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Aspectos clínicos-epidemiológicos e análise de poliomorfirmos de genes relacionados à resposta imune em retocolite ulcerativa e doença de CrohnTAVARES, Mayara Costa Mansur 02 September 2016 (has links)
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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.
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A galectina-3 na fisiologia e no câncer de tiróide: identificação de SNPs no gene LGALS3 e estudo funcional de galectina-3 in vitro e in vivo / Galectin-3 in thyroid physiology and cancer: identification of SNPs in the LGALS3 gene and functional study of galectin-3 in vitro and in vivo.Luciane Martins 17 April 2008 (has links)
Neste estudo, investigamos o envolvimento de galectina-3 na fisiologia e no câncer de tiróide usando vários modelos biológicos e metodologias. Observamos que o gene LGALS3 apresenta um SNP no códon 98, mas não observamos correlação entre os genótipos deste SNP e fenótipo de câncer de tiróide. Na linhagem de tiróide de rato PCCl3, mostramos que a indução da expressão do oncogene RET/PTC promove o aumento da expressão de galectina-3, no entanto, a expressão de galectina-3, por si só, não confere vantagem de proliferação à célula. Por outro lado, na linhagem de carcinoma papilífero de tiróide TPC-1, a galectina-3 contribui para a sobrevivência da célula tumoral e progressão do ciclo celular, aumentando a expressão de c-Myc, diminuindo a expressão de p21 e caspase-3, e favorecendo a ativação de importantes vias envolvidas no controle do ciclo celular. Além disto, em modelos in vivo e in vitro, a galectina-3 interferiu na função e diferenciação da célula folicular tiroidiana, exercendo um papel indireto na regulação da expressão da tireoglobulina e atividade de TTF-1. / In this study, we investigate the involvement of galectin-3 in thyroid physiology and cancer using several biological models and methodologies. We observed that LGALS3 gene presents a SNP in codon 98, but no correlation between the genotype and the phenotype of benign or malignant thyroid tumor was observed. In the rat thyroid cell line PCCl3, we showed that the conditional induction of RET/PTC oncogene expression promotes the increase of galectin-3 expression, however, galectin-3 expression itself did not confer a proliferative advantage to cell. On the other hand, in papillary thyroid carcinoma cell line TPC-1 the galectin-3 contributes to tumor cell survival and cell cycle progression, increasing c-Myc expression, decreasing p21 and caspase-3 expression and cooperating to activation of important signaling pathways which are involved in the cell cycle control. In addition, in vitro and in vivo models the galectin-3 interferes in the differentiation and function of thyroid follicular cell, playing an indirect role in the regulation of thyroglobulin expression and TTF-1 activity.
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Análise de polimorfismos de nucleotídeo único na cistite intersticial / Single nucleotide polymorphism analysis in interstitial cystitisValter Dell Acqua Cassão 08 December 2017 (has links)
IINTRODUÇÃO: A Cistite Intersticial (CI) ou Síndrome da Bexiga Dolorosa (SBD) é uma síndrome crônica caracterizada pela presença de dor ou desconforto vesical ou pélvico e sintomas miccionais como urgência e aumento da frequência miccional diurna e noturna, na ausência de outra afecção identificável que justifique esses sintomas. Não existe até o momento nenhum teste diagnóstico ou marcador que defina a CI. Desta forma seu diagnóstico é predominantemente clínico, baseado nos sinais e sintomas e dependente da exclusão de outras doenças urológicas. A dificuldade no diagnóstico e no tratamento dessas pacientes reflete o pouco que se sabe sobre sua fisiopatologia e sobre as alterações genéticas presentes na doença. A identificação de marcadores pode proporcionar um melhor entendimento e manejo desses aspectos da síndrome. Na tentativa de identificar marcadores genéticos que possam estar associados a CI, avaliamos a presença de alguns polimorfismos genéticos, os polimorfismos de nucleotídeo único (SNP), no DNA de pacientes com os critérios diagnósticos de CI e comparamos sua prevalência entre as pacientes e também com um grupo controle representativo da população geral. A correlação desses polimorfismos considerando a CI e a intensidade de dor nessas pacientes ainda não foi estudada na literatura. OBJETIVOS: Analisar a presença de polimorfismos (SNP) em amostras de sangue de pacientes com CI e correlacionar a presença dos polimorfismos com o quadro de dor crônica. MÉTODOS: Foram selecionadas 34 pacientes do sexo feminino com diagnóstico de CI de acordo com os critérios do NIDDK e 23 pacientes do grupo controle (mulheres saudáveis apenas com incontinência urinária de esforço). As pacientes com o diagnóstico de CI foram estratificadas em dois grupos de acordo com o grau dos sintomas de dor crônica. Foram selecionados 20 polimorfismos para análise: rs1800871, rs1800872, rs1800896, rs1800471, rs1800629, rs361525, rs1800497, rs6311, rs6277, rs6276, rs6313, rs2835859, rs11127292, rs2243248, rs6887695, rs3212227, rs1799971, rs12579350, rs3813034, rs6746030. A genotipagem foi realizada através da técnica de PCR em tempo real (q-PCR) e correlacionada com o diagnóstico de CI e com a intensidade dos sintomas álgicos. RESULTADOS: O alelo polimórfico (T) do SNP rs11127292 foi mais frequente nas pacientes com CI em relação ao grupo controle (p:0,01). O alelo polimórfico (T) do SNP rs6311 foi significativamente mais frequente nas pacientes com dor mais intensa (p:0,03). A frequência do alelo selvagem (A) do SNP rs1799971 foi maior em pacientes com dor leve a moderada (p:0,04). CONCLUSÕES: Foram identificadas algumas diferenças na frequência dos polimorfismos nas pacientes estudadas, o que sugere a existência de um papel relevante dos SNP associados tanto à CI quando na intensidade dos sintomas de dor crônica nestas pacientes / INTRODUCTION: Interstitial cystitis (IC) or painful bladder syndrome (PBS) is a chronic syndrome characterized by the presence of bladder/pelvic pain or discomfort and voiding symptoms such as urgency and increased urinary waking and night-time frequency in the absence of another identifiable cause to justify these symptoms. So far, there is no diagnostic test or marker to establish the presence of IC. Thus, the diagnosis is predominantly clinical, based on signs and symptoms and dependent on the exclusion of other urological diseases. The difficulty in the diagnosis and treatment of these patients reflects the little that is known about IC physiopathology and about the genetic background of the disease. The identification of new markers may provide a better understanding and management of the syndrome. As an attempt to identify genetic markers that may be associated with IC, we evaluated the presence of some genetic polymorphisms, single nucleotide polymorphisms (SNPs), in the DNA of patients with the diagnostic criteria of IC, and we compared their prevalence among IC patients and with a control group representative of the general population. The correlation of these polymorphisms considering IC and pain intensity in these patients has not been studied in the literature. OBJECTIVES: To assess the presence of polymorphisms (SNPs) in blood samples from IC patients and to correlate the presence of polymorphisms with chronic pain. METHODS: Thirty-four female patients with a diagnosis of IC according to the NIDDK criteria and 23 control subjects (healthy women with stress urinary incontinence) were selected. Patients with the diagnosis of IC were stratified into two groups according to the degree of symptoms of chronic pain. We selected 20 polymorphisms for analysis: rs1800871, rs1800876, rs1800471, rs1800629, rs361525, rs1800497, rs6311, rs6277, rs6276, rs6313, rs2835859, rs11127292, rs2243248, rs6887695, rs3212227, rs1799971, rs12579350, rs3813034, rs6746030. Genotyping was performed using the real-time PCR technique (q-PCR) and correlated with the diagnosis of IC and intensity of pain symptoms. RESULTS: The polymorphic allele (T) of the SNP rs11127292 occurred with more frequency in patients with IC compared to the control group (p= 0.01). The polymorphic allele (T) of SNP rs6311 occurred with more frequency in patients with severe pain (p= 0.03). The frequency of wild-type (A) SNP rs1799971 was higher in patients with mild to moderate pain (p= 0.04). CONCLUSION: The results indicated differences in polymorphism frequency in the patients studied, suggesting the existence of a relevant role of SNPs associated with both IC and intensity of chronic pain symptoms in these patients
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Influência do polimorfismo do gene MYH9 na doença renal progressiva em pacientes com nefrite lúpica / Influence of the MYH9 gene polymorphism in progressive kidney disease in patients with lupus nephritisVinicius Sardão Colares 20 January 2012 (has links)
INTRODUÇÃO: A nefrite lúpica é uma complicação frequente e de alta morbimortalidade do lúpus eritematoso sistêmico (LES). A evolução para insuficiência renal crônica terminal varia entre 8 e 15% dos casos, após um período de 5 anos. A fase inicial da nefrite se deve a uma atividade imunológica exacerbada que leva a sequelas renais, como a fibrose intersticial, sinéquias glomerulares, e glomeruloesclerose. Uma vez instalada, vários fatores aceleram a velocidade de progressão da insuficiência renal, como a presença de proteinúria residual, hipertensão arterial sistêmica e a etnia do paciente. Estudos recentes mostraram que a presença de polimorfismos do MYH9 são altamente prevalentes em pacientes com GESF (glomeruloesclerose focal e segmentar), nefropatia do HIV e em pacientes com doença renal crônica não diabética. Os polimorfismos do MYH9 mais relacionados com essas doenças são os do haplótipo E1, causados pelos polimorfismos rs4821480, rs2032487, rs4821481 e rs3752462, presentes principalmente na população negra e de hispano-americanos. No Brasil não há estudos sobre a prevalência desse gene. MÉTODOS: Nosso estudo analisou retrospectivamente 196 pacientes com nefrite lúpica, acompanhadas no ambulatório de glomerulopatias do Hospital das Clínicas da USP. Foram recuperados os dados clínicos e laboratoriais dos pacientes de janeiro de 1999 a dezembro de 2010. Foi feita análise dos polimorfismos do haplótipo E1 do gene do MYH9 (rs4821480, rs2032487, rs4821481 e rs3752462) e correlacionados com suas características clínicas e laboratoriais, apresentando como desfecho a duplicação da creatinina ou a evolução para doença renal crônica terminal. RESULTADOS: O tempo de seguimento médio dos pacientes foi de 6,1 anos, com a creatinina inicial média de 1,6 g/dL e proteinúria média de 3,9 g/dia. Dezenove pacientes não recuperaram função renal, mantendo-se em diálise. Dos 177 pacientes restantes 43 (24%) apresentaram o desfecho de duplicação (DC) da creatinina, ou necessidade de diálise (DRCT). Pacientes progressores eram tinham maior SLEDAI renal (10 vs 8,9 p=0,04), maior índice de cronicidade renal à biópsia (5 vs 2, p<0,001) e maior frequência de reativações da doença renal (flare renal) (82,9% x 53,8%, p=0,002), assim menores índices de remissão completa ou parcial (p<0,0001). Os 4 polimorfismos se segregam em conjunto, ou seja, como um haplótipo, pelo modelo de Hardy-Weinberg. Analisando separadamente cada polimorfismo, apenas o rs3752462, apresenta associação com o desfecho DC/DRCT, na análise por genótipo (CC/CT/TT, p=0,03) e quando feita análise TT/CT vs CC (p=0,02). Não houve relação dos polimorfismos com a etnia negra ou parda. Pacientes com haplótipo E1 eram progressores em 28% dos casos, conferindo um OR de 1,79 (IC 1,02 a 3,0) de DC/DRC. DISCUSSÃO: A presença do haplótipo E1 têm alta prevalência em pacientes portadores de nefrite lúpica no Brasil, sendo fator de risco para progressão da doença renal crônica / BACKGROUND: Lupus nephritis (LN) is a frequent complication with high morbidity and mortality of systemic lupus erythematosus (SLE). Chronic renal failure is observed in 8 to 15% of the patients after 5 years of follow up. LN is an inflammatory disease after a systemic autoimmune activation. Once inflammation is shutdown several renal and nonrenal factors, such as residual proteinuria, hypertension and ethnicity of the patient, may emerge and impose to the kidney a chronic phenotype (interstitial fibrosis, glomerular adhesions and glomerulosclerosis. Recently E1 haplotype (rs4821480, rs2032487, rs4821481 and rs3752462 polymorphisms) of the MYH9 gene was associated to progressive kidney diseases in patients with FSGS (focal segmental glomerulosclerosis), HIV nephropathy and non-diabetic chronic kidney disease, in african american and spanic american patients. In Brazil there is no data on this subject. METHODS: Retrospective analysis of 196 patients with LN followed in our outpatient glomerular disease ward were enrolled glomerulopathies. Patients clinical data from January 1999 to December 2010 were retrieved and MYH9 rs4821480, rs2032487, rs4821481 and rs3752462 polymorphisms were genotyped. Outcome was defined as doubling of serum creatinine, or end stage renal disease (ESRD). RESULTS: The mean follow-up of patients was 6.1 years, with an initial mean creatinine of 1.6 g/dL and mean proteinuria 3.9 g/day. On enrollment nineteen patients were on dialysis and did not recover renal function, they were withdraw from analyses of progressive kidney disease. On follow up, from 177 remaining patients, 43 (24%) showed the composite outcome: dialysis, or doubling creatinine. Progressors had higher renal SLEDAI (10 vs 8.9, p = 0.04), higher chronicity index at biopsy (5 vs 2, p <0.001) and more frequently renal flares (82, 9% vs. 53.8%, p=0.002), as well as lower rates of complete or partial remission (p <0.0001). The four polymorphisms segregate as a haplotype, according the Hardy-Weinberg model. Analysing each polymorphism, only TT/CT genotype from rs3752462 polymorphism was associated with the outcome of DC/ESRD (p = 0.02). E1 haplotype were associated with progression with an OR of 1.79 (CI 1.02 to 3.0). DISCUSSION: The presence of the E1 haplotype is associated with worse prognosis of chronic renal failure in lupus nephritis patients
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Matrix metalloproteinase-8 as a diagnostic tool for the inflammatory and malignant diseasesPradhan-Palikhe, P. (Pratikshya) 27 September 2011 (has links)
Abstract
Matrix metalloproteinases (MMPs) are the zinc-dependent endopeptidases which belong to a large family of proteases. MMPs are responsible for degradation and remodeling of extracellular matrix proteins during growth, organogenesis and tissue turnover. Besides their role in physiological processes, MMPs also influence various pathological processes, i.e., inflammatory diseases and cancers, in which MMPs may ultimately lead to unwanted tissue destruction. One of the most widely studied MMPs is MMP-8. MMP-8 was previously thought to be expressed only by neutrophils. Presently, it is evident that MMP-8 can be expressed in a wide range of cells such as macrophages, plasma cells, T-cells, endothelial cells, smooth muscle cells, oral epithelial cells, fibroblasts etc. MMP-8 has been previously studied in inflammation and malignancies. High serum MMP-8 concentration is associated with the presence of atherosclerosis and poor cardiovascular disease prognosis, while higher plasma MMP-8 levels protect against lymph node metastasis. Certain MMP-8 gene variations can alter promoter activity and subsequent gene expression. MMP-8 gene variation influences obstetrical outcomes, and lung and breast cancer prognosis. For our study, we hypothesized that systemic levels of MMP-8 correlate with its genetic variations and appear as novel risk markers for disease.
We aimed to address the potential role of MMPs and their regulators with a special focus on MMP-8 in distinct sets of inflammatory and malignant diseases, i.e. arterial diseases, and head and neck squamous cell cancer (HNSCC). We demonstrated that the combination of high serum MMP-8 and low myeloperoxidase (MPO) levels is an important risk marker for arterial disease. Further, we demonstrated that MMP-8 gene variation is protective against arterial diseases. Interestingly, we were able to demonstrate an association between MMP-8 gene variation and serum MMP-8 concentration in a healthy population. On the other hand, we showed that plasma tissue inhibitor of matrix metalloproteinases (TIMP-1) concentration is associated with survival in HNSCC patients and TIMP-1 genotype is associated with plasma TIMP-1 levels in women only.
Collectively, our study showed that serum MMP-8 levels can be used as an important risk marker in arterial disease and TIMP-1 levels in HNSCC patients. Based on our results, the hypothesis raised has been widely confirmed. Additionally, our study has warranted the need for further investigation involving a larger number of patients. If our results are replicable, serum MMP-8 and plasma TIMP-1 could be used to develop diagnostic tools as well as treatment regimes in clinics. / Tiivistelmä
Matriksin metalloproteinaasit (MMP:t) ovat sinkkiriippuvaisia endopeptidaaseja, jotka kuuluvat laajaan proteiineja pilkkovaan proteolyyttiseen entsyymi perheeseen. MMP:ien tehtävä on pilkkoa ja uudelleen muokata soluväliaineen proteiineja kasvun, elinten kehityksen ja kudosten uusiutumisen aikana, mutta MMP:t toimivat aktiivisesti myös patologisissa prosesseissa, kuten tulehdustiloissa ja syövissä. Syövissä MMP:en vaikutus voi johtaa ei-toivottuun kudostuhoon. Yksi laajimmin tutkituista MMP-ryhmän entsyymeistä on MMP-8, jonka alunpitäen ajateltiin ilmenevän vain neutrofiileissä. Nykytietämyksen mukaan MMP-8:aa ilmentyy myös mm. makrofaageissa, plasmasoluissa, T-soluissa, endoteelisoluissa, sileälihassoluissa, suun limakalvon epiteelisoluissa ja fibroplasteissa. MMP-8:aa on aikaisemmin tutkittu erityisesti tulehdustiloissa ja pahanlaatuisissa kasvaimissa. Korkean MMP-8 seerumipitoisuuden on havaittu liittyvän valtimokovettumatautiin ja huonoon ennusteeseen sydän- ja verisuonisairauksissa, kun taas kohonnut MMP-8:n pitoisuus plasmassa suojaa imusolmuke-etäpesäkkeiltä. Tiedetään, että tietyt muutokset MMP-8:n geenissä voivat muuttaa sen promoottoriaktiviteettia ja täten säädellä geenin ilmentymistä. MMP-8:n geenimuutokset vaikuttanevat raskaudenkulkuun sekä keuhko- ja rintasyövän ennusteeseen. Tutkimushypoteesimme mukaan MMP-8:n seerumipitoisuudet riippuvat vaihtelusta MMP-8:aa koodaavassa geenissä ja niitä voidaan pitää uusina riskinarvioinnin merkkiaineina tautitiloissa.
Tavoitteenamme oli osoittaa yleisesti MMP:ien ja erityisesti MMP-8:n sekä näiden proteinaasien säätelytekijöiden merkitys tietyissä tulehdustiloissa ja maligniteeteissa, kuten sepelvaltimotaudissa ja pään ja kaulan alueen syövissä. Havaitsimme, että korkea MMP-8 seerumipitoisuus ja alhainen myeloperoksidaasitaso yhdistyvät vahvasti valtimotautiriskiin. Lisäksi osoitimme, että tietty MMP-8:n geenimuunnos on suojaava tekijä valtimotaudille ja että MMP-8:n seerumikonsentraatio on siitä riippuvainen terveillä tutkituilla. Tämän lisäksi todensimme, että MMP:n kudosestäjän (tissue inhibitor of matrix metalloproteinases, TIMP-1) plasmapitoisuus liittyy pään ja kaulan alueen levyepiteelisyöpää sairastavien potilaiden eloonjääntiin ja että TIMP-1:n genotyyppi liittyy sen plasmapitoisuuteen ainoastaan naisilla.
Tulostemme mukaan seerumin MMP-8-pitoisuutta voidaan pitää hyvänä riskinarviointivälineenä verisuonitaudeissa sekä TIMP-1-pitoisuutta vastaavasti pään ja kaulan alueen levyepiteelisyövissä. Saadut tulokset tukevat olettamustamme, jonka mukaan MMP-8 on tärkeä tautimarkkeri. Tämä on lisännyt kiinnostusta selvittää MMP:ien merkitystä laajemmin muissa tulehdustiloissa ja syövissä. Jos tulokset saadaan toistetuksi laajemmassa tutkimusaineistossa, seerumin MMP-8:sta voidaan kehittää kliinisten ja analyyttisten laboratorioiden käyttöön sopiva diagnostinen menetelmä.
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Molecular Marker Applications in Oat (Avena Sativa L.) Breeding and Germplasm DiagnosticsBenazir Katarina, Marquez January 2014 (has links)
The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.
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Fatores genéticos associados ao clareamento espontâneo e resposta ao tratamento da infecção pelo vírus da hepatite C / Genetic factors associated with spontaneous clearance and response to treatment of hepatitis C infectionAna Catharina de Seixas Santos Nastri 17 October 2016 (has links)
O vírus da hepatite C (HCV) é uma importante causa de doença hepática crônica e de complicações associadas, tais como cirrose e hepatocarcinoma (HCC). Fatores virais e do hospedeiro são conhecidos preditores da terapia antiviral. Fatores do hospedeiro preditores da resposta viral sustentada (RVS) foram descobertos por estudos de associação genômica ampla (GWAS), correspondendo a polimorfismos de nucleotídeo único (SNPs) nos genes IFNL3 e IFNL4 (rs8099917, rs12979860 e rs368234815). O objetivo do presente trabalho foi verificar as frequências genotípicas dos SNPs rs8099917, rs12979860 e rs368234815 e avaliar a associação entre estes SNPs e a evolução clínica e a resposta ao tratamento da infecção pelo HCV tendo em conta a ancestralidade genética da população estudada. Neste estudo, foi observada a associação dos três polimorfismos tanto com o desfecho clínico quanto com a resposta ao tratamento com interferon peguilado (PEG-IFN) e ribavirina (RBV). Os polimorfismos rs12979860 e rs368234815 foram associados com aumento da sensibilidade (respectivamente 97,7%, IC 95% 87,2-100, e 93,3%, IC 95% 81,3-98,3) e com um maior valor preditivo de uma resposta positiva ao tratamento. Na análise multivariada ajustada por sexo, idade e ancestralidade genética, o haplótipo G/T/?G foi relacionado com a não-resposta ao tratamento (OR = 21,09, IC 95% 5,33-83,51; p < 0,001) e com uma chance maior de desenvolver infecção crônica (OR = 5,46, IC 95% 2,06-14,46; p=0,001), quando comparado com haplótipo T/C/TT. Estes resultados podem ajudar a ajustar políticas de tratamento para a infecção por HCV em populações com tais características genéticas, assim como nos permitem conhecer o perfil genético da nossa população em relação a esses polimorfismos / Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and associated complications such as liver cirrhosis and hepatocellular carcinoma (HCC). Viral and host factors are known to be predictors for anti-viral therapy. Host factors predictors of sustained viral response (SVR) were discovered by Genome-Wide Association Studies (GWAS), including single nucleotide polymorphisms (SNPs) near or on genes IFNL3 and IFNL4 (rs8099917, rs12979860 and rs368234815). The aim of the present work was verify the genotype frequencies of SNPs rs8099917, rs12979860 and rs368234815, and evaluate the association between these SNPs and HCV infection outcome taking into account the genetic ancestry of the population. In this study, there was an association of the three polymorphisms with both clinical outcome and response to treatment with pegylated interferon (PEG-IFN) and ribavirin (RBV). The polymorphisms rs12979860 and rs368234815 showed increased sensitivity (97.7%, 95% CI 87.2-100, and 93.3%, 95% CI 81.3-98.3 respectively) and greater predictive value of a positive response to treatment. In multivariable analysis adjusted by gender, age and genetic ancestry, the haplotype G/T/?G was related to non-response to treatment (OR = 21.09, 95% CI 5.33-83.51; p < 0.001) and to a higher chance to develop chronic infection (OR = 5.46, 95% CI 2.06-14.46; p=0.001) when compared to haplotype T/C/TT. These findings may help to adjust our treatment policies for HCV infection in populations with such genetic characteristics, as well as allowing us to get to know the genetic profile of our population for these polymorphisms
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A influência de polimorfismos de base única na metilação de DNA em genes de receptores olfatórios / Single nucleotide polymorphisms lead to differential DNA methylation in odorant receptor genesArtur Guazzelli Leme Silva 24 April 2018 (has links)
Os genes de receptores olfatórios (OR) pertencem a uma família de proteínas de membrana formada por cerca de 1000 genes no genoma de camundongo. Os genes OR são expressos de forma monogênica e monoalélica nos neurônios olfatórios (OSNs). No entanto, ainda não está claro o mecanismo que permite essa forma de expressão peculiar, sobretudo, qual o papel da metilação de DNA nesse processo. Nosso estudo determinou o padrão de metilação de DNA da região promotora e codificadora do gene Olfr17. Em células de epitélio olfatório (MOE) de camundongos adultos, observamos na região codificadora (CDS) do gene uma frequência de metilação em dinucleotídeos CpG 58%, enquanto que na sua região promotora ela foi bem mais baixa. Os níveis de metilação do Olfr17 em MOE de embrião (E15.5) e fígado foram similares aos observados em MOE de animais adultos. Em seguida, analisamos se a metilação de DNA pode regular a expressão gênica do Olfr17. Utilizando animais transgênicos onde os neurônios olfatórios que expressam Olfr17 também expressam GFP, pudemos selecionar neurônios olfatórios GFP+ e analisar a metilação do gene Olfr17, que está ativo nestas células. Verificamos que o padrão geral de metilação do Olfr17, tanto na região CDS como na região promotora, não se altera quando este gene está ativo. Este resultado indica que alterações na metilação do gene Olfr17 não são necessárias para que este receptor seja expresso. Finalmente, verificamos que a região promotora do gene Olfr17, de duas linhagens de camundongos diferentes, a C57BL/6 e a 129, possuem dois polimorfismos de base única (SNPs) que alteram o conteúdo CpG. Devido a estes SNPs, a linhagem 129 apresenta dois sítios CpG adicionais, inexistentes na linhagem C57BL/6. Nossas análises mostraram que estes CpGs são frequentemente metilados, o que torna o promotor do Olfr17 de 129 significativamente mais metilado que o promotor de C57BL/6. Em seguida, nós analisamos o nível de expressão no MOE dos dois alelos de Olfr17, o 129 e o C57BL/6, utilizando ensaios de RT-qPCR. Estes experimentos demonstraram que o nível de expressão do alelo 129, que possui 3 CpGs metiladas em seu promotor, é menor que o do alelo C57BL/6, que apresenta apenas uma CpG que é pouco metilada em seu promotor. Nossos resultados sugerem que as alterações na região promotora influenciam a probabilidade com que o gene OR é escolhido para ser expresso no MOE. / Olfactory receptor (OR) genes belong to a large family of membrane proteins composed of 1000 genes in the mouse genome. The OR genes are expressed in the olfactory sensory neurons (OSNs) in a monogenic and monoallelic fashion. However, the mechanisms that govern OR gene expression are unclear. Here we asked whether DNA methylation plays a role in the regulation of OR gene expression. We first determined the DNA methylation pattern in the coding (CDS) and promoter regions of the odorant receptor gene Olfr17. In olfactory epithelium (MOE) cells, the CpG methylation level in the CDS is 58% but is much lower in the promoter region of the gene. In embryonic MOE (E15.5) and liver, the levels of Olfr17 DNA methylation are similar to the ones shown in adult MOE. We next analyzed whether DNA methylation is involved in Olfr17 regulation. We isolated GFP+ neurons from transgenic mice that coexpress GFP with Olfr17, and analyzed the DNA methylation pattern of the Olfr17, which is active in these cells. We found that the general methylation pattern, both, in the coding and promoter regions is not altered in the active gene. These results indicate that changes in DNA methylation are not required for the activation of Olfr17. Finally, we found that the Olfr17 promoter region from two different mouse strains, C57BL/6 and 129, has two single-nucleotide polymorphisms (SNPs) that alter the CpG content. The SNPs lead to the existence of two additional CpGs in the 129 allele, which are absent in the C57BL/6 allele. These CpGs are frequently methylated, making the 129 Olfr17 promoter significantly more methylated than the Olfr17 promoter from C57BL/6. We next performed RT-qPCR experiments to analyze the expression levels of the 129 and C57BL/6 Olfr17 alleles in the MOE. These experiments showed that the expression level of the 129 Olfr17 allele, which contains three methylated CpGs in its promoter region, is lower than the one from C57BL/6, which contains only one, undermethylated CpG, in its promoter. Our results suggest that these promoter modifications regulate the probability of the OR gene choice.
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L’apport alimentaire en iode, sélénium dans les ongles, et risque du cancer différencié de la thyroïde : analyses d’études cas-témoins du consortium Epi-Thyr / Dietary Iodine Intake, Fingernail Selenium, and Risk of Differentiated Thyroid Cancer : Analyses of Case-Control Studies from Epi-Thyr ConsortiumRen, Yan 14 June 2017 (has links)
Contexte: L’iode est un micronutriment provenant des aliments. Il est établi que, dans les régions d'endémie goitreuse caractérisées par un apport d'iode insuffisant, l’incidence des goitres et des cancers différenciés de la thyroïde (CDT) de type folliculaire est plus élevée qu'ailleurs. En revanche, l’influence de l’apport alimentaire en iode sur le risque de CDT de type papillaire, forme représentant actuellement plus de 80% des CDTs dans la plupart des pays, ne fait pas l’objet d’un consensus. Il semble cependant que cette incidence soit plus élevée dans les îles du pacifique qu’ailleurs. Par ailleurs, les propriétés de protection redox du sélénium pourraient protéger la glande thyroïdienne et aider à maintenir la production d'hormones thyroïdiennes, mais la relation entre l’apport en sélénium et le CDT n’avait été que très peu étudiée.Objectifs: L’objectif général de ce travail de thèse était d'explorer la relation entre l'apport alimentaire en iode et le risque de CDT. Plus spécifiquement, il s’agissait 1) d’étudier la relation entre l’apport alimentaire en iode et le risque de CDT dans les cinq études cas-témoins du consortium Epi-Thyr, conduites en Nouvelle Calédonie, en Polynésie Française, en France métropolitaine (deux études) et à Cuba; 2) d’étudier l’interaction entre cet apport et quatre polymorphismes nucléotidiques (SNP) identifiés dans la plupart des études d’association pangénomiques (GWAS) comme associés au risque de CDT, ainsi qu’avec les facteurs de risque environnementaux connus ; et 3) d’évaluer l’intérêt du sélénium présent dans les ongles comme un bio-marqueur potentiel du risque de CDT.Matériel et Méthodes: La régression logistique conditionnelle a été utilisée pour analyser la relation entre l'apport alimentaire en iode et le risque de CDT d’abord dans l’étude Cuba incluant 203 cas et 212 témoins, puis dans l’ensemble des cinq études incluant au total 2162 cas et 2571 témoins. Les questionnaires alimentaires de ces cinq études étaient dérivés de ceux de l’étude de cohorte E3N. Les mesures de l’iode et du sélénium dans les aliments traditionnels polynésiens et cubains avaient été réalisées spécialement pour cette étude. Quatre SNPs avaient été génotypés, dont deux sur le gène FOXE1, un sur le gène ATM et un autre près du gène NKX2-1. Les mesures de l’iode, du sélénium et des autres oligoéléments métalliques avaient été réalisées dans les ongles des sujets de l’étude Polynésie Française.Résultats: Il n’a pas été observée, une association significative entre l’apport alimentaire en iode et le risque de CDT dans l’étude réalisée à Cuba. Dans l'ensemble des cinq études, la majorité des cas et des témoins ont été considérée comme présentant une carence légère en iode selon la classification du Réseau Mondial d'Iode (IGN). Bien que le risque de CDT ne soit pas lié à l'apport alimentaire en iode, ce risque était significativement réduit avec l’augmentation de la consommation de poisson, ceci de manière plus importante dans l'étude réalisée à Cuba que dans les autres. En outre, une augmentation de l’apport alimentaire en iode a été significativement associée à une diminution du risque de CDT uniquement dans l’étude réalisée en Polynésie Française et chez les Polynésiens. Une augmentation significative du risque de CDT associée au nombre de l'allèle mineur (A) du SNP rs965513 près de FOXE1 parmi les sujets qui ont consommé moins d'iode que la médiane dans l'étude réalisée à Cuba. Pour les femmes qui ont eu un nombre de grossesses élevé et qui étaient déficitaires en iode, l'augmentation de l'apport alimentaire en iode réduisait leur risque de CDT. Par ailleurs, il n’a pas été possible de mettre en évidence un intérêt du sélénium dans les ongles comme bio-marqueur prédictif du risque de CDT. / Context: Iodine is a trace element derived from food. In endemic goiter areas characterized by dietary iodine deficiency, it is established that the incidence of goiter and differentiated thyroid cancers (DTC) of follicular type is higher than elsewhere. On the other hand, the influence of dietary iodine intake in the risk of papillary thyroid cancer which currently representing more than 80% of DTCs in most countries, has not achieved a consensus. It appears, however, that this incidence is higher in the Pacific islands than elsewhere. In addition, the redox protection properties of selenium could protect the thyroid gland and help to maintain the production of thyroid hormones, but few studies evaluated the relationship between selenium intake and DTC.Objectives: The general objective of this thesis was to explore the relationship between dietary iodine intake and DTC risk. More specifically, it was 1) to study the relationship between dietary iodine intake and the risk of DTC in five case-control studies of Epi-Thyr consortium, carried out in New Caledonia, French Polynesia, Metropolitan France (two studies) and Cuba; 2) to investigate the interaction between this intake and four single-nucleotide polymorphisms (SNP) identified in most genome-wide association studies (GWAS) as associated with DTC risk, as well as the interaction with the well-established environmental risk factors; and 3) to evaluate the benefit of selenium present in fingernails as a potential bio-marker of DTC risk.Materials and Methods: Conditional logistic regression was used to analyze the relationship between dietary iodine intake and DTC risk first in the Cuba study including 203 cases and 212 controls, and then in the pooled analysis of the five studies including a total of 2162 cases and 2571 controls. The dietary questionnaires of these five studies were derived from those in the E3N cohort study. Measurements of iodine and selenium in traditional Polynesian and Cuban foods were specifically carried out for this pooled analysis. Four SNPs were genotyped, including two of FOXE1 gene, one of ATM gene and another near NKX2-1 gene. Measurements of iodine, selenium and other metal trace elements were made in the fingernails of the participants of the French Polynesia study.Results: There was no significant association between dietary iodine intake and DTC risk in the Cuba study. In the pooled analysis of the five studies, the majority of the cases and the controls was considered as being in mild dietary iodine deficiency according to the IGN classification. Although DTC risk was not found to be linked to dietary iodine intake, this risk significantly decreased with high fish consumption, this reduction in DTC risk per quartile of fish consumption was more important in the Cuba study than in the other studies. Additionally, higher dietary iodine intake significantly associated with lower DTC risk only in the French Polynesia study and in Polynesians. A strong increase in DTC risk associated with the number of the minor allele (A) of the SNP rs965513 near FOXE1, among participants who consumed less iodine than the median value in the Cuba study. For the women who had a high number of full term pregnancies and who were iodine deficient, increasing dietary iodine intake may reduce their risk of suffering from DTC. Moreover, it was not possible to demonstrate an interest in fingernail selenium as a biomarker that predicts DTC risk.
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Impact of pre-imputation SNP-filtering on genotype imputation resultsRoshyara, Nab Raj, Kirsten, Holger, Horn, Katrin, Ahnert, Peter, Scholz, Markus January 2014 (has links)
Background: Imputation of partially missing or unobserved genotypes is an indispensable tool for SNP data analyses. However, research and understanding of the impact of initial SNP-data quality control on imputation results is still limited. In this paper, we aim to evaluate the effect of different strategies of pre-imputation quality filtering on the performance of the widely used imputation algorithms MaCH and IMPUTE. Results: We considered three scenarios: imputation of partially missing genotypes with usage of an external reference panel, without usage of an external reference panel, as well as imputation of ompletely un-typed SNPs using an external reference panel. We first created various datasets applying different SNP quality filters and masking certain percentages of randomly selected high-quality SNPs. We imputed these SNPs and compared the results between the different filtering scenarios by using established and newly proposed measures of imputation quality. While the established measures assess certainty of imputation results, our newly proposed measures focus on the agreement with true genotypes. These measures showed that pre-imputation SNP-filtering might be detrimental regarding imputation quality. Moreover, the strongest drivers of imputation quality were in general the burden of missingness and the number of SNPs used for imputation. We also found that using a reference panel always improves imputation quality of partially missing genotypes. MaCH performed slightly better than IMPUTE2 in most of our scenarios. Again, these results were more pronounced when using our newly defined measures of imputation quality. Conclusion: Even a moderate filtering has a detrimental effect on the imputation quality. Therefore little or no SNP filtering prior to imputation appears to be the best strategy for imputing small to moderately sized datasets. Our results also showed that for these datasets, MaCH performs slightly better than IMPUTE2 in most scenarios at the cost of increased computing time.
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