disease, patients possessing the same genotype show great variation in pulmonary disease severity and progression. Genes involved in modulating the inflammatory response and genes increasing susceptibility to infection are proposed as modifiers of pulmonary disease severity. Polymorphisms selected for based on evidence that they affect the function of the gene and prevalence of the putative risk allele: 1) antiprotease gene alpha-1-antitrypsin (alpha-1-AT), 2) innate immunity genes: mannose binding lectin (MBL2) (promoter [G→C] at -221 and codon 52 (Arg52Cys, D allele), 54 (Gly54Asp, B allele), and 57 (Gly57Glu, C allele), and pulmonary surfactant genes SPA-1 (Arg219Trp), SPA-2 (Thr9Asn, Lys223Gln) and SPD (Thr11Met), 3) antioxidant genes GSTM1 and T1 (gene deletion polymorphisms), GSTP1 (Ile105Val) and GCLC repeats, 4) mucin genes (MUC2 and MUC5B). Pulmonary disease progression and survival in patients with chronic Burkholderia cepacia complex (BCC) infection were also investigated controlling for genomovar and RAPD type of the organism. BCC infection was associated with more severe pulmonary disease progression and worse survival. Alpha-1-AT genotype was not a major contributor to variability of pulmonary disease severity, but the results suggest that alpha-1-AT plasma levels during pulmonary infections may be affected by poor nutritional status. We showed similar pulmonary disease progression and MBL2 genotype. Contrary to the previous literature, wild-type MBL2 genotype was associated with steeper decline in pulmonary disease over time following chronic infection with BCC, but genotype was not associated with increased susceptibility to BCC infection. We showed inconsistant results for the pulmonary surfactant gene polymorphisms, GSTM1, T1 and GSTP1 polymorphisms, and number of repeats for GCLC and MUC5B depending on the phenotype investigated. We conclude that some of the variability in pulmonary disease severity and progression in CF is explained by polymorphisms in secondary genes. / Medicine, Faculty of / Medicine, Department of / Experimental Medicine, Division of / Graduate

<p> Obesity is a growing concern as 42.3% of people in the U.S were considered obese in the years 2017- 2018. Little is known about the genetic components that contribute to weight gain. In humans, the hormone glucagon is a major contributor to the body’s energy demand as it helps break down lipids. Therefore, learning more about this pathway could enable a range of therapeutics. In fact, studies have shown that glucagon treatments have helped patients with both weight loss and appetite suppression. In this project, we analyzed candidate genes that modify the glucagon pathway in <em>Drosophila melanogaster.</em> We reduced the expression of the fly version of the glucagon receptor (AKHR) in our model. This induces fat retention in the L3 larvae, which mimics obesity in humans. We then crossed our model to the DGRP and looked for natural variation in fat content using a density assay. The density assay examines the relative fat levels of the larvae by slowly increasing the amount of sucrose in water. This enables us to observe whether we have lean larvae which float later or fat larvae which float early on. We used the variation in floating concentration to identify candidate modifier genes through GWA or genome-wide association study. We crossed our <em>AKHR</em> RNAi model to RNAi for various candidate modifier genes that may enhance or suppress fat retention. We screened these candidates initially with the same density assay used in the original study. This resulted in four candidate genes that significantly impacted the density of the larvae: <em>THADA</em>, <em>AmyD</em>, <em>GluRIIC</em>, and <em>CG9826</em>. We further characterized these candidates using biochemical assays to analyze stored metabolites such as triglycerides, glucose, glycogen, and protein. These have been further analyzed under control, high sugar, and high fat conditions to see if the larvae are resistant to environmental changes. <em>CG9826</em> showed significant increase in stored fats across all environments. <em>THADA</em> RNAi showed an increase in fat in the high fat environment. Overexpression of <em>THADA</em> showed a decrease in fat storage in the high fat environment. Our goal is to advance our understanding of the glucagon signaling pathway, obesity, and lipid metabolism. We are also hopeful to provide candidate genes that can be regarded as future therapeutic targets. </p>