Dissertations / Theses on the topic 'Genes, Modifier'

Cystic Fibrosis is one of the most common genetic recessive diseases among Caucasians and is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene on chromosome 7. There are different classes of CFTR mutation, leading to differences in disease severity among patients. In addition to the CFTR genotype, secondary genetic factors, modifier genes, also influence CF phenotypes. Due to the dysfunction of CFTR protein and production of thickened mucus, bacterial infection in the lungs is favored and can lead to further clinical complications in CF patients. Pseudomonas aeruginosa is one of the most common bacteria detected among patients. The aim of this project was to investigate four candidate modifier genes, Factor B, Complement Factor 3, Toll-like Receptor 4 and Heme oxygenase-1, which might affect the status of Pseudomonas aeruginosa infection. A total of 22 single nucleotide polymorphisms (SNPs) were selected in these four genes and they were tested against five phenotypic traits, including age of diagnosis, FEV1% predicted andstandard deviation value, age of first Pseudomonas aeruginosa infection and Pseudomonas aeruginosa infection status. Among the selected SNPs, both case-control studies and family-based analysis were performed in order to establish any correlation between the genotypes and the phenotypes. In addition, haplotype analysis was performed to determine whether there was interaction between SNPs or whether there were unidentified SNPs in the vicinity of the selected ones that might contribute to the observed phenotypic traits. Among the 22 chosen SNPs, 13 of them were found to be significantly linked to one or more of the tested phenotypes. The three most significant associations were BF_2557 with lung function, HMOX1_9531 with lung function and BF_7202 with age of diagnosis. Several haplotypes were significantly associated with one of the five phenotypes. There was no evidence for the presence of unidentified SNPs or interaction between SNPs. Most of haplotype associations were likely due to the presence of a single SNP which was found to be significantly linked to the phenotype. Conclusively, both SNPs and haplotype analyses suggest that the four candidate genes are modifiers of disease severity in CF.

Von Willebrand Disease (VWD) is the most common bleeding disorder. In addition to known major genes, genetic modifiers, such as ABO blood group, affect quantitative outcome measures for VWD. The data consist of an 854-member Amish pedigree with established linkage of VWD to a locus within the Von Willebrand Factor (VWF) gene on chromosome 12. The DNA sequence of the causative mutation is known. Phenotypic information and genotypic data consisting of VWF mutation status and a genome screen of markers are available for 385 pedigree members. Genetic modifiers of the VWF mutation are investigated using known and new conditional linkage methods that search for modifier genes of a major gene with known mutation. The MCMC-based program LOKI was used to conduct multipoint linkage analysis of VWD outcome measures while controlling for the VWF mutation. Adjustment for the mutation did not eliminate the linkage signal on chromosome 12 in the same location as the VWF mutation. Evidence for QTLs was also found on six other chromosomes. Smod, a score statistic that detects evidence of a genetic modifier conditional on linkage to a major gene, was developed for sib pair data. To limit the modifier gene main effect, Smod was developed so that variance due to the modifier locus is bounded above by the variance of the interaction between major gene and modifier gene. The performance of Smod was compared to other published score statistics. Power to detect linkage to the modifier locus depended on major gene and modifier gene risk allele frequencies, relative contribution of the major gene main effect to the interaction effect, and the upper bound on the modifier gene main effect. The Amish pedigree was broken up into sib pair data and analyzed using Smod and other score statistics. Using these statistics, the strongest evidence for QTLs for VWD was also found on chromosome 12 in the region of the VWF mutation. Combined with the LOKI results, further analysis will help determine if intragenic modification is occurring or if linkage disequilibrium between the mutation and analyzed markers is driving results.

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
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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

Thesis (MSc)--University of Stellenbosch, 2002.
ENGLISH ABSTRACT: Variegate porphyria (VP, MIM 176200) is a low penetrance autosomal dominant disorder that stems from mutations in the protoporphyrinogen oxidase (PPOX) gene. VP is found in most populations, but has a high prevalence in the South African Afrikaner population with most patients inheriting the same PPOX mutation (R59W) from a common ancestor. The clinical manifestations of the disease include acute neurovisceral attacks and/or cutaneous photosensitivity. Great variation in the clinical presentation of VP is observed; even in members of the same family that share a common genetic background and that have been exposed to similar environmental factors. Candidate genes that may have an influence on phenotypic variation due to the regulatory function in the haem biosynthetic pathway include the two deltaaminolevulinic acid synthase (ALAS) genes and the porphobilinogen deaminase (PBGD) gene. Sequence homology searches between different species indicated that the ALAS-1, ALAS-2 and PBGD genes are highly conserved, indicating that these genes have an important function to fulfill in the haem biosynthetic pathway. The study population of 25 R59W individuals were divided in four categories according to their clinical presentation. The distribution of clinical symptoms observed in this study corresponds with results from previous studies. Conformation sensitive gel electrophoresis (CSGE), conventional single stranded conformation polymorphism analysis (SSCP) and two buffer SSCP analysis were implemented to screen for possible sequence variants. The exons of all three genes as well as the adjacent intronic sequences were investigated. A total of six sequence variation sites were identified of which five had previously been described single nucleotide polymorphisms (ALAS-1: 4713 T>C; PBGD: -64 C>T, 3581 A>G, 6479 G>T, 7064 C>A)] and a novel 8bp deletion (PBGD: 4582_ 4589del). No sequence variant was identified in the ALAS-2 gene. The CSGE method proved to have the highest sensitivity (83%), identifying five of six sequence variant sites. The conventional SSCP method identified only three (50%) sequence variant sites, while the two buffer system detected two (33%) of the sequence variants. The 4713 T>C SNP in exon 4 of the ALAS-1 gene and the -64 C>T SNP in the PBGD gene were selected for further investigation due to their location in the respective genes. These sequence variants were typed in 50 patients and 50 control subjects matched for ethnic background. The relationship between variation at these loci and clinical features was investigated. No statistical significant association was observed for either of the 4713 T>C SNP (P= 0.717) or the -64 C>T SNP (P= 0.931). Genetic modifying factors make a variable contribution to the total clinical picture and are difficult to identify in small populations. Due to the fact that we only had a limited number of VP samples, association cannot be ruled out. This study does, however, provide insight into investigational approaches that should be undertaken in future research concerning the ALAS and PBGD genes. Further knowledge concerning the haem biosynthetic pathway could ultimately lead to the understanding and assessment of the clinical expression observed in individuals with VP.
AFRIKAANSE OPSOMMING: Variegate porfirie (VP, MIM 176200) is 'n lae penetrasie outosomaal dominante siekte wat veroorsaak word deur mutasies in die protoporfirienogeen oksidase (PPOX) geen. VP word gevind in die meeste populasies, maar het 'n hoë voorkoms in die Suid- Afrikaanse populasie waar meeste pasiente dieselfde PPOX mutasie (R59W) van 'n gemeenskaplike voorouer oorgeërf het. VP word gekenmerk deur akute neuroviserale aanvalle en/of fotosensitiewe vel. Groot variasie word egter waargeneem in die kliniese uitdrukking van VP, selfs in lede van dieselfde familie wat 'n gemeenskaplike genetiese agtergrond deel en wat blootgestel is aan dieselfde omgewingsfaktore. Kandidaat gene wat as gevolg van hulle regulatoriese funksie in die heem biosintetiese padweg 'n effek op die ekspressie van VP mag hê, sluit in die twee deltaaminolevuliniese suur sintase (ALAS) en die porfobilinogeen deaminase (PBGD) gene. Homologie ondersoeke van die ALAS-1, ALAS-2 en PBGD gene in verskillende spesies dui daarop dat die gene hoogs gekonserveerd is en dus gevolglik 'n belangrike funksie in die heem biosintetiese padweg vertolk. Die studie populasie van 25 R59W individue is verdeel in vier kategorieë op grond van hulle kliniese simptome. Die verspreiding van die kliniese simptome wat waargeneem is tydens hierdie studie stem ooreen met die resultate van vorige studies. Konformasie sensitiewe gel elektroforese (CSGE), konvensionele enkelstring konformasie polimorfisme analise (SSCP) en twee buffer SSCP analise is gebruik vir die identifisering van genetiese variasie. Die eksons van al drie gene, sowel as die aangrensende intron volgordes, is ondersoek. 'n Totaal van ses areas van genetiese variasie is geïdentifiseer, waarvan vyf reeds beskryfde polimorfismes is (ALAS-1: 4713 T>C; PBGD: -64 C>T, 3581 A>G, 6479 G>T, 7064 C>A) en 'n nuwe 8bp delesie (PBGD: 4582_ 4589del). Geen genetiese volgorde variasie is gevind in die ALAS-2 geen nie. Die CSGE metode het die hoogste sensitiwiteit getoon (83%) en het vyf van die ses volgorde variasies geïdentifiseer. Die konvensionele SSCP metode het slegs drie volgorde variasies geïdentifiseer (50%), terwyl die twee buffer deteksie-sisteem twee variasies geïdentifiseer (33%) het. Die 4713 T>C polimorfisme in ekson 4 van die ALAS-1 geen en die -64 C>T polimorfisme in die PBGD geen, is geselekteer vir verdere ondersoek as gevolg van hulle posisie in die respektiewe gene. Die volgorde variasies is getipeer in 50 R59W pasiënte sowel as in 'n kontrole groep van 50 individue met dieselfde etniese agtergrond. Die verband tussen die variasie by die lokusse en die kliniese kenmerke is ondersoek. Geen statisties beduidende assosiasie is waargeneem vir hetsy die 4713 T>C SNP (P= 0.717) of die -64 C>T SNP (P= 0.931). Genetiese modifiserende faktore word moeilik geïdentifiseer in klein populasies omdat hulle afsonderlike bydra tot die geheelbeeld van die kliniese simptome so varieerbaar is. 'n Relatiewe klein groep van VP pasiënte was tydens die studie beskikbaar en dus kan assosiasie nie uitgesluit word nie. Die studie verskaf egter insig in verband met toekomstige benaderings wat volg kan word in verdere ondersoeke van die ALAS en PBGD gene. Verdere kennis in verband met die heem biosihtetiese padweg kan uiteiHdelik lei tot die verduideliking en assesering van die kliHiese uitdrukking in vI=' individue.

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.

Orientador: Carmen Silvia Bertuzzo
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas
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Resumo: A Fibrose Cística é uma alteração genética que cursa principalmente com manifestações pulmonares e pancreáticas. A correlação genótipo-fenótipo da fibrose cística é motivo de árduos estudos. Somente a correlação com a insuficiência pancreática foi encontrada. Percebeu-se, também, que o curso e a gravidade da manifestação pulmonar não estão correlacionados com o genótipo CFTR. A doença pulmonar pode ser influenciada por fatores ambientais e por fatores genéticos. Genes modificadores podem influenciar na gravidade do fenótipo dos fibrocísticos através de vários mecanismos. O objetivo desse projeto foi analisar alguns genes modificadores, MBL2, TGFB1 e CD14, e correlacionar com a gravidade do quadro pulmonar dos fibrocísticos. Verificar a presença dos alelos 'delta'F508 e a gravidade do quadro pulmonar nos paciente fibrocísticos. A análise de polimorfismos no gene MBL2 e no gene TGF- 'beta'1 no códon 10 na posição + 869, foi realizada através da técnica da reação em cadeia da polimerase alelo específica. A genotipagem do polimorfismo C-159T, no gene CD14 foi realizada através da reação em cadeia da polimerase e digestão enzimática. Em nossa casuística, os polimorfismos do gene MBL2 não foram associados com a gravidade do quadro pulmonar em pacientes fibrocísticos. Com relação ao polimorfismo T869C no gene TGFB1, encontramos apenas associação do heterozigoto TC com quadro pulmonar leve (P=0,04). Para o polimorfismo C-159T no gene CD14, obtivemos um predomínio de pacientes com o genótipo TT (P=0,0009), mas não houve discriminação com relação à gravidade do quadro pulmonar. Com isso concluímos que houve uma associação entre o genótipo TC do polimorfismo T869C (TGF-'beta'1) e o quadro pulmonar leve nos fibrocísticos. Com relação ao gene CD14, o genótipo TT parece ser um fator de risco para o quadro pulmonar, mas não um fator modulador da gravidade. Em nossa casuística, não existiu associação entre pacientes homozigotos para a mutação 'delta'F508 e a gravidade do quadro pulmonar
Abstract: Cystic fibrosis is a genetic alteration characterized mainly by pancreatic and pulmonary manifestations. The genotype-phenotype correlation in cystic fibrosis has been the subject of arduous studies. A correlation between cystic fibrosis and pancreatic insufficiency, as well as to the fact that the occurrence and severity of pulmonary manifestations are not correlated with CFTR genotype, has been observed. Pulmonary illness can be influenced by environmental and genetic factors. Modifier genes can influence the phenotype severity of patients with cystic fibrosis through some mechanisms. The objective of this study was to analyze some modifier genes, such as MBL2, TGFB1 and CD14, and to correlate them with the gravity of the pulmonary picture of patients with cystic fibrosis and to also verify the presence of the alleles 'delta'F508 and the gravity of the pulmonary picture in these patients. The analysis of MBL2 and TGF-'beta'1 gene polymorphisms at codon 10, in the position + 869, was carried out using the technique of allele-specific polymerase chain reaction. The genotyping of the CD14/-159 polymorphism was performed by polymerase chain reaction and enzymatic digestion. In our casuistic, the polymorphism of the MBL2 gene was not associated with the gravity of the pulmonary picture in patients with cystic fibrosis. Regarding the T869C polymorphism in the TGFB1 gene, we found only an association of heterozygote TC with a mild pulmonary picture (P=0,04). In the C-159T polymorphism of the CD14 gene, we observed an accumulation of patients with genotype TT (P=0,0009), but did not have a discrimination regarding the gravity of the pulmonary picture. Therefore we concluded that there was an association between the genotype TC of the T869C polymorphism (TGF-'beta'1) and the mild pulmonary picture in the patients with cystic fibrosis. Regarding the CD14 gene, the TT genotype seems to be a risk factor for the pulmonary picture, but not a gravity modulating factor. In our casuistic, we found no association between 'delta'F508 homozygote patients for the mutation and the gravity of the pulmonary picture
Doutorado
Ciencias Biomedicas
Mestre em Ciências Médicas

Orientador: Carmen Silvia Bertuzzo
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas
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Resumo: A fibrose cística (FC) é uma doença autossômica recessiva com características de doença complexa. Complicações clínicas parece ser fator decisivo para o prognóstico dos pacientes. Os polimorfismos nos genes ADRA2A e TCF7L2 são importantes para elucidar parte da variabilidade encontrada nas características clínicas de doenças inflamatórias, incluindo a FC, que tem a Diabetes Mellitus como uma importante co-morbidade. Os objetivos deste estudo foram determinar a frequência do polimorfismo rs12255372 no gene TCF7L2 e sua associação com Diabetes Mellitus em pacientes com fibrose cística, e investigar a associação de 27 variáveis clínicas da FC com os polimorfismos rs553668 e rs10885122 do gene ADRA2A. Em nosso estudo, 145 pacientes foram avaliados em relação ao genótipo do polimorfismo rs12255372 no gene TCF7L2 e 176 pacientes foram avaliados em relação à associação dos polimorfismos rs553668 e rs10885122 no gene ADRA2A com 27 variáveis clínicas da FC. Todos os pacientes em atendimento no Ambulatório de Pediatria da Faculdade de Ciências Médicas da UNICAMP foram confirmados como tendo fibrose cística por dois testes de suor alterados (valor de sódio e de cloro superior a 60 mmol / L) e por análise de diferencial do epitélio da membrana do intestino através da dosagem de CFTR pela câmara Ussing. A identificação das mutações do gene CFTR foi realizada no laboratório de Genética Molecular da FCM/Unicamp. O rastreio do polimorfismo rs12255372 foi feito através da técnica de PCR associada à digestão enzimática específica. O rastreio dos polimorfismos rs553668 e rs10885122 no gene ADRA2A foi feito por PCR ARMS. Uma comparação genotípica foi realizada com as 27 variáveis clínicas, da FC considerando as mutações do gene CFTR. Encontramos associações clínicas, sem considerar as mutações no gene CFTR, com as variáveis categóricas: raça [para o polimorfismo rs553668 (p = 0,002), grupo haplotípico (p = 0,014)], íleo Meconial [para o polimorfismo rs553668 (p = 0,030) Quando consideradas as duas mutações no gene CFTR, encontramos associações com as variáveis íleo meconial (p = 0,0012) e IMC [para o polimorfismo rs553668 (p = 0,014)]. A associação com dados numéricos, sem considerar as mutações no gene CFTR, foi positiva para a idade ao diagnóstico [para o polimorfismo rs553668 (p = 0,022)]. Considerando as duas mutações no gene CFTR, a associação com dados numéricos foi positiva para o Escore de Bhalla [para o polimorfismo rs553668 (p = 0,014)], Escore de Shwachman-Kulczycki [para o polimorfismo rs553668 (p = 0,008) e haplótipos (p = 0,050)]. Os polimorfismos rs553668 e rs10885122 no gene ADRA2A parecem ser moduladores da gravidade da FC em nossa amostra. Em nossa amostra, não houve associação entre o polimorfismo rs12255372 no gene TCF7L2 e a Diabetes Mellitus
Abstract: Cystic fibrosis (CF) is an autosomal recessive disease with characteristics of complex disease. Clinical complications appear to be a decisive factor in the prognosis of patients. The ADRA2A and TCF7L2 gene polymorphisms are important to elucidate part of the variability encountered in clinical characteristics in inflammatory diseases, including CF, which has diabetes-associated as an important comorbidity. The aims of this study ware to determine the frequency of polymorphism rs12255372 in the TCF7L2 gene and its association with Diabetes Mellitus in Cystic Fibrosis patients and to investigate the association of 27 CF clinical variables with ADRA2A polymorphisms. In our study, 145 patients were evaluated in relation to the genotype of the rs12255372 polymorphism in the TCF7L2 gene. 176 patients were evaluated in relation to associate rs553668 and rs10885122 polymorphisms in the ADRA2A gene with 27 CF clinical variables. All patients in attendance at the Pediatric Clinic at the Faculty of Medical Sciences, UNICAMP, were confirmed as having cystic fibrosis by two altered sweat tests (sodium and chlorine value greater than 60 mmol/L) and by analysis of differential membrane epithelium of the intestine by the dosage of active CFTR through the Ussing chamber. The identification of CFTR gene mutations was performed in the laboratory of Molecular Genetics, FCM/Unicamp. The rs12255372 polymorphism was screening by PCR method associated with specific enzymatic digestion. The rs553668 and rs10885122 polymorphisms in ADRA2A gene were screening by ARMS-PCR. A genotypic comparison was performed with 27 CF clinical variables, considering CFTR mutations. We found clinical associations, without considering the mutations in the CFTR gene, with categorical variables: race [for polymorphism rs553668 (p = 0.002), haplotype group (p = 0.014)], meconium ileus [for polymorphism rs553668 (p = 0.030). Considering the two mutations in the CFTR gene, we find associations with categorical variables meconium ileus (p = 0.0012) and BMI [for polymorphism rs553668 (p = 0.014)]. The association with numerical data, without considering the mutations in the CFTR gene, was positive for age at diagnosis [for polymorphism rs553668 (p = 0.022)]. Considering the two mutations in the CFTR gene, the association with numerical data was positive for Bhalla score [for polymorphism rs553668 (p = 0.014)], Shwachman-Kulczycki score [for polymorphism rs553668 (p = 0.008) and haplotypes (p = 0.050)]. Polymorphisms rs553668 and rs10885122 in ADRA2A gene appear to be modulators of CF severity in our sample. In our sample, there was no association between the polymorphism rs12255372 in the TCF7L2 gene and Diabetes Mellitus
Doutorado
Clinica Medica
Doutora em Clínica Médica

Herz-Kreislauf-Erkrankungen als Folge arteriosklerotischer Prozesse sind die häufigste Todesursache weltweit. Lipidstoffwechselstörungen sind ein wichtiger Risikofaktor für die Pathogenese der Arteriosklerose. Komplexe Phänotypen, wie z.B. der Lipidstoffwechsel, werden durch eine Vielzahl von genetischen und Umweltfaktoren beeinflusst. Obwohl der Lipidstoffwechsel biochemisch gut charakterisiert ist und viele Gene, die für Proteine innerhalb des Lipidstoffwechsels kodieren bekannt sind, sind die spezifischen genetischen Faktoren, die die Variabilität des Lipidstoffwechsels beeinflussen, weitgehend unbekannt. Die vorgelegten Studien zeigen verschiedene Ansätze, wie genetische Faktoren, die die Variabilität des Lipidstoffwechsels beeinflussen, identifiziert und quantifiziert werden können. Dabei wird ein besonderer Schwerpunkt auf die Untersuchung der Variabilität im nicht-pathologischen Bereich des Stoffwechsels gelegt. Im Rahmen der durchgeführten Arbeiten wurden: 1. modifizierende Genorte bei familiären Hyperlipidämien identifiziert. Dieser Ansatz wurde am Beispiel von zwei Familien mit familiärer Hypercholesterinämie aus Israel und Syrien illustriert. Mit Hilfe der Familie aus Israel wurde ein Genort, der für einen Cholesterin-senkenden Effekt verantwortlich ist, kartiert. Mit Hilfe der Familie aus Syrien wurde ein Gen für die Ausprägung von Xanthomen postuliert. 1. der Einfluß von Genen und Genorten auf die Variabilität des Lipidstoffwechsels in einer Zwillingspopulation nachgewiesen. Dieser Anstz wurde anhand von Genorten auf Chromosom 13q (Cholesterin-senkender Genort), auf Chromosom 8 (Lipioprotein Lipase und Makrophagen Scavenger Rezeptor) und dem PPAR?-Gen auf Chromosom 3 illsutriert. 3. der Einfluß einzelner genetischer Varianten in sechs Kandidatengenen des Lipidstoffwechsels in einer familienbasierten Stichprobe quantifiziert. 4. ein mathematisches Modell des Lipidstoffwechsels entwickelt, mit dem Ziel, sich der Komplexität des Stoffwechsels sowohl von experimenteller als auch von theoretischer Seite her zu nähern.
Cardiovascular disease resultung from atherosclerotic processes are the most commonest cause of death worldwide. Lipid disturbances are a major risk factor in the pathogenesis of atherosclerosis. Complex phenotypes, e.g. lipid metabolism, are influenced by a variety of genetic and environmental factors. Although lipid metabolism is well characterized biochemically and many genes, coding for proteins of lipid metabolism are known, the specific genetic variants, influencing the variability of lipid metabolism are largely unknown. The studies presented show different approaches to the identification of genetic factors contributing quantitatively and qualitatively to the variability of lipid metabolism. This work puts an emphasis on the variability in the non-pathological range of lipid concentrations. The following issues are addressed in the context of this work: 1. Identification of modifying genes of familial lipid disorders. This approach is illustrated for two families with familial hypercholesterolemia from Israel and Syria. The family from Israel allowed the mapping and identification of a cholesterol-lowering gene locus. The family from Syria helped postulating a giant xanthoma gene. 2. The influence of genes and gene loci on the variability of lipid metabolism using a twin cohort. This approach was illustrated for gene loci on chromosome 13q (cholesterol-lowering gene locus), chromosome 8 (Lipoprotein lipase and macrophage scavenger receptor gene locus), and the PPAR?-gene on chromosome 3. 3. The influence of single nucleotide polymorphisms in six lipid metabolism relevant genes using a family based association approach. 5. A mathematical model of lipid metabolism was developed. The goal was to approach the complexity of lipid metabolism experimentally as well as theoretically.

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

Gene expression technologies allow expression levels to be compared across treatments for thousands of genes simultaneously. Statistical methods exist for identifying differentially expressed (DE) genes and gene sets while controlling multiple testing error. Most methods do not take into account the distribution of effect sizes or the overrepresentation of observed patterns. This paper compares a recently proposed modified q-value method that takes into account such patterns to a traditional q-value method for experiments with three treatments. The results of simulation studies performed suggest that the proposed methods improve upon the traditional method in the identification of DE genes in certain settings, but are outperformed by the traditional method in other settings. Analysis of data sets from real microarray.

CD8 T cells recognize complexes of MHC class I and peptide on the surface of target cells. MHC class I antigen presentation is a long pathway, in which proteins are degraded by proteasomes to generating oligopeptides, which may be further trimmed by aminopeptidases in the cytosol. Peptides are transported into the ER, where they may be further trimmed by ER lumenal aminopeptidases and bind to newly-synthesized MHC class I complexes. Proteins degraded by the proteasome are generally tagged with ubiquitin by a combination of ubiquitin-conjugating enzymes and ubiquitin ligases. UBC9 is one ubiquitin conjugating enzyme, which does not conjugate ubiquitin, but instead conjugates small ubiquitin-like molecules (SUMO) to target protein. UBC9 has been found to regulate the functions of many proteins in vivo, most importantly by modifying nuclear transportation and function. Curing [During] my thesis work, I studied the function of UBC9 in MHC class I antigen presentation. UBC9 over-expression in COS cells co-expressing ovalbumin markedly increased presentation SIINFEKL (the immunodominant epitope from ovalbumin in the context of H-2Kb), and UBC9 overexpression increased cell surface H-2Kbin general, suggesting that Ubc9 increased MHC class I antigen presentation by increasing peptide supply. UBC9 did not increase synthesis or degradation of ovalbumin. In transient transfection experiments, Ubc9 increased presentation of SIINFEKL precursors that did, and that did not, depend on proteasomes for processing, as well as SIINFEKL precursors targeted to the ER, bypassing cytosolic processing altogether. However, a C-terminal extended precursor of SIINFEKL, which requires only proteasomal processing before presentation, was the most markedly affected by UBC9 overexpression. This suggested that UBC9 was affecting the pattern of cleavages made by proteasomes in ways that enhance the generation of the C-terminus of SIINFEKL. Because presentation of SIINFEKL itself (which requires no further proteolytic processing) was also enhanced, UBC9 must also affect steps in the class I pathway that occur after the generation of the mature epitopes. UBC9 did not affect the rate of peptide degradation in cytosolic extracts or in intact cells. These findings suggested that UBC9 might have multiple effects on the MHC class I antigen presentation pathway. Immunofluorescent microscopy demonstrated that UBC9 increased the expression of the beta subunits of immunoproteasomes (LMP2, LMP7, and MECL1) as well as of TAP1 and tapasin. In contrast, UBC9 expression did not increase levels of calnexin, calreticulin, ERp57, or Protein disulfide isomerase (PDI). Similarly, levels of leucine aminopeptidase were not increased in UBC9-transfected cells. Therefore, UBC9 overexpression increases the levels of some but not all components of the class I pathway. UBC9 overexpression increased protein levels of MECL1, LMP2 or LMP7 that were under the control of viral promoters, and levels of MECL1 mRNA were similar in control vector and UBC9 transfected cells. Therefore, UBC9 did not increase the level of expression of these subunits through increased transcription. Pulse-chase experiments showed that UBC9 overexpression reduced the degradation of MECL1. Therefore, UBC9 increases the levels of at least some of these components of the MHC class I antigen presentation pathway by increasing their stability. To know the biological significance of UBC9 in MHC class I antigen presentation, I used small interfering RNA (siRNA) to knock down UBC9. Though UBC9 can be successfully knocked down by siRNA, the UBC9-negative cells became very sick, and were not suitable for the study of MHC class I antigen presentation. There are three forms of SUMO molecules in mammalian cells: SUMO-1, SUMO-2 and SUMO-3. My study suggested that SUMO-2 may be involved in UBC9's regulation of MHC class I antigen presentation, since mutant SUMO-2 blocked UBC9's ability to increase H-2Kb-SIINFEKL levels on the cell surface after the cells were loaded with ovalbumin. To further study the function of UBC9, I mutated the active amino acid Cys 93 of UBC9 to Ser (UBC9OH). Unexpectedly, this mutant form (UBC9OH) has very similar effects as wild-type UBC9, increasing Kb-SIINFEKL levels at the cells surface. This suggested that UBC9 protein regulates MHC class I antigen presentation pathway proteins by direct or indirect protein interaction, rather than (or as well as) by SUMO conjugation. Taking account of SUMO-2 results, I propose that wild-type UBC9 (either transfected or endogenous) conjugates SUMO-2 to its substrates, and then UBC9 (wild-type or mutant) interacts with its sumoylated targets, thus affecting protein functions. I also studied heat shock protein Hsp27, which is known to be a substrate for UBC9 in vivo. Hsp27 is expressed in a variety of tissues in the absence of stress, and may regulate actin dynamics. Hsp27 overexpression decreased generation of H-2Kb-SIINFEKL complexes from SIINFEKL precursors that did, and did not, require proteasomes for processing, or that were targeted to the ER. Hsp27 over-expression did not affect protein synthesis, and globally decreased cell surface H2-Kb and H2-Dblevels, but did not affect HLA-A0302 level. Hsp27 overexpression inhibits the presentation of ER-localized SIINFEKL. Taken together, my data suggested that HSP27 may inhibit MHC class I antigen presentation by affecting MHC class I molecules itself rather than peptide supply. After Hsp27 was eliminated with siRNA, the effects were very similar to those seen with Hsp27 overexpression. Levels of H-2Kb-SIINFEKL decreased, and overall cell surface H-2Kb and H-2Db levels decreased. It is possible that when Hsp27 is over-expressed, it acts as a dominant negative form, conferring a similar phenotype to Hsp27 knockdown. These observations suggest that Hsp27 plays an important role in MHC class I antigen presentation.

L'hémochromatose génétique de type 1 est caractérisée par une surcharge en fer dans les organes parenchymateux. Elle est provoquée par une mutation ponctuelle (C282Y) du gène HFE, très fréquente dans les populations originaires du nord ouest de l'Europe. Des études épidémiologiques récentes mettent en évidence une pénétrance incomplète et une variabilité de l'expressivité de la maladie. Ceci peut s'expliquer par l'action de facteurs non génétiques (âge, alimentation, dons de sang réguliers. . . ) et génétiques. Pour étudier l'action de ces derniers dans l'intensité de la surcharge hépatique, nous avons utilisé un modèle murin d'hémochromatose : les souris Hfe-/-. L'étude comparative de 4 souches de souris consanguines (C57BL/6, CBA, DBA/2 et 129/Sv) a montré des différences de régulation du métabolisme du fer selon les souches. L'analyse de souris Hfe-/- sous deux fonds génétiques distincts (C57BL/6 et DBA/2) a révélé que l'intensité de la surcharge en fer varie en fonction de la souche et fait intervenir d'autres gènes qui modulent l'action de HFE. Nous avons démontré que les souris Hfe-/- des deux fonds génétiques varient, non seulement par l'intensité de la surcharge mais aussi par les régulations transcriptionnelles mises en jeu dans le duodénum. Par une approche de criblage du génome, nous avons identifié quatre régions chromosomiques avec un lod score significatif d'une liaison génétique. Enfin, le niveau hépatique d'expression des ARNm de diverses molécules dont l'hepcidine a été dosé chez des souris Hfe-/- de deux souches (C57BL/6 et DBA/2). Bien que nous n'ayons pas mis en évidence de différence significative de l'expression de l'ARNm de l'hepcidine 1 entre les souris Hfe+/+ et Hfe-/-, nos résultats révèlent que l'expression des ARNm de l'hepcidine 1 et 2 varie selon la souche de souris
Type 1 genetic hemochromatosis is characterised by an iron overload in parenchyme organs. A mutation (C282Y) in the HFE gene is the cause of the disease which is very frequent in the populations of North West Europe origins. Recent epidemiological studies revealed an incomplete penetrance and a variable expression of the disease. Involvement of non genetic factors (age, nutrition, regular blood donations. . . ) and of genetic factors can explain this picture. To characterise the role of the genetic factors in hepatic iron loading, we have used the Hfe-/- mouse as a murine model of hereditary hemochromatosis. The comparative study of 4 consanguineous mouse strains (DBA/2, C57BL/6, CBA and 129/Sv) showed differences in the regulation of iron metabolism between strains. Hfe-/- mice with two different genetic backgrounds (C57BL/6 and DBA/2) showed differences on iron overload levels which are controlled by other genes modulating HFE gene. We showed that in these two Hfe-/- strains, the iron overload levels and the transcriptional regulations in duodenum are different. Screening the whole genome, four chromosomic regions with a significant LOD score of genetic linkage were identified. The mRNA expression was quantified for hepcidin and other molecules among the two strains of Hfe-/- mice. Though there was no significant differences in hepcidin 1 mRNA levels between the Hfe-/- and Hfe+/+ mice, our results showed that there was higher mRNA expression for hepcidin 1 than for hepcidin 2 in C57BL/6 mice and the opposite was observed in DBA/2 mice

Background: We aimed to increase the knowledge regarding the familial arrhythmogenic disorder Long QT Syndrome (LQTS) and its recessive variant Jervell and Lange-Nielsen Syndrome (JLNS) in Sweden, including prevalences and clinical phenotypes. A specific focus was directed towards two KCNQ1 mutations –p.Y111C and p.R518X- commonly identified in Swedish LQTS index cases. Methods: Cases and families with LQTS (p.Y111C or p.R518X) and JLNS were recruited via regional clinical practices, national referrals to the Clinical Genetics laboratory, Umeå University Hospital, and a national inventory. Molecular genetics methods were used for case ascertainment. Clinical data was obtained via medical records, a questionnaire, and/or an interview. Electrocardiograms were manually assessed. In p.R518X heterozygotes intra-familial phenotypic variability (QTc and cardiac events) was assessed by analysis of sequence variants (modifier genes). The origins of the mutations p.Y111C and p.R518X were investigated using genealogical and haplotype analysis (microsatellite markers). In families sharing a common haplotype mutation age and associated prevalence was analyzed using ESTIAGE and DMLE computer software. Results: We identified p.Y111C (170 mutation-carriers) and p.R518X (101 mutation-carriers) as two major causes of LQTS/JLNS in Sweden. LQTS phenotype was revealed to be relatively benign in p.Y111C and p.R518X (annual incidence of life-threatening cardiac events, before therapy 0.05% and 0.04%, respectively). Gender-specific effects of genetic modifiers on phenotypic expression were seen. A founder origin, approximately 600-700 years ago in two northern river valleys was established for p.Y111C and p.R518X, and a high prevalence of LQTS founder descendants suggested. A minimum JLNS prevalence of 1:200 000 in preadolescent Swedish children was revealed. JLNS phenotype was mainly severe, with a cumulative incidence of life-threatening cardiac events of 53% (annual incidence rate before therapy 5%) and four sudden deaths. Possible founder effects regarding four KCNQ1 mutations; p.Y111C (8%), p.R518X (50%), c.572_576del (17%) and p.Q530X (8%) together explained 83% of the JLNS mutation-spectrum in Sweden, consisting of 8 KCNQ1 mutations. Conclusion: The high prevalence of p.Y111C- and p.R518X-related LQTS as well as JLNS revealed in Sweden could be explained by the combination of mild clinical phenotypes in heterozygotes and strong founder effects present during the population development of northern Sweden. Increased knowledge regarding the occurrence of LQTS and JLNS as well as mutation- and/or genotype-specific data constitute prerequisites for possible improvement of patient management.

La hipomagnesèmia familiar amb hipercalciúria i nefrocalcinosi (HFHNC) és una tubulopatia minoritària autosòmica recessiva causada per mutacions als gens CLDN16 o CLDN19, que codifiquen per la claudina-16 i -19, respectivament, que s’expressen a la porció gruixuda de la nansa ascendent de Henle, i estan implicades en el transport iònic paracel·lular. Aquesta malaltia es caracteritza per la pèrdua urinària massiva de calci i magnesi, nefrocalcinosi bilateral i progressió inexorable de la malaltia renal crònica, que desencadena en fallida renal. Addicionalment, la majoria de pacients amb mutacions a CLDN19 també desenvolupen alteracions oculars, ja que aquest s’expressa a les cèl·lules epitelials de la retina. Característicament, existeix una gran variabilitat fenotípica entre els pacients, inclús entre aquells que comparteixen la mutació c.59G>A; p.G20D a CLDN19 (mutació Hispànica), i entre membres d’una mateixa família. Aquest fenomen suggereix que possiblement existeixen altres processos moleculars que determinen la progressió clínica dels pacients. Sota aquesta hipòtesi, aquest treball s’ha focalitzat en l’estudi dels factors genètics i epigenètics que podrien modular la progressió de la malaltia renal. Per això, s’han obtingut les dades clíniques i mostres d’orina i sang de 30 pacients afectes d’HFHNC i 6 individus control d’arreu d’Espanya, essent la majoria dels pacients diagnosticats d’HFHNC en aquest territori. L’anàlisi de les dades clíniques va permetre avaluar les diferències en l’evolució de la malaltia renal en funció del sexe i el genotip, classificar els pacients segons la pèrdua anual de funció renal (progressió renal ràpida, moderada i lenta), identificar biomarcadors clínics de pronòstic, i evidenciar l’alta variabilitat fenotípica intrafamiliar. L’estudi de variants gèniques en homozigosi associades als fenotips més extrems (progressió ràpida i lenta) s’ha realitzat amb les dades obtingudes de la seqüenciació massiva de l’exoma dels 30 pacients de la cohort. Seguint aquesta estratègia, s’han identificat un total de 45 variants gèniques. D’entre aquestes, per la funció fisiològica dels gens on es localitzen, en destaquen la rs11207827 (al gen PATJ) i la rs1050171 (al gen EGFR). Per determinar els factors epigenètics implicats en la fisiopatologia de la HFHNC i en la seva progressió, s’han utilitzat els urinary exosome-like vesicles (uEVs) com a font no invasiva d’informació dels processos cel·lulars renals. Mitjançant microarrays, s’ha analitzat el perfil d’expressió dels miRNAs continguts als uEVs dels 20 pacients que mantenien els ronyons natius funcionals identificant-se 24 miRNAs diferencialment expressats en el conjunt de pacients respecte el grup control, i 43 en el subconjunt dels pacients homozigots per la mutació p.G20D a CLDN19. La comparació de pacients d’ambdós sexes, va mostrar únicament la infraexpressió del miR 1915 5p en aquells de sexe masculí. Per últim, s’han identificat 4 miRNAs diferencialment expressats en els pacients d’HFHNC amb progressió renal moderada, en comparació amb el de progressió lenta, i 8 en el subgrup de pacients homozigots per la mutació p.G20D a CLDN19. La biologia de sistemes i l’ús de xarxes neuronals d’intel·ligència artificial han permès associar els resultats obtinguts amb processos biològics crucials en la fisiopatologia de la HFHNC, com la fibrosi renal i el transport de calci i magnesi, entre d’altres. Aquest treball ha permès incrementar el coneixement de la fisiopatologia de la HFHNC i determinar factors clínics, genètics i epigenètics implicats en la progressió de la malaltia renal i identificar nous possibles biomarcadors pronòstics de la HFHNC, i dianes terapèutiques que podrien permetre modular la severitat de la malaltia i, en el millor dels casos, curar-la.
La hipomagnesemia familiar con hipercalciuria y nefrocalcinosis (HFHNC) es una tubulopatía minoritaria autosómica recesiva causada por mutaciones en los genes CLDN16 o CLDN19, que codifican para la claudina-16 y -19, respectivamente, expresadas en la porción gruesa del asa ascendente de Henle, e implicadas en el transporte iónico paracelular. Esta enfermedad se caracteriza por la pérdida urinaria de calcio y magnesio, nefrocalcinosis bilateral y progresión inexorable de la enfermedad renal crónica, que desencadena en fallo renal. Adicionalmente, la mayoría de pacientes con mutaciones en CLDN19 también desarrollan alteraciones oculares, ya que este se expresa en las células epiteliales de la retina. Existe una gran variabilidad fenotípica entre pacientes, incluso entre aquellos que comparten la mutación c.59G>A; p.G20D en CLDN19 (mutación Hispánica), y entre miembros de una misma familia. Este fenómeno sugiere que, más allá de la mutación causante de la enfermedad, posiblemente existen otros procesos moleculares que determinan la progresión clínica de los pacientes. Bajo esta hipótesis, este trabajo se ha focalizado en el estudio de los factores genéticos y epigenéticos que podrían modular la progresión de la enfermedad renal. Para ello, se han obtenido los datos clínicos, orina y sangre de 30 pacientes afectos de HFHNC y 6 individuos control de diferentes lugares de España, siendo estos la mayoría de pacientes diagnosticados de HFHNC en este territorio. El análisis de los datos clínicos permitió evaluar las diferencias en la evolución de la enfermedad renal en función del sexo y del genotipo, clasificar los pacientes según la pérdida anual de función renal (progresión renal rápida, moderada y lenta), identificar biomarcadores clínicos de pronóstico, y evidenciar la alta variabilidad fenotípica intrafamiliar. El estudio para la identificación de variantes génicas en homocigosis asociadas a los fenotipos más extremos (progresión renal rápida y lenta) se realizó con los datos obtenidos de la secuenciación masiva del exoma de los 30 pacientes de la cohorte. Con esta estrategia, se identificaron 45 variantes génicas. De entre estas, por la función fisiológica de los genes donde se localizan, destacan la rs11207827 (en el gen PATJ) y la rs1050171 (en el gen EGFR). Para determinar los factores epigenéticos implicados en la fisiopatología de la HFHNC y en su progresión, se utilizaron los urinary exosome-like vesicles (uEVs) como fuente no invasiva de información de procesos celulares renales. Mediante microarrays, se analizó el perfil de expresión de los miRNAs contenidos en los uEVs de los 20 pacientes que mantenían los riñones nativos funcionales, identificándose 24 miRNAs diferencialmente expresados en el total de pacientes respecto al grupo control, y 43 en el subconjunto de pacientes homocigotos para la mutación p.G20D en CLDN19. La comparación de pacientes de ambos sexos mostro únicamente la infraexpresión del miR-1915-5p en aquellos de sexo masculino. Finalmente, se identificaron 4 miRNAs diferencialmente expresados en los pacientes con progresión renal moderada, en comparación con el de progresión lenta, y 8 en el subgrupo de pacientes homocigotos para la mutación p.G20D en CLDN19. La biología de sistemas y el uso de redes neuronales de inteligencia artificial han permitido asociar los resultados obtenidos con procesos biológicos cruciales en la fisiopatología de la HFHNC, como la fibrosis renal y el transporte de calcio y magnesio, entre otros. Este trabajo ha permitido incrementar el conocimiento de la fisiopatología de la HFHNC y determinar factores clínicos, genéticos y epigenéticos implicados en la disfunción renal. Desde el punto de vista traslacional, se han identificado nuevos posibles biomarcadores pronósticos de la HFHNC, y dianas terapéuticas que podrían permitir modular la severidad de la enfermedad y, en el mejor de los casos, curarla.
Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is a rare autosomal recessive tubulopathy caused by mutations in either CLDN16 or CLDN19 genes, which encode for claudin-16 and -19, respectively, expressed in the thick ascending loop of Henle, and involved in paracellular ion transport. This disease is characterized by urinary loss of calcium and magnesium, bilateral nephrocalcinosis, and inexorable progression of chronic renal disease leading to renal failure. Besides, most patients with CLDN19 mutations also develop ocular anomalies, as it is expressed in the retinal epithelial cells. There is great phenotypic variability among patients, even in those who share the c.59G>A; p.G20D mutation in CLDN19 (Hispanic mutation), and also among members of the same family. This phenomenon suggests that, beyond the mutation causing the disease, other molecular processes could determine the clinical progression of patients. Under this hypothesis, this work has focused on the study of genetic and epigenetic factors that could modulate renal disease progression. For this purpose, clinical data, urine and blood from 30 patients affected by FHHNC and 6 control individuals were collected from around Spain, being them the majority of patients diagnosed of FHHNC in this territory. The analysis of the clinical data allowed evaluating the differences in the evolution of the renal disease according to sex and genotype, classifying patients according to the annual decline of renal function (fast, moderate and slow renal progression), identifying clinical biomarkers of prognosis, and evidencing the high intrafamilial phenotypic variability. The study for the identification of gene variants in homozygosis associated with both extreme phenotypes (fast and slow renal progression) was carried out with data obtained from exome sequencing of the 30 patients included in the cohort. With this strategy, 45 gene variants were identified. Among these, due to the physiological function of the genes where they are located, the rs11207827 (in the PATJ gene) and the rs1050171 (in the EGFR gene) were highlighted. To determine the epigenetic factors involved in FHHNC physiopathology and disease progression, the urinary exosome-like vesicles (uEVs) were used as a non-invasive source of information on renal cellular processes. Microarray technique was used to analyze the expression pattern of miRNAs contained in uEVs of the 20 patients who maintained functional native kidneys. Twenty-four miRNAs were identified differentially expressed in all patients when compared with the control group, and 43 in the subset of patients homozygous for the p.G20D mutation in CLDN19. The comparison of patients of both sexes showed only the under-expression of the miR-1915-5p in males. Finally, 4 miRNAs were differentially expressed in patients with moderate to slow progression of renal disease, and 8 within the subgroup of patients homozygous for the p.G20D mutation in CLDN19. Systems biology and the use of artificial neuronal networks have allowed to associate the results obtained with crucial biological processes in FHHNC physiopathology such as renal fibrosis and calcium and magnesium transport, among others. This work, through two complementary strategies, has allowed increasing the knowledge of the physiopathology of FHHNC and, for the first time, determining clinical, genetic and epigenetic factors involved in renal disease progression. From a translational perspective, this thesis has identified new possible prognostic biomarkers of FHHNC as well as novel therapeutic targets that could allow modulating the severity of the disease and, in the best case, to cure it.

A Neoplasia endócrina múltipla tipo 1 (NEM1; OMIM 131100) é uma síndrome endócrina hereditária, que envolve tumores nas glândulas paratireóides, pâncreas endócrino/duodeno e hipófise. Mutações germinativas no gene supressor de tumor MEN1 são identificadas em aproximadamente 80% dos casos familiais. Os casos restantes podem apresentar grandes deleções no gene MEN1 (raras), não identificáveis ao seqüenciamento direto, ou mutações em outros genes, ainda pouco conhecidos. Recentemente, mutações germinativas em genes que codificam quinases dependentes de ciclinas, como o gene supressor de tumor p27Kip1, foram identificadas em cerca de 1-2% dos pacientes NEM1 sem mutação no gene MEN1. Esses pacientes apresentam uma clínica similar à NEM1, sendo chamada de NEM-like ou NEM4. Estudos in vitro mostraram que a proteína codificada pelo gene MEN1, MENIN, controla a expressão gênica de p27Kip1, indicando que ambos os genes fazem parte da mesma via celular supressora de tumor. Devido à correlação genótipo-fenótipo ser muito fraca nessa síndrome e à grande variabilidade fenotípica encontrada em pacientes com NEM1 (mesmo entre indivíduos/familiares que possuem mesma mutação no gene MEN1), no presente estudo investigamos a hipótese do envolvimento do gene p27Kip1, e de outro gene supressor de tumor recentemente associado com um fenótipo tumores hipofisários famílias, o gene AIP, como possíveis moduladores de fenótipo entre os pacientes com NEM1 de uma extensa família brasileira com a mutação germinativa MEN1 c.308delC e ampla variabilidade fenotípica. Dentre uma série de variáveis clínicas investigadas, observamos um possível papel modulador de fenótipo do gene p27Kip1 nesta família com NEM1. Foi encontrada associação significante entre o genótipo do polimorfismo p.V109G do gene p27Kip1, localizado em um domínio de ligação com a proteína p38 (que é um regulador negativo de p27 por levar à degradação dessa proteína), com os seguintes aspectos clínicos: maior agressividade do tumor hipofisário (macro vs. microadenomas), precocidade no desenvolvimento do tumor pancreático, e presença de carcinóides e metástases nos pacientes analisados (p< 0,05). Não foi observada nenhuma associação do gene AIP e o fenótipo dos pacientes com NEM1. O presente estudo investigou, pela primeira vez, o status germinativo do gene p27Kip1 em pacientes com mutação MEN1 e identificou uma associação significante em relação à susceptibilidade e agressividade dos tumores na coorte estudada
Multiple endocrine neoplasia type 1 (MEN1) is an inherited tumoral syndrome that involves tumors in the parathyroids, anterior pituitary and in the pancreatic islet(s) cells. Germline mutations in the tumor suppressor gene MEN1 are detectable through direct sequencing in the majority (80%) of the patients with familial MEN1. The remaining patients may present large MEN1 gene deletions, not detectable through direct sequencing, or mutations in other genes, so far largely unknown. Recently, rare mutations in genes that encode cyclin-dependent kinases, as p27Kip1, have been reported in approximately 1-2% of the patients without a MEN1 mutation. These patients were reported as presenting a MEN1-like (or the MEN4) syndrome phenotype. In vitro studies have demonstrated that the protein encoded by the MEN1 gene, MENIN, controls the expression of the p27Kip1 gene and, therefore, these two genes seem to act in the same intracellular tumor suppressor pathway. Due to the lack of genotype-phenotype correlation in MEN1 and the large clinical variability usually observed within unrelated patients carrying the same MEN1 mutation, we hypothesized that p27Kip1 (as well as AIP gene, recently associated with familial predisposition to pituitary tumors) may act as phenotypic modifying gene(s) in the MEN1 syndrome. Herein, we analyzed possible correlations between p27Kip1 genotype and a number of clinical features. We identified significant statistic associations between the p.V109G p27Kip1 polymorphism and phenotype manifestations, indicating a potential role of p27Kip1 in modifying MEN1 phenotype, as follows: pituitary tumor size; early development of pancreatic tumors, and presence of carcinoids and metastasis (p< 0,05). In addition, a possible association with the AIP gene was excluded. The present study analyzed, for the first time, the germline status of p27Kip1 gene in MEN1-mutated patients and identified a potential interaction between the genotype of this tumor suppressor gene in regulating susceptibility and the tumor aggressiveness in MEN1 patients

In this thesis I show that macrophages (both cell lines and primary cultures) can be transfected by recombinant adenoviruses expressing -galactosidase (A-gal/Av1Bng), that the macrophages become activated by the transfection process and can be easily manipulated to localise to inflamed glomeruli after direct injection into the renal artery of rats with an experimentally induced glomerular inflammation caused by nephrotoxic nephritis. The injection of transfected macrophages reduces the severity of injury in this model of glomerulonephritis as shown by a reduction in the degree of albuminuria. This approach provides a favourable system for gene delivery in inflammatory disease and shows that both the functional properties of the transfected macrophage as well the transgene it is engineered to produce are relevant for in vivo gene transfer. This approach has also been used to determine the effect of macrophages expressing active TGF-1 on the development of glomerular inflammation. TGF-1 expressing macrophages localised efficiently to inflamed glomeruli and produced the cytokine in vivo. These cells produced a reduction in the level of albuminuria compared to unmodified disease but not in comparison to injection of macrophages transfected with adenovirus expressing -galactosidase. In addition there was no alteration in the infiltration by ED1 positive macrophages. Thus TGF-1 expressed in this manner appears unable to significantly modulate glomerular inflammatory disease and the potential reasons for this are discussed. The system I have developed of macrophage transfection and delivery provides a valuable approach to study and modulate inflammatory disease.

T-Zellrezeptor (TZR)-Gentherapie zeigte erste Erfolge in klinischen Studien, jedoch wurden gleichzeitig Risikofaktoren deutlich. Ein Risikofaktor ist das falsche Paaren der transferierten TZR-Ketten mit den endogenen, was zu TZR-Molekülen von unbekannter Spezifität führt und die Oberflächenexpression und somit auch die Funktionalität des transgenen TZR reduziert. Dieser Aspekt wurde in generierten T-Zellklonen mit einer konstitutiven/endogenen TZR-Expression sowie einer zweiten induzierbaren/transgenen TZR-Expression untersucht. Es konnte gezeigt werden, dass nach Induktion der transgenen TZR-Expression der endogene TZR seine Funktionalität verlor, obwohl er noch auf der Oberfläche detektierbar war. Als Ursachen wurden neben einer reduzierten Oberflächenexpression des endogenen TZR auch falsch gepaarte TZR-Moleküle, die mit Hilfe der Fluoreszenz-Resonanz-Energie-Transfer-Methode detektiert wurden, gefunden. Die Modifikation des TZR durch den Einbau einer zweiten Cystein-Brücke, was das Paaren der korrespondierenden TZR-Ketten stabilisieren soll, führte in den T-Zellklonen zu keiner Reduktion der falsch-paarenden TZR-Moleküle. In primären Wildtyp-T-Zellen verbesserte sich das richtige Paaren des transgenen TZR leicht und konnte durch Codon-Optimierung der TZR-Gene weiter verbessert werden. Der zweite untersuchte Risikofaktor ist die Insertionsmutagenese durch den retroviralen Vektor. Die sichere Verwendbarkeit von differenzierten T-Zellen für die TZR-Gentherapie wurde in einem Tiermodel mit wiederholter T-Zellstimulierung, um weitere Mutationen während der Zellteilung zu provozieren, analysiert. Im Laufe der Zeit reicherten sich die transferierten T-Zellen in den Tieren dramatisch an, aber entwickelten sich nicht zu T-Zelllymphomen. Die Proliferationskapazität und die Funktionalität der transferierten T-Zellen wurden bestätigt. Die Polyklonalität der TZR-gen-modifizierten T-Zellen wurde mit Hilfe der linear-amplifizierten Polymerasekettenreaktion nachgewiesen.
T cell receptor (TCR) gene therapy is a new therapy for cancer which showed first clinical success but at the same time risk factors evolved. One risk factor is the mispairing of the TCR chains with the endogenous TCR chains which leads to TCRs with unknown specificities and to a reduced expression and functionality of the transferred TCR. This aspect was analyzed in dual TCR T cell clones which had one constitutive/endogenous TCR expression as well as a second inducible/transgenic TCR expression. It could be shown that the endogenous TCR lost its functionality after induction of the transgenic TCR expression although it was still detectable on the cell surface. The reason was found in the lower surface expression level of the endogenous TCR as well as in mispaired TCR dimers detected by fluorescence resonance energy transfer (FRET) technique. Modification of the TCR by insertion of a second cysteine bridge which should stabilize the pairing of the corresponding TCR chains did not reduce the TCR mispairing in the T cell clones. In primary wild-type cells, the pairing of the transgenic TCR improved slightly and could be further improved by codon-optimization of the TCR genes. The second analyzed possible side effect of TCR gene therapy is the insertional mutagenesis by the retroviral vector. The safety of differentiated T cells for TCR gene therapy was analyzed in an animal model with a repetitive T cell stimulation to provide the opportunity for mutations to occur during cell division. Over time, transferred T cells increased dramatically in the recipient mice, but did not lead to T cell lymphomas. The proliferative capacity and the functionality of transferred T cells were confirmed. The polyclonality of the TCR gene-modified T cells could be confirmed by linear amplification-mediated polymerase-chain reaction.

The long-term implications of deregulation of glucose metabolism, manifesting itself as diabetes is significant. Whilst treatments for the disease are progressing, often they require multiple daily insulin injections. This may be difficult for diabetics in poorer nations. This thesis examines the possibility of utilising keratinocytes and melanocytes transfected with either normal or furin-modified proinsulin constructs, to process and secrete mature insulin via secreted protein pathways. The advantage of this approach is that it may allow normalisation of basal glucose levels, which in turn may prevent or delay the onset of many of the complications associated with diabetes. The results confirmed that keratinocytes and melanocytes are able to process and secrete mature insulin from a furin-modified proinsulin construct, thus validating this approach and paving the way for skin grafts of genetically modified cells to be used as a possible treatment for diabetes. Whilst the results regarding the ability of these cells to process a normal proinsulin construct are inconclusive, they highlight areas of interest that could help to resolve this issue
Master of Science (Hons.)

Understanding the genetic foundations of schizophrenia and the resultant symptom manifestations is an important step as we work toward development of new prevention and treatment strategies. This work has sought better understanding of this disease through use of three subject cohorts and two studies using simulated data exploring features of complex disease. First, we probed the symptoms of schizophrenia in subjects of African and European ancestry drawn from the Genetic Association Information Network (GAIN) schizophrenia study and found significant differences between groups, particularly in affective symptoms. The genetic basis of symptom variation was then explored in a selection of candidate genes in two Irish samples, the Irish Study of High Density Schizophrenia Families (ISHDSF) and Irish Case-Control Study of Schizophrenia (ICCSS). We found a significant association of PAH with delusions, GABRB3 with hallucinations, and SNAP25 with both of these symptom factors. AKT1 alleles conferred greater Schneiderian symptoms, but dysbindin, MAOB, and SLC6A4 were not related to any symptom dimensions. Simulated data were used to probe the parameters necessary to detect susceptibility genes as modifiers in a scenario in which two disease groups with incompletely overlapping symptom profiles are examined together. The heterogeneous genetic underpinnings and variable symptom manifestation of schizophrenia make the findings from this study particularly relevant to this disease. Convergent lines of evidence implicating myelin and synaptic dysfunction in schizophrenia prompted us to test related gene networks for association with this disease in two populations, African-ancestry and European-ancestry, from the GAIN study. Some evidence supporting myelin-related genes in the etiology of schizophrenia was presented but only in the African-ancestry group. Epistatic (gene-gene) interactions may confer much greater disease risk than single-gene results would indicate, but their detection is often difficult. The final study included here explored two approaches to family-based epistasis detection under a range of epistatic models. The haplotype relative risk (HRR) approach yields greater power for detection under conditions of dominance, but the Cordell approach is more powerful under most other models. Together, these studies provide a modest advancement in our understanding of schizophrenia and the methodological avenues available for future studies of this disease.

WWOX is a tumour suppressor gene, as demonstrated by increased neoplasia incidence in Wwox-knock-out animals, and is frequently disrupted in human cancers. WWOX expression reconstitution abolishes xenograft growth of lung, pancreatic, breast, ovarian and prostate cancer cells. The tumoursuppressive function of WWOX is suggested to be related to pro-apoptotic effects or interactions with potentially oncogenic transcription factors leading to their cytoplasmic sequestration and trans-activity inhibition. In physiology WWOX might be involved in metabolism. Our group demonstrated that WWOX reconstitution in ovarian cancer cells inhibits xenograft growth but this was not accompanied by altered in vitro growth or apoptosis rates. Rather, WWOX transfection reduced cancer cell adhesion to extracellular matrix due to reduction of integrin α3 binding. Additionally, our group postulated that natural polymorphic variants of WWOX are linked to ovarian cancer clinicopathological features. The hypotheses behind this work were that WWOX regulates gene expression or promotes apoptosis in ovarian cancer. Further, this project aimed at confirming the associations of WWOX polymorphisms. I demonstrate no link between WWOX status and the subcellular localization of putative WWOX-binding transcription factors or the expression of their target genes in ovarian cancer cells. The phenotypic consequences of WWOX expression manipulation do not appear to be explained by transcriptional changes. I show that WWOX increases apoptosis rates in ovarian cancer cells exposed to the chemotherapy agent paclitaxel, but not cisplatin. This is independent of the anti-mitotic function of taxanes and unrelated to integrin regulation. Rather, WWOX promotes cell death during taxane-induced endoplasmic reticulum stress. I propose WWOX-driven cell death during endoplasmic reticulum stress might be also linked to anti-tumorigenic effects in vivo. A validation study did not confirm the link between WWOX genetic variants and ovarian cancer pathology. There is also no link between WWOX polymorphisms and bone metabolism, a trait affected in WWOX-knock-out animals.

Chimeric Immune Receptors (CIR) consisting of a carcinoembryonic antigen (CEA)specific single chain antibody fragment (scFv), fused to the CD3s signalling chain from the T-cell receptor (TCR), induce T-cell activation on CEA ligation. The study sought to investigate some of the structural aspects of CIRs with the objective of potentially optimising CIR function. Analysis of several model systems identified Jurkat T-cells as a useful model for assessing CIR-mediated responses to antigen. CIR-expressing Jurkat T-cells demonstrated a dose-dependent increase in CD69 expression in response to CEA. Jurkat T-cells expressing a CIR with the wild-type CD3s transmembrane domain exhibited a significantly higher surface expression of the TCR associated CD3e than cells expressing receptors with any other transmembrane domain. This upregulation of TCR-associated but not TCR-non associated receptors was abrogated by a transmembrane C2G mutation, which effectively prevented dimerisation, or by replacing the transmembrane domain with a heterologous non-dimerising domain. The concentration of CEA required for 50% maximal CD69 expression (ECso) was also significantly increased by both of these modifications. Moving the disulphide bridge to the extracellular domain, but not any other position in the transmembrane domain, permitted redimerisation and partially restored optimal receptor function. This difference in function may be attributed to TCR interactions as wild-type dimeric but not monomeric receptors, as well as inducing an upregulation in TCR complexes in Jurkat T-cells, could also reconstitute TCR expression in CD3s deficient MA5.8 cells. Potential TCR-CIR interactions were further investigated by mutational analysis to the charged transmembrane D6 residue responsible for wild-type CD3s-TCR interactions. Conservative D6N/E/Q mutations permitted dimerisation but significantly impacted on receptor efficiency; however, non-conservative D6K mutations affected receptor dimerisation and had a more severe impact on receptor function. This knowledge obtained from this study was applied to clone a novel CD28-fusion receptor containing the CD3s transmembrane domain with analysis in Jurkat T-cells demonstrating this CIR had a significantly lower ECso than existing CD28-fusion receptors containing the CD28 transmembrane domain. The second aim of this study was to investigate the role of CD2 as a novel costimulatory module. scFv.CD2.CD3s and scFv.CD28.CD2.CD3s activated Jurkat T-cells more efficiently than scFv.CD28.CD3s. However, in primary human T-cells only scFv.CD2.CD3s expressed at levels to observe functional responses. In these cells CD2 costimulation induced higher IFNy secretion than CD28 costimulation. In summary the report highlights the importance of the CD3s transmembrane domain in optimal CIR function and demonstrates the potential for CD2-based CIRs for future clinical trials.

The Chalcone Synthase (CHS) gene codes for the first step of biosynthesis of the purple pigment anthocyanin. In this study, transgenic Arabidopsis plants with a hairpin construct homologous to part of the CHS coding sequence were used in a genetic screen to identify modifiers of hairpin silencing. Some putative genetic modifiers were identified, but these appear to be the result of transgene:transgene interaction based on shared promoter homology rather than being due to second site suppressors in the Arabidopsis genome. New transgenic Arabidopsis lines were made with hairpin constructs directed to either the promoter or the reading frame of the CHS gene and both types of transgenic showed an anthocyanin-deficient phenotype. For each construct a representative single-insert homozygous transgenic line was selected for subsequent work. Both transgenic lines showed increased methylation of their respective target site and contained short interfering RNA (siRNA) homologous to their target site. A collection of 59 putative modifiers of CHS silencing were tested with both transgenic lines using segregation analysis of the anthocyanin-deficient phenotype in the F₂ generation of appropriate crosses. Mutants in AGO4, AGO6, DRD1, DRM2, NRPD2a and NRPE1 act as recessive second site modifiers of the CHS promoter hairpin line phenotype. These mutants are associated with a decrease in DNA methylation at the hairpin target site. Mutant alleles of the DCL4 and HEN1 genes reduce silencing of the CHS coding sequence hairpin. The reduction in silencing is greater in mutants that are hemizygous for the hairpin construct than in those that are homozygous for it. The increase in siRNA in the construct homozygotes, compared to that in the hemizygotes, is perhaps sufficient to overcome any modification of the phenotype by mutants of DCL4 and HEN1.

The overall goal of our research was to design a vector for efficient delivery of therapeutic genes/drugs to brain. Specifically, this research work was focused on designing PEGylated liposomes surface modified with the receptor targeting protein, transferrin and cell penetrating peptides (CPPs) for targeting and improving the delivery of desired therapeutic agent to brain. Various CPPs including poly-L-arginine, TAT, Penetratin and Mastoparan were investigated for their influence on transport of transferrin receptor targeted liposomes across brain endothelial cells. The dual-modified liposomes were synthesized using thin film hydration and post-insertion technique. The biocompatibility of the liposomes was evaluated at increasing concentrations to obtain an optimum value for safe and effective delivery of drugs or genes. The liposomes showed excellent cellular, blood and tissue compatibility at the optimized concentration. In addition, the combination of targeting ligand transferrin and CPPs resulted in considerable translocation of the therapeutic agent across cellular and brain endothelial barriers both in vitro and in vivo. Among different Tf-CPP liposomes, the Tf-Penetratin liposomes showed maximum translocation of the drug across the brain endothelial barrier (approximately 15% across in vitro and 4% across in vivo BBB) and efficient cellular transport of the encapsulated drug (approximately 90-98%) in various cell lines. In addition, Tf-poly-L-arginine and Tf-Penetratin liposomes showed improved transfection efficiencies in various cell lines. The Tf-Penetratin and Tf-TAT liposomes demonstrated excellent cellular biocompatibility and no hemolytic activity upto 200nM phospholipid concentration. In vivo efficacy of the liposomes was evaluated by performing biodistribution studies in in adult Sprague Dawley rats. The liposomes were intended for delivery of small molecule drug, doxorubicin and pDNA to brain. The dual modified liposomes showed significantly (p<0.05) higher transport of encapsulated agents in rat brain as compared to single ligand (Tf) or plain liposomes. Histological examination of the tissues, from various organs, did not show any signs of toxicity including necrosis, inflammation, fibrosis etc. The study underlines the potential of bifunctional liposomes as high-efficiency and low-toxicity gene delivery system for the treatment of central nervous system disorders.

Multiple Endocrine Neoplasia Type 1 (MEN1) is an autosomal dominant disorder characterized by the combined occurrence of pituitary, pancreatic islet and parathyroid tumours. MEN1-associated tumours show loss of heterozygosity and the MEN1 gene encodes a putative tumour-suppressor, menin, whose over-expression in vitro inhibits cell proliferation. MEN1-associated tumours present earlier, are more aggressive and more difficult to treat than sporadic endocrine tumours. Strategies for earlier identification of index cases and novel therapies may contribute towards reduced morbidity and mortality from the condition. In this study, I first investigated the safety and efficacy of MEN1 gene replacement therapy using a modified adenoviral vector in pituitary tumours of heterozygous Men1 knockout mice. This revealed that MEN1 gene replacement was safe, effective and induced reduction of tumour cell proliferation. I also performed an in vivo phage-displayed peptide library screening study in heterozygous Men1 knockout mice to identify novel peptides that specifically bind pancreatic islet tumours. This identified one peptide sequence that likely targets pancreatic islet tumours. To further elucidate the role of menin I carried out phenotypic characterization of the mouse model for MEN1 in two mouse strains to investigate the effect of different genetic backgrounds and the potential for genetic modifiers on tumour phenotype. The frequency of pituitary and adrenal tumours was significantly influenced by the mouse strain, demonstrating the importance of genetic background on MEN1 tumour occurrence, implicating the role of genetic modifiers. Finally, I investigated the prevalence of MEN1 mutations in a cohort of patients presenting with primary hyperparathyroidism under 40 years of age. This revealed that 6% of under 40 year-olds with apparently sporadic parathyroid tumours have MEN1 mutations, and are likely to present with multiple parathyroid tumours. Pre-operative genetic screening of under 40 year-old patients with multiglandular parathyroid disease may reduce post-operative recurrence of hyperparathyroidism in those patients with MEN1 mutations.