Campylobacter jejuni is the commonest cause of bacterial foodborne gastroenteritis in industrialised countries. Despite its significance, it remains unclear how C. jejuni is disseminated in the environment, whether particular strains are more pathogenic than others, and by what routes this bacterium is transmitted to humans. One major factor hampering this knowledge is the lack of a standardised method for fingerprinting C. jejuni. Therefore, the overall aim of this project was to develop systematic and novel genotyping methods for C. jejuni. Chapter Three describes the use of single nucleotide polymorphisms (SNPs) derived from the multilocus sequence typing (MLST) database of C. jejuni and the closely related Campylobacter coli for genotyping these pathogens. The MLST database contains DNA sequence data for over 4000 strains, making it the largest comparative database available for these organisms. Using the in-house software package "Minimum SNPs", seven SNPs were identified from the C. jejuni/C. coli MLST database that gave a Simpson's Index of Diversity (D), or resolving power, of 0.98. An allele-specific real-time PCR method was developed and tested on 154 Australian C. jejuni and C. coli isolates. The major advantage of the seven SNPs over MLST is that they are cheaper, faster and simpler to interrogate than the sequence-based MLST method. When the SNP profiles were combined with sequencing of the rapidly evolving flaA short variable region (flaA SVR) locus, the genotype distributions were comparable to those obtained by MLST-flaA SVR. Recent technological advances have facilitated the characterisation of entire bacterial genomes using comparative genome hybridisation (CGH) microarrays. Chapter Four of this thesis explores the large volume of CGH data generated for C. jejuni and eight binary genes (genes present in some strains but absent in others) were identified that provided complete discrimination of 20 epidemiologically unrelated strains of C. jejuni. Real-time PCR assays were developed for the eight binary genes and tested on the Australian isolates. The results from this study showed that the SNP-binary assay provided a sufficient replacement for the more laborious MLST-flaA SVR sequencing method. The clustered regularly interspaced short palindromic repeat (CRISPR) region is comprised of tandem repeats, with one half of the repeat region highly conserved and the other half highly diverse in sequence. Recent advances in real-time PCR enabled the interrogation of these repeat regions in C. jejuni using high-resolution melt differentiation of PCR products. It was found that the CRISPR loci discriminated epidemiologically distinct isolates that were indistinguishable by the other typing methods (Chapter Five). Importantly, the combinatorial SNP-binary-CRISPR assay provided resolution comparable to the current 'gold standard' genotyping methodology, pulsed-field gel electrophoresis. Chapter Six describes a novel third module of "Minimum SNPs", 'Not-N', to identify genetic targets diagnostic for strain populations of interest from the remaining population. The applicability of Not-N was tested using bacterial and viral sequence databases. Due to the weakly clonal population structure of C. jejuni and C. coli, Not-N was inefficient at identifying small numbers of SNPs for the major MLST clonal complexes. In contrast, Not-N completely discriminated the 13 major subtypes of hepatitis C virus using 15 SNPs, and identified binary gene targets superior to those previously found for phylogenetic clades of C. jejuni, Yersinia enterocolitica and Clostridium difficile, demonstrating the utility of this additional module of "Minimum SNPs". Taken together, the presented work demonstrates the potentially far-reaching applications of novel and systematic genotyping assays to characterise bacterial pathogens with high accuracy and discriminatory power. This project has exploited known genetic diversity of C. jejuni to develop highly targeted assays that are akin to the resolution of the current 'gold standard' typing methods. By targeting differentially evolving genetic markers, an epidemiologically relevant, high-resolution fingerprint of the isolate in question can be determined at a fraction of the time, effort and cost of current genotyping procedures. The outcomes from this study will pave the way for improved diagnostics for many clinically significant pathogens as the concept of hierarchal combinatorial genotyping gains momentum amongst infectious disease specialists and public health-related agencies.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen that is endemic in hospitals all over the world. It has more recently emerged as a serious threat to the general public in the form of community-acquired MRSA. MRSA has been implicated in a wide variety of diseases, ranging from skin infections and food poisoning to more severe and potentially fatal conditions, including; endocarditis, septicaemia and necrotising pneumonia. Treatment of MRSA disease is complicated and can be unsuccessful due to the bacterium's remarkable ability to develop antibiotic resistance. The considerable economic and public health burden imposed by MRSA has fuelled attempts by researchers to understand the evolution of virulent and antibiotic resistant strains and thereby improve epidemiological management strategies. Central to MRSA transmission management strategies is the implementation of active surveillance programs, via which unique genetic fingerprints, or genotypes, of each strain can be identified. Despite numerous advances in MRSA genotyping methodology, there remains a need for a rapid, reproducible, cost-effective method that is capable of producing a high level of genotype discrimination, whilst being suitable for high throughput use. Consequently, the fundamental aim of this thesis was to develop a novel MRSA genotyping strategy incorporating these benefits. This thesis explored the possibility that the development of more efficient genotyping strategies could be achieved through careful identification, and then simple interrogation, of multiple, unlinked DNA loci that exhibit progressively increasing mutation rates. The baseline component of the MRSA genotyping strategy described in this thesis is the allele-specific real-time PCR interrogation of slowly evolving core single nucleotide polymorphisms (SNPs). The genotyping SNP set was identified previously from the Multi-locus sequence typing (MLST) sequence database using an in-house software package named Minimum SNPs. As discussed in Chapter Three, the genotyping utility of the SNP set was validated on 107 diverse Australian MRSA isolates, which were largely clustered into groups of related strains as defined by MLST. To increase the resolution of the SNP genotyping method, a selection of binary virulence genes and antimicrobial resistance plasmids were tested that were successful at sub typing the SNP groups. A comprehensive MRSA genotyping strategy requires characterisation of the clonal background as well as interrogation of the hypervariable Staphylococcal Cassette Chromosome mec (SCCmec) that carries the β-lactam resistance gene, mecA. SCCmec genotyping defines the MRSA lineages; however, current SCCmec genotyping methods have struggled to handle the increasing number of SCCmec elements resulting from a recent explosion of comparative genomic analyses. Chapter Four of this thesis collates the known SCCmec binary marker diversity and demonstrates the ability of Minimum SNPs to identify systematically a minimal set of binary markers capable of generating maximum genotyping resolution. A number of binary targets were identified that indeed permit high resolution genotyping of the SCCmec element. Furthermore, the SCCmec genotyping targets are amenable for combinatorial use with the MLST genotyping SNPs and therefore are suitable as the second component of the MRSA genotyping strategy. To increase genotyping resolution of the slowly evolving MLST SNPs and the SCCmec binary markers, the analysis of a hypervariable repeat region was required. Sequence analysis of the Staphylococcal protein A (spa) repeat region has been conducted frequently with great success. Chapter Five describes the characterisation of the tandem repeats in the spa gene using real-time PCR and high resolution melting (HRM) analysis. Since the melting rate and precise point of dissociation of double stranded DNA is dependent on the size and sequence of the PCR amplicon, the HRM method was used successfully to identify 20 of 22 spa sequence types, without the need for DNA sequencing. The accumulation of comparative genomic information has allowed the systematic identification of key MRSA genomic polymorphisms to genotype MRSA efficiently. If implemented in its entirety, the strategy described in this thesis would produce efficient and deep-rooted genotypes. For example, an unknown MRSA isolate would be positioned within the MLST defined population structure, categorised based on its SCCmec lineage, then subtyped based on the polymorphic spa repeat region. Overall, by combining the genotyping methods described here, an integrated and novel MRSA genotyping strategy results that is efficacious for both long and short term investigations. Furthermore, an additional benefit is that each component can be performed easily and cost-effectively on a standard real-time PCR platform.

Melanopsin (Opn4) is the opsin photopigment of intrinsically photosensitive retinal ganglion cells (ipRGCs). It has a conserved opsin structure and activation mechanism, yet demonstrates unusual functional properties that suggest it will possess unique structure-function relationships. The aim of this thesis was to characterise key OPN4 residues by examining the impact of non-synonymous mutations on melanopsin function. A genotype-driven screen of a chemically-mutagenized mouse archive led to the identification of a novel Opn4 mutant, S310A, located at a known opsin spectral tuning site. Action spectra from ipRGC and pupil light responses (PLR) of Opn4^S310A mice revealed no change in wavelength of peak sensitivity. However, Opn4^S310A PLR was significantly less sensitive at longer wavelengths, consistent with a short-wavelength shift in spectral sensitivity. This suggests S310A acts as a spectral tuning site in melanopsin. Next, the impact of naturally-occurring missense variants in human melanopsin (hOPN4) was examined in vitro. Fluorescent calcium imaging of 16 hOPN4 variants expressed in HEK293 cells revealed four hOPN4 variants abolished or attenuated responses to light (Y146C, R168C, G208S and S308F). These variants were located in conserved opsin motifs for chromophore binding or hydrogen-bond networks, functional roles apparently shared by melanopsin. Finally, two hOPN4 single nucleotide polymorphisms (SNPs) P10L and T394I, associated with abnormal non-image forming behaviour in humans, were explored in vivo. Using targeted viral-delivery of hOPN4 SNPs to mouse ipRGCs, a range of OPN4-driven behaviours, such as circadian photoentrainment and pupil light responses, were found to be comparable with hOPN4 WT control. Multi-electrode array recordings of ipRGCs transduced with hOPN4 T394I virus had significantly attenuated sensitivity and faster response offset, indicating this site may be functionally important for melanopsin activity but compensatory rod and cone input limits changes to non-image forming behaviour.

No description available.

Plus de 170 millions d'individus sont infectés par le VHC dans le monde et 37 millions par le VIH. La coinfection VIH/VHC est fréquente et représente un élément clé de la prise en charge des patients infectés par le VIH. Depuis l'arrivée des HAART, les maladies du foie sont devenues la cause principale de mortalité chez les patients coinfectés VIH/VHC. L'évolution naturelle et le pronostic de l'hépatite C sont plus sévères en cas de coinfection par le VIH du fait d'une fibrose accélérée et d'une évolution rapide vers la cirrhose et ses complications. Certains facteurs accélérant la fibrose hépatique sont clairs aujourd'hui comme: l'absence de recours au traitement anti-VHC, la réplication active du VHC et la consommation excessive d'alcool. De plus, il existe de plus en plus de preuves que les variants génétiques contribuent à la fibrose hépatique chez les patients monoinfectés par le VHC, mais cet aspect a été peu étudié dans la coinfection VIH/VHC.Durant ma thèse, j'ai eu accès aux données d'un échantillon de 494 patients coinfectés génotypés issu de la cohorte ANRS CO13 HEPAVIH. L'histoire naturelle du VIH et du VHC y est renseignée de manière très détaillée et le suivi clinique des patients permet d'avoir des informations précises sur l'état de fibrose hépatique. J'ai pu alors réaliser deux études d'association « génome-entier » pour identifier des polymorphismes associés à la sévérité de la fibrose à l'aide de données complètes de 292 patients. La première étude a mis en évidence une association entre la quantification de l'élasticité hépatique par Fibroscan® et un locus, également répliqué dans la monoinfection par le VHC. Cette association a permis d'identifier deux gènes impliqués dans des mécanismes de maintien de structure et de signalisation cellulaire (CAV3) mais aussi dans la réplication du VHC (RAD18). La seconde étude a identifié deux associations significatives en comparant deux groupes de scores METAVIR (F0F1F2 vs F3F4), en particulier dans le gène CTNND2 qui est impliqué dans un réseau d'interaction associé à des mécanismes moléculaires lié à des maladies hépatiques.Ces deux études sont en cours de publication dans des revues scientifiques internationales à comité de lecture. Ces nouvelles perspectives dans la compréhension des mécanismes de fibrose dans le contexte de la coinfection VIH/VHC pourraient aider à l'identification de nouvelles cibles pour la création de médicaments ou de tests diagnostiques afin d'améliorer les soins des patients. / Over 170 million people worldwide are infected by HCV and 37 million by HIV. Both viruses share the same modes of transmission, and HIV/HCV coinfection is common and represents a key element in the management of patients infected with HIV. Since the appearance of HAART, liver diseases have become the leading cause of death in HIV/HCV coinfected patients. The natural history and prognosis of hepatitis C are more severe in case of coinfection with HIV due to accelerated rate of fibrosis progression and rapid progression to cirrhosis and its complications. Factors accelerating liver fibrosis are known today such as the lack of recourse to anti-HCV treatment, active HCV replication and excessive alcohol consumption. There is increasing evidence that genetic variants contribute to liver fibrosis in HCV monoinfection, but this aspect has been little studied in HIV/HCV coinfection.I have exploited the genotype information from 494 coinfected patients from the cohort ANRS CO13 HEPAVIH. These patients are very-well documented regarding the history of their HIV/HCV infection and are very carefully followed-up, especially regarding the status of liver fibrosis. I have performed two genome-wide association studies to identify polymorphisms associated with the severity of fibrosis from complete data of 292 patients. The first study has dealt with the quantification of liver stiffness by Fibroscan® and an association with the 3p25 region has been identified, also replicated in monoinfection HCV. Two genes involved in cell signaling and structure of holding mechanisms (CAV3) but also in HCV replication (RAD18) appear as good candidates. The second study has unraveled two significant associations by comparing the METAVIR score group (F0F1F2 vs F3F4), especially in the CTNND2 gene implicated in a network of interactions with molecular mechanisms involved in liver diseases.These results are under publications in peer-review international scientific journals. These new insights into the molecular mechanisms of liver fibrosis in patients with HIV/HCV co- infection may help to define new targets for drug development or new diagnostic tests, to improve patient care.

Citocinas são moléculas que controlam e modulam a atividade de numerosas células por se ligarem a seus receptores específicos. As diferenças observadas na produção de citocinas entre indivíduos podem ser, pelo menos em parte, explicadas pelos polimorfismos genéticos como o polimorfismo de um único nucleotídeo (SNP). Em 181 indivíduos saudáveis não-aparentados da cidade do Rio de Janeiro (região Sudeste - Brasil), nós analisamos os polimorfismos de citocinas em genes que codificam para Fator de Necrose Tumoral-alfa (TNF-a), Fator de Crescimento Transformante-beta (TGF-b), Interleucina-10, Interleucina-6 e Interferon-gama (IFN-g). Reação em cadeia da polimerase utilizando-se iniciadores sequencia-específicos foi realizada com auxílio do kit comercial CytGen (One Lambda Inc. Canoga Park, CA, USA). Ao todo, 8 polimorfismos foram analisados: TNF-a (-308G/A); TGF-b (códon 10C/T, códon 25C/G); IL-10 (-1082A/G, -819T/C, -592A/C); IL-6 (-174C/G) e IFN-g (+874T/A). Os dados observados foram comparados a três grupos de população de diferentes regiões do Brasil (São Paulo, Paraná e Bahia) e a três populações de outros continentes (Itália, Eslováquia e Negros Norte-Americanos). O teste qui-quadrado foi utilizado para as comparações. Nossa análise da população do Rio de Janeiro mostrou que os as freqüências alélicas em IL-10, IL-6 e IFN-g são desigualmente distribuídos entre Brancos, Mulatos e Negros (p<0,05). A comparação com populações de outras regiões do Brasil revelou que Rio de Janeiro e Bahia possuem freqüências alélicas e genotípicas de TGF-b (códon 25) estatisticamente diferentes (p=0,004 e p=0,002, respectivamente). Ainda, a freqüência alélica na população do Rio de Janeiro é significativamente diferente quando comparada à população da Itália [IL-6 (-174), p=0,0092; e IFN-g (+874) p=0,0418)]; Eslováquia [IL-10(-1082), p=0,006; IL-6(-174), p=0,0002; e IFN-g(+874), p=0,0335]; e Afro-Americanos [IL-10(-819), p=0,0446; IL-6(-174), p<0,0001; e IFN-g(+874), p<0,0001]. Adicionalmente, observamos que a diferença na distribuição dos haplótipos em IL-10 (-1082/-819/-592) na população do Rio de Janeiro em comparação com a da Itália (p=0,0293) e Afro-Americanos (p=0,0025) é significativa. Portanto, concluímos que os polimorfismos em IL-10, IL-6 e IFN-g estão distribuídos de acordo com a etnia na população do Rio de Janeiro. A população do Rio de Janeiro possui freqüências de polimorfismos diferentes das populações de Bahia, Itália, Eslováquia e Afro-Americanos, mas semelhantes à população de São Paulo/Paraná. Nossas observações poderão ser úteis para futuros estudos e associação entre polimorfismos genéticos de citocinas e doenças na população do Rio de Janeiro. / Cytokines are molecules that control and modulate the activities of numerous target cells via binding to specific receptors. The observed differences in the cytokine production among individuals can be, at least, explained by genetic polymorphisms like single nucleotide polymorphism (SNP). In 181 unrelated healthy Brazilian individuals from Rio de Janeiro City, we investigated the polymorphisms of cytokine genes encoding Tumor Necrosis Factor-alpha (TNFA), Transforming Growth Factorbeta (TGFB), Interleukin (IL)-10, IL-6, and Interferon-gamma (IFNG). Polymerase chain reaction using sequence-specific primers genotyping was performed for these gene cytokines using the avaiable comercial kit CytGen (One Lambda Inc., CA, USA). Eight polymorphisms were tested: TNF-a (-308G/A); TGF-b (códon 10C/T, códon 25C/G); IL-10 (-1082A/G, -819T/C, -592A/C); IL-6 (-174G/C) and IFN-g (+874T/A). Chi-square test was used for comparisons. Observed data were compared to three other populations from different regions of Brazil (São Paulo, Paraná and Bahia) and three populations of other countries (Italy, Slovakia and North American Blacks). Our analysis from Rio de Janeiro population showed that the alleles frequencies in IL-10, IL-6 and IFN-g are unevenly distributed among Whites, Blacks and Mulatos (p<0.05). The comparison with populations from other regions of Brazil showed that Rio de Janeiro and Bahia have genotypic and allelic frequencies of TGF-b (códon 25) statistically different (p=0,004 and p=0,002, respectively). Also, the allelic frequency in the population of Rio de Janeiro is significantly different when compared to the population of Italy [IL-6 (-174), p=0.0092, and IFN-g (+874), p=0.0418] ; Slovak [IL-10 (-1082), p=0006; IL-6 (-174), p=0.0002, and IFN-g (+874), p=0.0335] and Afro-Americans [IL-10 (-819), p=0.0446, IL-6 (-174), p<0.0001, and IFN-g (+874), p<0.0001]. Additionally, we observed that the distribution of haplotypes in IL-10 (-1082/-819/-592) in the population of Rio de Janeiro in comparison with that of Italy (p = 0.0293) and Afro-Americans (p =0,0025) is statistically different. Therefore, we conclude that the polymorphisms in IL-10, IL-6 and IFN-g are distributed according to ethnicity in the population of Rio de Janeiro. The population of Rio de Janeiro have different frequencies of polymorphisms of the population of Bahia, Italy, Slovak and Afro-American, but similar to the population of São Paulo/Paraná. Our observations may be useful for future studies in association between genetic polymorphisms of cytokines and disease in the Rio de Janeiro population.

Made available in DSpace on 2014-12-17T15:32:28Z (GMT). No. of bitstreams: 1 Tese_GeorgeJFN.pdf: 2720479 bytes, checksum: 6d72db8b12a0e5f743d69a67430d66b7 (MD5) Previous issue date: 2010-02-18 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / Matrix metalloproteinase-7 (MMP-7) and -9 (MMP-9) modulate important functions strictly related to the development, invasion and metastasis of several human cancers among them the squamous cell carcinoma of the tongue (SCCT). However, individual genetic factors such as the functional single nucleotide polymorphisms (SNPs) influence the pattern of protein expression of these MMPs and thus may be related to the variability observed in the clinical behavior of patients with SCCT. In this context, the present cross-sectional study aimed to evaluate the association between the frequency of the functional SNPs MMP-7 -181 A/G and MMP-9 -1562 C/T and the clinical (age, gender and metastasis) and pathological (malignancy histological grading and immunohistochemistry expression) features of SCCT cases. Genotyping of these SNPs were performed by PCR-RFLP on DNA samples from 71 cases of SCCT and 60 individuals without cancer who constitute the control group. Among the results of this research, it was observed that the frequency of the polymorphic alleles MMP-7 -181 G and MMP-9 -1562 T in SCCT patients was 28% and 12%, respectively, and the frequency of the heterozygotes A/G (PR = 2.00; p < 0.001) and C/T (PR = 1.54; p = 0.014) were significantly higher in the patient group than in the controls. The prevalence of patients carrying the combination of SNPs studied was significantly associated with SCCT cases (PR = 2.00; p = 0.011) and metastasis (PR = 2.00; p < 0.001). Furthermore, with the frequency of SNPs analyzed, the age, gender, histological grading and immunoreactivity of MMP-7 and MMP-9 formed clinical and pathological parameters relevant to the identification of population subgroups more related to the development of SCCT and metastasis. Based on these results, it is suggested that the protein expression levels of MMP-7 and -9 substantially influence the balance between their pro- and anticancer biological functions and hence the clinicopathological profile of the squamous cell carcinoma of the tongue / As metaloproteinases da matriz extracelular-7 (MMP-7) e -9 (MMP-9) modulam importantes fun??es relacionadas ao desenvolvimento, invas?o e met?stase de diversos c?nceres humanos, dentre os quais o carcinoma epiderm?ide de l?ngua (CEL). Entretanto, fatores gen?ticos individuais, tais como polimorfismos de nucleot?deo ?nico (SNPs) funcionais, influenciam no padr?o de express?o proteica dessas MMPs, podendo estar relacionados ? variabilidade no comportamento cl?nico tumoral observado em pacientes com CEL. Neste contexto, o presente trabalho objetivou, atrav?s de an?lise em sec??o transversal, estudar a associa??o entre a frequ?ncia dos SNPs funcionais MMP-7 -181 A/G e MMP-9 -1562 C/T e as caracter?sticas cl?nicas (idade, sexo e met?stase) e patol?gicas (grada??o histol?gica e express?o imuno-histoqu?mica) em uma s?rie de casos de CEL. A genotipagem dos referidos SNPs foi executada por PCR-RFLP em amostras de DNA de 71 casos de CEL e de 60 indiv?duos sem c?ncer, que constitu?ram o grupo controle. Dentre os resultados da presente pesquisa, evidenciou-se que a frequ?ncia dos alelos polim?rficos MMP-7 -181 G e MMP-9 -1562 T nos pacientes com CEL foi de 28% e 12%, respectivamente, sendo as frequ?ncias dos heterozigotos A/G (RP = 2.00; p < 0.001) e C/T (RP = 1.54; p = 0.014) significativamente maiores neste grupo de pacientes que no grupo controle. A preval?ncia dos pacientes portadores da combina??o dos SNPs estudados associou-se significativamente aos casos de CEL (RP = 2.00; p = 0.011) e ? met?stase (RP = 2.00; p < 0.001). Ademais, junto ? frequ?ncia dos SNPs analisados, a idade, sexo, grada??o histol?gica e imunoexpress?o da MMP-7 e -9 constitu?ram par?metros clinicopatol?gicos relevantes para a identifica??o de subgrupos populacionais mais predispostos ao desenvolvimento do CEL e met?stase. Frente a estes resultados, sugere-se que os n?veis de express?o da MMP-7 e -9 influenciam consideravelmente no balan?o entre suas fun??es pr? e antineopl?sicas e, consequentemente, no perfil clinicopatol?gico do carcinoma epiderm?ide de l?ngua.

Citocinas são moléculas que controlam e modulam a atividade de numerosas células por se ligarem a seus receptores específicos. As diferenças observadas na produção de citocinas entre indivíduos podem ser, pelo menos em parte, explicadas pelos polimorfismos genéticos como o polimorfismo de um único nucleotídeo (SNP). Em 181 indivíduos saudáveis não-aparentados da cidade do Rio de Janeiro (região Sudeste - Brasil), nós analisamos os polimorfismos de citocinas em genes que codificam para Fator de Necrose Tumoral-alfa (TNF-a), Fator de Crescimento Transformante-beta (TGF-b), Interleucina-10, Interleucina-6 e Interferon-gama (IFN-g). Reação em cadeia da polimerase utilizando-se iniciadores sequencia-específicos foi realizada com auxílio do kit comercial CytGen (One Lambda Inc. Canoga Park, CA, USA). Ao todo, 8 polimorfismos foram analisados: TNF-a (-308G/A); TGF-b (códon 10C/T, códon 25C/G); IL-10 (-1082A/G, -819T/C, -592A/C); IL-6 (-174C/G) e IFN-g (+874T/A). Os dados observados foram comparados a três grupos de população de diferentes regiões do Brasil (São Paulo, Paraná e Bahia) e a três populações de outros continentes (Itália, Eslováquia e Negros Norte-Americanos). O teste qui-quadrado foi utilizado para as comparações. Nossa análise da população do Rio de Janeiro mostrou que os as freqüências alélicas em IL-10, IL-6 e IFN-g são desigualmente distribuídos entre Brancos, Mulatos e Negros (p<0,05). A comparação com populações de outras regiões do Brasil revelou que Rio de Janeiro e Bahia possuem freqüências alélicas e genotípicas de TGF-b (códon 25) estatisticamente diferentes (p=0,004 e p=0,002, respectivamente). Ainda, a freqüência alélica na população do Rio de Janeiro é significativamente diferente quando comparada à população da Itália [IL-6 (-174), p=0,0092; e IFN-g (+874) p=0,0418)]; Eslováquia [IL-10(-1082), p=0,006; IL-6(-174), p=0,0002; e IFN-g(+874), p=0,0335]; e Afro-Americanos [IL-10(-819), p=0,0446; IL-6(-174), p<0,0001; e IFN-g(+874), p<0,0001]. Adicionalmente, observamos que a diferença na distribuição dos haplótipos em IL-10 (-1082/-819/-592) na população do Rio de Janeiro em comparação com a da Itália (p=0,0293) e Afro-Americanos (p=0,0025) é significativa. Portanto, concluímos que os polimorfismos em IL-10, IL-6 e IFN-g estão distribuídos de acordo com a etnia na população do Rio de Janeiro. A população do Rio de Janeiro possui freqüências de polimorfismos diferentes das populações de Bahia, Itália, Eslováquia e Afro-Americanos, mas semelhantes à população de São Paulo/Paraná. Nossas observações poderão ser úteis para futuros estudos e associação entre polimorfismos genéticos de citocinas e doenças na população do Rio de Janeiro. / Cytokines are molecules that control and modulate the activities of numerous target cells via binding to specific receptors. The observed differences in the cytokine production among individuals can be, at least, explained by genetic polymorphisms like single nucleotide polymorphism (SNP). In 181 unrelated healthy Brazilian individuals from Rio de Janeiro City, we investigated the polymorphisms of cytokine genes encoding Tumor Necrosis Factor-alpha (TNFA), Transforming Growth Factorbeta (TGFB), Interleukin (IL)-10, IL-6, and Interferon-gamma (IFNG). Polymerase chain reaction using sequence-specific primers genotyping was performed for these gene cytokines using the avaiable comercial kit CytGen (One Lambda Inc., CA, USA). Eight polymorphisms were tested: TNF-a (-308G/A); TGF-b (códon 10C/T, códon 25C/G); IL-10 (-1082A/G, -819T/C, -592A/C); IL-6 (-174G/C) and IFN-g (+874T/A). Chi-square test was used for comparisons. Observed data were compared to three other populations from different regions of Brazil (São Paulo, Paraná and Bahia) and three populations of other countries (Italy, Slovakia and North American Blacks). Our analysis from Rio de Janeiro population showed that the alleles frequencies in IL-10, IL-6 and IFN-g are unevenly distributed among Whites, Blacks and Mulatos (p<0.05). The comparison with populations from other regions of Brazil showed that Rio de Janeiro and Bahia have genotypic and allelic frequencies of TGF-b (códon 25) statistically different (p=0,004 and p=0,002, respectively). Also, the allelic frequency in the population of Rio de Janeiro is significantly different when compared to the population of Italy [IL-6 (-174), p=0.0092, and IFN-g (+874), p=0.0418] ; Slovak [IL-10 (-1082), p=0006; IL-6 (-174), p=0.0002, and IFN-g (+874), p=0.0335] and Afro-Americans [IL-10 (-819), p=0.0446, IL-6 (-174), p<0.0001, and IFN-g (+874), p<0.0001]. Additionally, we observed that the distribution of haplotypes in IL-10 (-1082/-819/-592) in the population of Rio de Janeiro in comparison with that of Italy (p = 0.0293) and Afro-Americans (p =0,0025) is statistically different. Therefore, we conclude that the polymorphisms in IL-10, IL-6 and IFN-g are distributed according to ethnicity in the population of Rio de Janeiro. The population of Rio de Janeiro have different frequencies of polymorphisms of the population of Bahia, Italy, Slovak and Afro-American, but similar to the population of São Paulo/Paraná. Our observations may be useful for future studies in association between genetic polymorphisms of cytokines and disease in the Rio de Janeiro population.

Introdução: A variação genética em genes que codificam a absorção, distribuição, metabolismo e excreção (ADME) de medicamentos frequentemente afeta a farmacocinética da droga e resulta na variabilidade da eficácia e segurança do medicamento. No entanto, a frequência da variação genética nos genes ADME diferem entre as populações. O objetivo deste estudo foi analisar as variações genéticas nos genes ADME nos pacientes brasileiros portadores do vírus da hepatite C e comparar com outros bancos de dados (1000 Genomes Project e Exome Aggregation Consortium). Métodos: Um total de 147 genes ADME foram genotipados em 100 amostras por sequenciamento de DNA genômico usando SureSelectXT (Agilent) e MiSeq, NextSeq (Illumina). Resultados: Um total de 2004 SNPs em 147 genes foram analisados, incluindo enzimas de fase I (n=50), enzimas de fase II (n=37) e transportadores (n=60). Uma coleção de variantes genéticas indica que há pelo menos 2 vezes mais variações do que semelhanças entre os pacientes com hepatite C e os principais grupos continentais. Estas diferenças foram observadas em vários genes relevantes, incluindo CYP1A2, CYP3A4, NAT2, ABCB1 e SLCO1B1. Além disso, pacientes auto declarados como branco, pardo, negro e asiático também apresentaram diferenças de frequência alélica quando comparados à europeus, americanos mixos, africanos e asiáticos nos polimorfismos dos genes CYP1A1, CYP2B6, GSTP1 e ABCG2, respectivamente. Conclusão: Concluímos que os pacientes com hepatite C tem uma frequência alélica de genes ADME diferente dos outros bancos de dados. Embora a personalização do tratamento medicamentoso com base no genótipo individual, e não na etnia, possa ser a mais apropriada, as diferenças nas frequências alélicas entre os continentes devem ser consideradas ao projetar ensaios clínicos de novos medicamentos / Background: Genetic variation in genes encoding drug absorption, distribution, metabolism, and excretion (ADME) proteins often affects the drug pharmacokinetics and results in variability in drug efficacy and safety. However, the frequency of genetic variation in the ADME genes differ among populations. The aim of this study was to analyze the genetic variations in the ADME genes in Brazilian patients with hepatitis C and to compare to other databases (1000 Genomes Project e Exome Aggregation Consortium). Methods: A total of 147 ADME were genotyped in 100 samples from Brazil by targeted genomic DNA sequencing using SureSelectXT (Agilent) and MiSeq, NextSeq (Illumina). Results: A total of 2004 SNPs in 147 genes that were analyzed, including phase I enzymes (n=50), phase II enzymes (n=37), drug transporters (n=60). We provide a collection of genetic variants that indicate that there are at least 2-times more variation than similarities between patients with hepatitis C and major continental groups. These differences were observed in several relevant genes including CYP1A2, CYP3A4, NAT2, ABCB1 and SLCO1B1. Moreover, white, brown, black and Asian self-reported patients also showed allele frequency differences when compared to European, mixed American, African and Asian for polymorphisms of the genes CYP1A1, CYP2B6, GSTP1 and ABCG2. respectively. Conclusion: We conclude that the hepatitis C patients has an allele frequency of ADME genes different from other data bases. While personalization of drug treatment based on individual genotype rather than ethnicity may be more appropriate, differences in allelic frequencies across continents should be considered when designing clinical trials of new drugs

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-04-07T12:49:00Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Mayara final [08-09-2016].pdf: 6000027 bytes, checksum: 8aba9ff907d1176a530d19ec2bb6fad1 (MD5) / Made available in DSpace on 2017-04-07T12:49:00Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Mayara final [08-09-2016].pdf: 6000027 bytes, checksum: 8aba9ff907d1176a530d19ec2bb6fad1 (MD5) Previous issue date: 2015-09-02 / CAPES / Doença inflamatória intestinal descreve um grupo heterogêneo de doenças inflamatórias crônicas do trato gastrointestinal. Os dois principais tipos de DII são retocolite ulcerativa idiopática e doença de Crohn. A patogênese dessas doenças é caracterizada pela inflamação persistente no intestino, envolvendo uma interação entre fatores genéticos, ambientais e imunológicos. Foram investigados aspectos clínico-epidemiológicos e analisados os polimorfismos dos genes da reposta imune em pacientes brasileiros com doença inflamatória intestinal em diferentes formas anátomo-clínicas. Um total de 101 pacientes foram analisados (43 - retocolite ulcerativa idiopática e 58 - doença de Crohn) para os polimorfismos dos genes do fator de necrose tumoral alfa (TNF-α -308 G/A; rs1800629), interleucina-10 (IL-10 -1082 G/A; rs1800896), domínio do recrutamento e ativação da caspase 15/receptor tipo NOD2 (CARD15/NOD2; rs2066844 e rs2066845), receptor tipo NOD contendo domínio pirina – NLRP1 (rs12150220), NLRP3 (rs35829419) e interleucina -1beta (IL-1β -511T/C; rs16944). A forma anatómica-clínica de DC predominante foi a fistulizante (29,31%), seguida por inflamatória (27,58%) e estenosante (27,58%). O grupo controle foi composto por 91 indivíduos saudáveis. Os genes do receptor tipo NOD contendo domínio pirina 1 e 3 e do domínio do recrutamento e ativação da caspase 15/receptor tipo NOD2 variantes R702W e G908R não foram associados à susceptibilidade a doença inflamatória intestinal. Em relação ao polimorfismo da interleucina 10, nenhuma diferença estatística foi encontrada entre os genótipos e alelos para a doença inflamatória intestinal comparado aos controles. Fator de necrose tumoral alfa mostrou uma associação estatisticamente significativa entre pacientes e controles de retocolite ulcerativa idiopática que sugere que a presença do alelo A predispõe o aparecimento de retocolite ulcerativa idiopática, mas não doença de Crohn. Verificou-se ainda que o genótipo AG da interleucina 1 foi associado com o desenvolvimento de retocolite ulcerativa idiopática. Os resultados sugerem que os polimorfismos de única base do fator de necrose tumoral alfa e da interleucina 1 estão envolvidos com a retocolite ulcerativa idiopática e podem contribuir para a patogênese na população brasileira estudada. / Inflammatory bowel disease describes a heterogeneous group of chronic inflammatory diseases of the gastrointestinal tract. The two main types of inflammatory bowel disease are ulcerative colitis and Crohn disease. The pathogenesis of the disease is characterized by unpredictable attacks of inflammation of the intestine, besides involving an interaction between genetic, environmental and immunological factors. Clinical and epidemiological aspects were investigated and the polymorphisms of genes of the immune response in Brazilian patients with inflammatory bowel disease in different anatomic-clinical forms were analyzed. A total of 101 patients were analyzed (43 - ulcerative colitis and 58 - Crohn disease) for the tumour necrosis factor alpha (TNF-α -308 G/A; rs1800629), interleukin-10 (IL-10 -1082 G/A; rs1800896), caspase activation and recruitment domains 15/ NOD like receptor 2 (CARD15/NOD2; rs2066844 and rs2066845), NOD like receptor pyrin domain containing – NLRP1 (rs12150220), NLRP3 (rs35829419) and interleukin-1beta (IL-1β 511T/C; rs16944) genes polymorphisms. The anatomic-clinical form of Crohn disease predominant was the fistulizing (29.31%), followed by inflammatory (27.58%) and stricturing (27.58%). A control group was composed by 91 healthy subjects group. NOD like receptor pyrin domain containing 1 and 3 and caspase activation and recruitment domains 15/ NOD like receptor 2 genes R702W and G908R variants were not associated to inflammatory bowel disease susceptibility. With respect to the polymorphism of interleukin-10, no statistical difference was found between the genotypes and alleles for inflammatory bowel disease compared to controls. Tumour necrosis factor alpha showed a statistically significant association between ulcerative colitis patients and controls which suggests that the presence of A allele predisposes the onset of ulcerative colitis but not Crohn disease. It was found yet that AG genotype of interleukin-1beta was associated with the development of ulcerative colitis. The results suggest that the tumour necrosis factor alpha and interleukin-1beta single nucleotide polymorphisms are involved with ulcerative colitis and may be contributing to pathogenesis in Brazilian population.