Recentemente, estudos de Genome Wide Association (GWA) identificaram uma nova região cromossômica, 18q22, como de susceptibilidade ao Diabetes tipo 1 autoimune (DM1A). Nesta região localiza-se o gene CD226, responsável por codificar uma molécula de adesão leucocitária (CD226) envolvida no processo de adesão celular, diferenciação de células T CD4+ virgens, citotoxicidade induzida por células natural killer (NK) e produção de citocinas. Até o momento, apenas o polimorfismo rs763361 A/G foi relacionado ao diabetes autoimune e pouco é conhecido quanto ao envolvimento de outras variantes do CD226, associadas a outras doenças autoimunes, na patogênese do DM1A. Com o objetivo de definir as variantes polimórficas relacionadas à susceptibilidade ao DM1A, às suas características fenotípicas e outras manifestações de autoimunidade, 532 pacientes diabéticos tipo 1A e 594 controles normais foram envolvidos neste estudo. Inicialmente, em um subgrupo de 106 diabéticos e 102 controles, as regiões codificadoras e flanqueadoras do gene CD226, obtidas do DNA genômico de leucócitos do sangue periférico, foram amplificadas pela técnica de Reação em Cadeia da Polimerase e submetidas à sequenciamento direto. Em uma segunda etapa, os polimorfismos rs763361, rs1788101 e rs727088 foram genotipados pelo ensaio TaqMan nos demais pacientes e controles. Resultados: foram identificadas 12 variantes no gene CD226, sete com frequência acima de 5%. Nenhuma variante nova foi encontrada. A variante rs727088 não estava em equilíbrio de Hardy Weinberg no grupo controle. Os genótipos AA da variante rs763361 e CC do rs727088 foram associados ao risco de DM1A e estavam em desequilíbrio de ligação. O genótipo do haplótipo ACAC, formado pelas variantes de risco, predominou nos pacientes diabéticos. Tanto o genótipo AA do rs763361 como o CC do rs727088 e o genótipo do haplótipo ACAC foram associados com menores valores de peptídeo C em pacientes com até dois anos de duração da doença. Nenhum polimorfismo influiu na presença de autoanticorpos pancreáticos e extra-pancreáticos. Conclusão: O genótipo AA da variante rs763361 do gene CD226 predispõe ao diabetes autoimune na nossa população, assim como a menores valores de Peptídeo C, contribuindo para a maior agressividade da doença. Dados da variante rs727088 devem ser analisados com cautela devido à falta de equilíbrio de Hardy Weinberg no grupo dos controles / Recently, Genome Wide Association (GWA) studies identified a new locus, 18q22, as a canditate to Type 1 A, or immune mediated diabetes (T1AD) susceptibility. This locus harbors the CD226 gene, responsible for encoding the leukocyte adhesion molecule (CD226) involved in cell adhesion, differentiation of naïve CD4+T cells, cytotoxicity induced by natural killer (NK) cells and cytokine production. Although just one single nucleotide polymorphism (SNP) rs763361 A/G had been related to T1AD, little is known about the involvement of new variants of CD226, implicated in other autoimmune disorders, in the pathogenesis of T1AD. In order to identify polymorphic variants related to T1AD susceptibility and their influences in phenotypic characteristics and other manifestations of autoimmunity, 532 type 1A diabetic patients and 594 health controls were enrolled in this study. Initially, in a subset of 106 diabetics and 102 controls, coding and flanking regions of CD226 gene obtained from genomic DNA extraction were amplified by polymerase chain reaction technique and subjected to direct sequencing. In a second step, the polymorphisms rs763361, rs727088 and rs1788101 were genotyped by TaqMan assay in the remaining patients and controls. Results: 12 variants in CD226 gene, seven of them with frequency above 5 % where identified. We did not found new variants. The variant rs727088 was not in Hardy Weinberg equilibrium in the control group. The genotypes AA (OR=1.45; p=0.005) and CC (OR=1.41; p=0.01) related to rs763361 and rs727088 variants respectively, were associated with risk of T1AD. Both predominated in female (p<0.01). Further, these variants were in linkage disequilibrium. The genotype haplotype ACAC formed by the risk variants was more frequent in patients with diabetes (30.5% x 25.6%; OR=1.42; p=0.014). The AA genotype of rs763361, the CC genotype and ACAC genotype haplotype were associated with lower levels of C-peptide in patients with no more than two years of disease course. The presence of pancreatic and extra-pancreatic autoantibodies was not associated with CD226 SNPs. Conclusion: The AA genotype of rs763361 variant of the gene CD226 predisposes to autoimmune diabetes in our population, as well as to lower levels of C-peptide, contributing to the aggressiveness of the disease. It predominated in female. Data of rs727088 variant should be analyzed with caution due to the lack of Hardy Weinberg equilibrium in the control group

Recentemente, estudos de Genome Wide Association (GWA) identificaram uma nova região cromossômica, 18q22, como de susceptibilidade ao Diabetes tipo 1 autoimune (DM1A). Nesta região localiza-se o gene CD226, responsável por codificar uma molécula de adesão leucocitária (CD226) envolvida no processo de adesão celular, diferenciação de células T CD4+ virgens, citotoxicidade induzida por células natural killer (NK) e produção de citocinas. Até o momento, apenas o polimorfismo rs763361 A/G foi relacionado ao diabetes autoimune e pouco é conhecido quanto ao envolvimento de outras variantes do CD226, associadas a outras doenças autoimunes, na patogênese do DM1A. Com o objetivo de definir as variantes polimórficas relacionadas à susceptibilidade ao DM1A, às suas características fenotípicas e outras manifestações de autoimunidade, 532 pacientes diabéticos tipo 1A e 594 controles normais foram envolvidos neste estudo. Inicialmente, em um subgrupo de 106 diabéticos e 102 controles, as regiões codificadoras e flanqueadoras do gene CD226, obtidas do DNA genômico de leucócitos do sangue periférico, foram amplificadas pela técnica de Reação em Cadeia da Polimerase e submetidas à sequenciamento direto. Em uma segunda etapa, os polimorfismos rs763361, rs1788101 e rs727088 foram genotipados pelo ensaio TaqMan nos demais pacientes e controles. Resultados: foram identificadas 12 variantes no gene CD226, sete com frequência acima de 5%. Nenhuma variante nova foi encontrada. A variante rs727088 não estava em equilíbrio de Hardy Weinberg no grupo controle. Os genótipos AA da variante rs763361 e CC do rs727088 foram associados ao risco de DM1A e estavam em desequilíbrio de ligação. O genótipo do haplótipo ACAC, formado pelas variantes de risco, predominou nos pacientes diabéticos. Tanto o genótipo AA do rs763361 como o CC do rs727088 e o genótipo do haplótipo ACAC foram associados com menores valores de peptídeo C em pacientes com até dois anos de duração da doença. Nenhum polimorfismo influiu na presença de autoanticorpos pancreáticos e extra-pancreáticos. Conclusão: O genótipo AA da variante rs763361 do gene CD226 predispõe ao diabetes autoimune na nossa população, assim como a menores valores de Peptídeo C, contribuindo para a maior agressividade da doença. Dados da variante rs727088 devem ser analisados com cautela devido à falta de equilíbrio de Hardy Weinberg no grupo dos controles / Recently, Genome Wide Association (GWA) studies identified a new locus, 18q22, as a canditate to Type 1 A, or immune mediated diabetes (T1AD) susceptibility. This locus harbors the CD226 gene, responsible for encoding the leukocyte adhesion molecule (CD226) involved in cell adhesion, differentiation of naïve CD4+T cells, cytotoxicity induced by natural killer (NK) cells and cytokine production. Although just one single nucleotide polymorphism (SNP) rs763361 A/G had been related to T1AD, little is known about the involvement of new variants of CD226, implicated in other autoimmune disorders, in the pathogenesis of T1AD. In order to identify polymorphic variants related to T1AD susceptibility and their influences in phenotypic characteristics and other manifestations of autoimmunity, 532 type 1A diabetic patients and 594 health controls were enrolled in this study. Initially, in a subset of 106 diabetics and 102 controls, coding and flanking regions of CD226 gene obtained from genomic DNA extraction were amplified by polymerase chain reaction technique and subjected to direct sequencing. In a second step, the polymorphisms rs763361, rs727088 and rs1788101 were genotyped by TaqMan assay in the remaining patients and controls. Results: 12 variants in CD226 gene, seven of them with frequency above 5 % where identified. We did not found new variants. The variant rs727088 was not in Hardy Weinberg equilibrium in the control group. The genotypes AA (OR=1.45; p=0.005) and CC (OR=1.41; p=0.01) related to rs763361 and rs727088 variants respectively, were associated with risk of T1AD. Both predominated in female (p<0.01). Further, these variants were in linkage disequilibrium. The genotype haplotype ACAC formed by the risk variants was more frequent in patients with diabetes (30.5% x 25.6%; OR=1.42; p=0.014). The AA genotype of rs763361, the CC genotype and ACAC genotype haplotype were associated with lower levels of C-peptide in patients with no more than two years of disease course. The presence of pancreatic and extra-pancreatic autoantibodies was not associated with CD226 SNPs. Conclusion: The AA genotype of rs763361 variant of the gene CD226 predisposes to autoimmune diabetes in our population, as well as to lower levels of C-peptide, contributing to the aggressiveness of the disease. It predominated in female. Data of rs727088 variant should be analyzed with caution due to the lack of Hardy Weinberg equilibrium in the control group

Systemic lupus erythematosus (SLE) is a chronic and complex autoimmune disorder characterized by a failure in the mechanism of self-tolerance and production of autoantibodies, potentially affecting any organ in the body. The genetic factors behind the disease have been extensively studied in the past years and to date a list of more than 30 loci have been associated with SLE. However, very little is known about the functional significance of the risk variants. In this thesis, we focused on the analysis of SLE-associated variants in three genes: interferon regulatory factor 5 (IRF5), CD226 and the microRNA 146a. In paper I, we analyzed four polymorphisms in the IRF5 gene in a large set of individuals from different populations. We replicated a strong association of a promoter indel in our meta-analysis, but expression analysis indicated that it is rather another variant, SNP rs10954213 in the poly(A) signal of the gene that is in fact the major contributor to the altered gene expression in leukocytes. In manuscript II, we further characterized the regulation of IRF5 expression, showing that this gene can be up-regulated by estrogen in PBMCs and monocytes, regardless of the genotype, which could to some extent, explain the sex-bias of SLE. In paper III, we investigated the association of CD226 with SLE and the potential functional effect of the associated variants. The genetic analysis showed an association of a three-SNP-haplotype located at the 3’UTR region of the gene. The risk haplotype correlated with lower CD226 protein expression on the surface of cytotoxic and helper T cells, as well as in NK T cells. Reporter assays pointed to rs727088 in the 3’UTR as the main responsible variant for altered gene expression. In paper IV, we described the association of a variant in microRNA miR-146a, involved in the interferon pathway, with SLE in Europeans, which could in addition be correlated with decreased expression of both mature and primary miR-146a in leukocytes. In summary, we have investigated the genetic association of three genes with SLE in a large cohort of individuals and identified variants responsible for functional alterations of these genes, providing further insight into the pathogenesis of SLE.

Systemic lupus erythematosus (SLE) is a chronic and systemic autoimmune disease that primarily affects women during the childbearing years. SLE is characterized by the production of autoantibodies against nucleic acids and their interacting proteins. The exact molecular mechanisms leading to the breakdown of self-tolerance remain to a large extent unknown, but it is well established that they are influenced by both non-genetic (i.e. environmental and hormonal) and genetic factors. SLE is a complex, polygenic disease. Several susceptibility variants have been identified in SLE. However, the functional role in disease pathogenesis for the majority of them remains largely unknown. This thesis includes case-control association studies where the role of the genes TNFSF4 (Paper I), STAT4 (Paper II), CD226 (Paper III), and BLK (Papers IV and V) in the susceptibility of developing SLE was investigated. The primary focus was on the identification of the functional variants underlying the association. For each of these genes, fine mapping was performed using single nucleotide polymorphisms (SNPs), the linkage disequilibrium (LD) was characterized, and the association was narrowed down to specific haplotypes by means of several different statistical genetic strategies. Candidate variants were prioritized for further functional analysis on the basis of their potential effect on the gene function, their association, and/or biological plausibility. In Paper I, the association of TNFSF4 with SLE was validated and attributed to a risk haplotype tagged by SNPs rs1234317-T and rs12039904-T. Paper II provides evidence supporting the presence of at least two independent genetic effects within the STAT4 gene represented by rs3821236-A and rs7574865-A, which correlated with increased levels of gene expression. In Paper III, a functional allele in CD226 (rs727088-C) was identified, which was responsible for decreased levels in both mRNA and protein expression. In Paper IV, two independent genetic effects in the BLK gene were demonstrated. The first one comprised multiple regulatory variants in high LD that were enriched for NFκB and IRF4 binding sites and correlated with low BLK mRNA levels. The second was a low-frequency missense substitution (Ala71Thr) that decreased the BLK protein half-life. In Paper V, a genetic epistatic interaction between BANK1 rs10516487 (GG) and BLK rs2736340 (TT+TC) was demonstrated. Additional molecular analyses established that these molecules interact physically.   These studies have contributed to the dissection of the genetic architecture of SLE. They highlight the allelic heterogeneity of the disease and provide functional links to the associated variants, which has significantly aided in the understanding of SLE disease pathogenesis.