Systems biology approaches for the design of novel Saccharomyces cerevisiae winemaking strains for enhanced flavour compounds synthesis

Tese de Doutoramento em Biologia Ambiental e Molecular

O polimorfismo VNTR no gene codificador do antagonista do receptor da interleucina-1 está associado com a doença arterial coronariana

FUNDAMENTO: A Doença Arterial Coronariana (DAC) é a aterosclerose das artérias coronárias que transportam o sangue para o coração. A aterosclerose é uma doença inflamatória. As variações gênicas das citocinas - como as associadas à família IL1 - fazem parte da patogênese da aterosclerose. OBJETIVO: O objetivo deste estudo foi determinar a relação entre os polimorfismos da família IL1 (VNTR do IL1RN, posições -511 e +3953 do IL1B) e a DAC na população turca. MÉTODOS: Um total de 427 indivíduos foram submetidos à angiografia coronariana e em seguida divididos da seguinte forma: 170 no grupo controle e 257 no grupo de pacientes com DAC. Os sujeitos com DAC foram divididos em dois subgrupos: 91 no grupo de Doença Coronariana em um único vaso (Single Vessel Disease - SVD) e 166 no grupo Doença Coronariana em múltiplos vasos (Multiple Vessel Disease - MVD). Os genótipos de IL1RN e IL1B (-511, +3953) foram determinados por reação em cadeia da polimerase (RCP), seguida de análise da digestão por enzima de restrição. RESULTADOS: Não foram observadas diferenças significantes nas distribuições de genótipos de IL1RN e IL1B (-511 e +3953) entre os sujeitos com DAC e os controles, ou entre sujeitos com MVD e controles. No entanto, observou-se uma relação significante no genótipo IL1RN 2/2 entre sujeitos portadores de SVD e controles (P= 0,016, x2: 10,289, OR: 2,94IC 95% 1,183 - 7,229). Tampouco foi observada diferença estatisticamente significante nas freqüências dos alelos de IL1RN e IL1B (-511 e +3953) entre os sujeitos com DAC e controles, os sujeitos com MVD e controles, ou ainda os sujeitos SVD e controles. CONCLUSÃO: Não foi observada nenhuma relação na freqüência alélica e nem na distribuição genotípica dos polimorfismos de IL1RN e IL1B entre sujeitos com DAC e grupos controle. No entanto, o genótipo IL1RN 2/2 pode representar um fator de risco para sujeitos com SVD na população turca.

Homocisteína e polimorfismos dos genes MTHFR e VEGF: impacto na doença arterial coronariana

FUNDAMENTO: Polimorfismos em genes relacionados ao desenvolvimento da aterosclerose, angiogênese e metabolismo da homocisteína (Hcy) podem ser fatores de risco para a doença arterial coronariana (DAC). OBJETIVO: Avaliar o efeito dos polimorfismos VEGF C-2578A e MTHFR C677T na DAC e a associação desses polimorfismos com a gravidade e a extensão das lesões ateroscleróticas e concentrações de Hcy. MÉTODOS: 244 indivíduos foram avaliados através de angiografia coronariana e incluídos no estudo (145 com DAC e 99 indivíduos-controle). Os polimorfismos VEGF C-2578A e MTHFR C677T foram investigados através das técnicas de PCR-SSCP e PCR-RFLP, respectivamente. Os níveis de homocisteína plasmática foram mensurados através de cromatografia líquida/espectrometria de massa seqüencial (CL/EMS). RESULTADOS: Não houve diferença significante em relação à distribuição de alelos e genótipos entre os grupos, para ambos os polimorfismos. A análise univariada mostrou uma freqüência maior do genótipo VEGF -2578AA no grupo com doença em três vasos (p=0,044). Além disso, o genótipo VEGF -2578CA foi observado mais freqüentemente entre indivíduos com <95% de estenose (p=0,010). Após ajuste para outros fatores de risco para DAC em um modelo multivariado, observou-se que o polimorfismo VEGF C-2578A não era um correlato independente da DAC (p=0,688). O polimorfismo MTHFR não mostrou qualquer relação com a extensão e/ou gravidade da DAC. O polimorfismo MTHFR C677T não mostrou uma associação direta com hiperhomocisteinemia ou aumento das concentrações médias de Hcy no plasma. CONCLUSÃO: Embora haja uma aparente associação entre o polimorfismo VEGF C-2578A e o desenvolvimento de aterosclerose coronariana, essa associação não é independente dos fatores de risco cardiovasculares convencionais.

Gravidade da lesão angiográfica coronariana e polimorfismo da APOE nas síndromes coronarianas agudas

FUNDAMENTO: Existem evidências de associação entre o polimorfismo da apolipoproteína E (APOE) e a doença coronariana, entretanto há controvérsias. OBJETIVO: Avaliar a associação entre o número de vasos coronarianos acometidos por obstrução significativa definida por angiografia, o polimorfismo da APOE e as variáveis clínicas. MÉTODOS: Estudo transversal multicêntrico que envolveu 207 pacientes (138 homens) com síndrome coronariana aguda (SCA) em Niterói (RJ - Brasil), os quais realizaram angiografia coronariana e determinação do genótipo para o polimorfismo APOE *2*3*4, pelo método de Restriction Fragment Length Polymorphism (RFLP). RESULTADOS: A frequência dos alelos APOE *2 foi de 6,8%, *3 foi de 82,5%, e *4 foi de 10,7%. Quanto ao número de vasos lesados, 27% dos pacientes apresentavam obstrução uniarterial, 33,8%, biarterial, e 39,1%, triarterial ou de tronco da coronária esquerda. O grau de lesão multivascular não se relacionou com a presença do alelo *4 (p = 0,78), mas com a idade > 55 anos (p = 0,025), o ex-tabagismo (p = 0,004) e a dislipidemia (p = 0,05) na análise multivariada e com doença arterial coronariana prévia (p = 0,05), diabete (p = 0,038) e síndrome metabólica (p = 0,021) na análise univariada. A prevalência de dislipidemia, diabete e hipertensão arterial sistêmica (HAS) foi elevada em relação a estudos semelhantes, com aumento progressivo da prevalência de HAS (p = 0,59) e de diabete (p = 0,06), de acordo com o número de vasos lesados. CONCLUSÃO: O polimorfismo da APOE não se associou ao número de vasos coronarianos com obstrução significativa em qualquer faixa etária. Por outro lado, a idade > 55 anos, o ex-tabagismo e a dislipidemia associaram-se à lesão multivascular.

Influência de combinações genéticas nos níveis de HDL-c em uma população do sul do Brasil

FUNDAMENTO: Baixos níveis de HDL-c são importantes preditores de doença coronariana, a primeira causa de morte no mundo todo. Muitos fatores afetam os níveis de HDL-c, tais como os polimorfismos de genes que codificam proteínas-chave para a via de transporte reverso de colesterol. OBJETIVO: Investigar a influência de sete polimorfismos dos genes CETP, APOA1, ABCA1 e SCARB1 genes nos níveis de HDL-c em uma população da região sul do Brasil. MÉTODOS: Os polimorfismos foram investigados em uma amostra de 500 indivíduos de descendência europeia, mas os níveis de HDL-c de somente 360 indivíduos foram ajustados para cofatores usando regressão linear múltipla no estudo de associação. A amostra foi dividida em tercis de acordo com os níveis ajustados de HDL-c e frequências de alelos e haplótipos foram comparadas entre o 1º e o 3º tercis dos níveis ajustados de HDL-c. RESULTADOS: Quando as combinações dos alelos de risco foram testadas, a frequência de combinações alélicas em três genes (haplótipo 1 do gene APOA1, variante 2S do gene SCARB1, e alelo B1 do gene CETP) foi significantemente mais alta no tercil inferior dos níveis ajustados de HDL-c (28,3%) do que no tercil superior (14,9%; p=0,008), o que indica que a presença dessas variantes aumentou 2,26 vezes a chance de ter níveis de HDL-C < 39,8 mg/dl. CONCLUSÃO: Espera-se que esses marcadores, quando estudados separadamente, tenham uma pequena influência na característica que está sendo analisada, mas uma influência maior foi detectada quando os marcadores foram estudados em combinação. Em uma população da região sul do Brasil, nossos dados mostraram uma influência significante das combinações das variantes dos genes APOA1, SCARB1 e CETP nos níveis de HDL-c.

Desarrollo de una colección de Líneas Casi Isogénicas (NIL) para el estudio de caracteres de interés agronómico en especies del género Fragaria

Fragaria vesca posee varias características que la hacen interesante como especie modelo en la familia Rosaceae. Además, su naturaleza diploide permite sortear la complejidad genética de la fresa cultivada. Considerando que los genomas de las especies diploides y octoploides de Fragaria mantienen una relación de sintenia y colinearidad, estamos desarrollando una colección de Líneas Casi Isogénicas (NIL) en Fragaria diploide, usando Fragaria bucharica, una variedad asiática, como donante de introgresiones y Fragaria vesca var. Reine des Vallées, una variedad francesa comúnmente cultivada en España para usos industriales, como parental recurrente. Para obtener introgresiones de F. bucharica en un fondo genético homogéneo de F. vesca, se desarrolló un retrocruzamiento y se obtuvo una población BC1 que fue analizada para la presencia de alelos de F. bucharica a lo largo de los 7 grupos de ligamiento (LG) del mapa de referencia de Fragaria. Los individuos con bajo número de introgresiones de gran tamaño, que en conjunto abarcaron todo el genoma de F. bucharica, fueron seleccionados y retrocruzados con el parental recurrente. La descendencia fue analizada para los loci segregantes y los individuos BC2 con 1 ó 2 introgresiones fueron seleccionados como líneas donadoras de introgresiones de las NIL. Hasta el momento se han descrito tres fenotipos dominantes diferentes bajo condiciones de invernadero en varias NIL heterozigóticas: Las plantas con introgresiones en LG2 presentan estolones. Las plantas con introgresiones en LG1 y LG3 presentan floración temprana. Las plantas con introgresiones en LG6 presentan floración estacional. Actualmente se está trabajando en la selección y caracterización de introgresiones de pequeño tamaño mediante la autofecundación de las líneas seleccionadas. La caracterización fenotípica de los recombinantes seleccionados permitirá localizar y estimar los patrones de herencia de los genes implicados en los caracteres descritos, además de la identificación de nuevos caracteres recesivos que aparecerán en homozigosis.

Frequency of Fabry disease in male and female haemodialysis patients in Spain

BACKGROUND: Fabry disease (FD), an X-linked lysosomal storage disorder, is caused by a reduced activity of the lysosomal enzyme alpha-galactosidase A. The disorder ultimately leads to organ damage (including renal failure) in males and females. However, heterozygous females usually present a milder phenotype with a later onset and a slower progression. METHODS: A combined enzymatic and genetic strategy was used, measuring the activity of alpha-galactosidase A and genotyping the alpha-galactosidase A gene (GLA) in dried blood samples (DBS) of 911 patients undergoing haemodialysis in centers across Spain. RESULTS: GLA alterations were found in seven unrelated patients (4 males and 3 females). Two novel mutations (p.Gly346AlafsX347 and p.Val199GlyfsX203) were identified as well as a previously described mutation, R118C. The R118C mutation was present in 60% of unrelated patients with GLA causal mutations. The D313Y alteration, considered by some authors as a pseudo-deficiency allele, was also found in two out of seven patients. CONCLUSIONS: Excluding the controversial D313Y alteration, FD presents a frequency of one in 182 individuals (0.55%) within this population of males and females undergoing haemodialysis. Moreover, our findings suggest that a number of patients with unexplained and atypical symptoms of renal disease may have FD. Screening programmes for FD in populations of individuals presenting severe kidney dysfunction, cardiac alterations or cerebrovascular disease may lead to the diagnosis of FD in those patients, the study of their families and eventually the implementation of a specific therapy.

Multiple sclerosis risk variant HLA-DRB1*1501 associates with high expression of DRB1 gene in different human populations.

The human leukocyte antigen (HLA) DRB1*1501 has been consistently associated with multiple sclerosis (MS) in nearly all populations tested. This points to a specific antigen presentation as the pathogenic mechanism though this does not fully explain the disease association. The identification of expression quantitative trait loci (eQTL) for genes in the HLA locus poses the question of the role of gene expression in MS susceptibility. We analyzed the eQTLs in the HLA region with respect to MS-associated HLA-variants obtained from genome-wide association studies (GWAS). We found that the Tag of DRB1*1501, rs3135388 A allele, correlated with high expression of DRB1, DRB5 and DQB1 genes in a Caucasian population. In quantitative terms, the MS-risk AA genotype carriers of rs3135388 were associated with 15.7-, 5.2- and 8.3-fold higher expression of DQB1, DRB5 and DRB1, respectively, than the non-risk GG carriers. The haplotype analysis of expression-associated variants in a Spanish MS cohort revealed that high expression of DRB1 and DQB1 alone did not contribute to the disease. However, in Caucasian, Asian and African American populations, the DRB1*1501 allele was always highly expressed. In other immune related diseases such as type 1 diabetes, inflammatory bowel disease, ulcerative colitis, asthma and IgA deficiency, the best GWAS-associated HLA SNPs were also eQTLs for different HLA Class II genes. Our data suggest that the DR/DQ expression levels, together with specific structural properties of alleles, seem to be the causal effect in MS and in other immunopathologies rather than specific antigen presentation alone.

CD40: Novel Association with Crohn's Disease and Replication in Multiple Sclerosis Susceptibility

Background: A functional polymorphism located at 21 from the start codon of the CD40 gene, rs1883832, was previously reported to disrupt a Kozak sequence essential for translation. It has been consistently associated with Graves’ disease risk in populations of different ethnicity and genetic proxies of this variant evaluated in genome-wide association studies have shown evidence of an effect in rheumatoid arthritis and multiple sclerosis (MS) susceptibility. However, the protective allele associated with Graves’ disease or rheumatoid arthritis has shown a risk role in MS, an effect that we aimed to replicate in the present work. We hypothesized that this functional polymorphism might also show an association with other complex autoimmune condition such as inflammatory bowel disease, given the CD40 overexpression previously observed in Crohn’s disease (CD) lesions. Methodology: Genotyping of rs1883832C.T was performed in 1564 MS, 1102 CD and 969 ulcerative colitis (UC) Spanish patients and in 2948 ethnically matched controls by TaqMan chemistry. Principal Findings: The observed effect of the minor allele rs1883832T was replicated in our independent Spanish MS cohort [p= 0.025; OR (95% CI)= 1.12 (1.01–1.23)]. The frequency of the minor allele was also significantly higher in CD patients than in controls [p= 0.002; OR (95% CI)= 1.19 (1.06–1.33)]. This increased predisposition was not detected in UC patients [p= 0.5; OR (95% CI)= 1.04 (0.93–1.17)]. Conclusion: The impact of CD40 rs1883832 on MS and CD risk points to a common signaling shared by these autoimmune conditions

Genetic analysis of caveolin-1 and eNOS genes in colorectal cancer.

Caveolae are involved in physical compartmentalization between different groups of signaling events. Its main component, CAV1, modulates different pathways in cellular physiology. The emerging evidence pointing to the role of CAV1 in cancer led us to study whether different alleles of this gene are associated with colorectal cancer (CRC). Since one of the most characterized enzymes regulated by CAV1 is eNOS, we decided to include both genes in this study. We analyzed five SNPs in 360 unrelated CRC patients and 550 controls from the general population. Two of these SNPs were located within eNOS and three within the CAV1 gene. Although haplotype distribution was not associated with CRC, haplotype TiA (CAV1) was associated with familiar forms of CRC (p<0.05). This was especially evident in CRC antecedents and nuclear forms of CRC. If both CG (eNOS) and TiA (CAV1) haplotypes were taken together, this association increased in significance. Thus, we propose that CAV1, either alone or together with eNOS alleles, might modify CRC heritability.

IL2RA/CD25 gene polymorphisms: uneven association with multiple sclerosis (MS) and type 1 diabetes (T1D).

BACKGROUND: IL-2 receptor (IL2R) alpha is the specific component of the high affinity IL2R system involved in the immune response and in the control of autoimmunity. METHODS AND RESULTS: Here we perform a replication and fine mapping of the IL2RA gene region analyzing 3 SNPs previously associated with multiple sclerosis (MS) and 5 SNPs associated with type 1 diabetes (T1D) in a collection of 798 MS patients and 927 matched Caucasian controls from the south of Spain. We observed association with MS in 6 of 8 SNPs. The rs1570538, at the 3'- UTR extreme of the gene, previously reported to have a weak association with MS, is replicated here (P = 0.032). The most associated T1D SNP (rs41295061) was not associated with MS in the present study. However, the rs35285258, belonging to another independent group of SNPs associated with T1D, showed the maximal association in this study but different risk allele. We replicated the association of only one (rs2104286) of the two IL2RA SNPs identified in the recently performed genome-wide association study of MS. CONCLUSIONS: These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.

The TT genotype of the STAT4 rs7574865 polymorphism is associated with high disease activity and disability in patients with early arthritis

BACKGROUND The number of copies of the HLA-DRB1 shared epitope, and the minor alleles of the STAT4 rs7574865 and the PTPN22 rs2476601 polymorphisms have all been linked with an increased risk of developing rheumatoid arthritis. In the present study, we investigated the effects of these genetic variants on disease activity and disability in patients with early arthritis. METHODOLOGY AND RESULTS We studied 640 patients with early arthritis (76% women; median age, 52 years), recording disease-related variables every 6 months during a 2-year follow-up. HLA-DRB1 alleles were determined by PCR-SSO, while rs7574865 and rs2476601 were genotyped with the Taqman 5' allelic discrimination assay. Multivariate analysis was performed using generalized estimating equations for repeated measures. After adjusting for confounding variables such as gender, age and ACPA, the TT genotype of rs7574865 in STAT4 was associated with increased disease activity (DAS28) as compared with the GG genotype (β coefficient [95% confidence interval] = 0.42 [0.01-0.83], p = 0.044). Conversely, the presence of the T allele of rs2476601 in PTPN22 was associated with diminished disease activity during follow-up in a dose-dependent manner (CT genotype = -0.27 [-0.56- -0.01], p = 0.042; TT genotype = -0.68 [-1.64- -0.27], p = 0.162). After adjustment for gender, age and disease activity, homozygosity for the T allele of rs7574865 in STAT4 was associated with greater disability as compared with the GG genotype. CONCLUSIONS Our data suggest that patients with early arthritis who are homozygous for the T allele of rs7574865 in STAT4 may develop a more severe form of the disease with increased disease activity and disability.

Evidence of new risk genetic factor to systemic lupus erythematosus: the UBASH3A gene

The ubiquitin associated and Src-homology 3 (SH3) domain containing A (UBASH3a) is a suppressor of T-cell receptor signaling, underscoring antigen presentation to T-cells as a critical shared mechanism of diseases pathogenesis. The aim of the present study was to determine whether the UBASH3a gene influence the susceptibility to systemic lupus erythematosus (SLE) in Caucasian populations. We evaluated five UBASH3a polymorphisms (rs2277798, rs2277800, rs9976767, rs13048049 and rs17114930), using TaqMan® allelic discrimination assays, in a discovery cohort that included 906 SLE patients and 1165 healthy controls from Spain. The SNPs that exhibit statistical significance difference were evaluated in a German replication cohort of 360 SLE patients and 379 healthy controls. The case-control analysis in the Spanish population showed a significant association between the rs9976767 and SLE (Pc = 9.9E-03 OR = 1.21 95%CI = 1.07-1.37) and a trend of association for the rs2277798 analysis (P = 0.09 OR = 0.9 95%CI = 0.79-1.02). The replication in a German cohort and the meta-analysis confirmed that the rs9976767 (Pc = 0.02; Pc = 2.4E-04, for German cohort and meta-analysis, respectively) and rs2277798 (Pc = 0.013; Pc = 4.7E-03, for German cohort and meta-analysis, respectively) UBASH3a variants are susceptibility factors for SLE. Finally, a conditional regression analysis suggested that the most likely genetic variation responsible for the association was the rs9976767 polymorphism. Our results suggest that UBASH3a gene plays a role in the susceptibility to SLE. Moreover, our study indicates that UBASH3a can be considered as a common genetic factor in autoimmune diseases.

Lack of association between the protein tyrosine phosphatase non-receptor type 22 R263Q and R620W functional genetic variants and endogenous non-anterior uveitis.

OBJECTIVE Endogenous uveitis is a major cause of visual loss mediated by the immune system. The protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene encodes a lymphoid-specific phosphatase that plays a key role in T-cell receptor (TCR) signaling. Two independent functional missense single nucleotide polymorphisms (SNPs) located within the PTPN22 gene (R263Q and R620W) have been associated with different autoimmune disorders. We aimed to analyze for the first time the influence of these PTPN22 genetic variants on endogenous non-anterior uveitis susceptibility. METHODS We performed a case-control study of 217 patients with endogenous non-anterior uveitis and 718 healthy controls from a Spanish population. The PTPN22 polymorphisms (rs33996649 and rs2476601) were genotyped using TaqMan allelic discrimination assays. The allele, genotype, carriers, and allelic combination frequencies were compared between cases and controls with χ(2) analysis or Fisher's exact test. RESULTS Our results showed no influence of the studied SNPs in the global susceptibility analysis (rs33996649: allelic P- value=0.92, odds ratio=0.97, 95% confidence interval=0.54-1.75; rs2476601: allelic P- value=0.86, odds ratio=1.04, 95% confidence interval=0.68-1.59). Similarly, the allelic combination analysis did not provide additional information. CONCLUSIONS Our results suggest that the studied polymorphisms of the PTPN22 gene do not play an important role in the pathophysiology of endogenous non-anterior uveitis.

Selected ABCB1, ABCB4 and ABCC2 Polymorphisms Do Not Enhance the Risk of Drug-Induced Hepatotoxicity in a Spanish Cohort.

BACKGROUND AND AIMS Flawed ABC transporter functions may contribute to increased risk of drug-induced liver injury (DILI). We aimed to analyse the influence of genetic variations in ABC transporters on the risk of DILI development and clinical presentations in a large Spanish DILI cohort. METHODS A total of ten polymorphisms in ABCB1 (1236T>C, 2677G>T,A, 3435T>C), ABCB4 (1954A>G) and ABCC2 (-1774G>del, -1549A>G, -24C>T, 1249G>A, 3972C>T and 4544G>A) were genotyped using Taqman 5' allelic discrimination assays or sequencing in 141 Spanish DILI patients and 161 controls. The influence of specific genotypes, alleles and haplotypes on the risk of DILI development and clinical presentations was analysed. RESULTS None of the individual polymorphisms or haplotypes was found to be associated with DILI development. Carriers homozygous for the ABCC2 -1774del allele were however only found in DILI patients. Hence, this genotype could potentially be associated with increased risk, though its low frequency in our Spanish cohort prevented a final conclusion. Furthermore, carriers homozygous for the ABCC2 -1774G/-1549A/-24T/1249G/3972T/4544G haplotype were found to have a higher propensity for total bilirubin elevations when developing DILI. CONCLUSIONS Our findings do not support a role for the analysed polymorphisms in the ABCB1, ABCB4 and ABCC2 transporter genes in DILI development in Spanish patients. The ABCC2 -1774deldel genotype was however restricted to DILI cases and could potentially contribute to enhanced DILI susceptibility.