Validation of RNA extraction procedures focused on micro RNA expression analysis.

The sampling procedure is a crucial step in every kind of experiment. This is also true in gene expression profiling experiments, where high quality and sufficient quantity of extracted RNA plays a significant role in the experimental outcome. We have compared five different RNA extraction protocols from peripheral blood/PBMCs with the aim to define the most suitable method for the miRNA expression profiling experiments. Convincing results in terms of highest quantity and quality were obtained by the TRIzol-chloroform extraction method. The total RNA obtained using this method contained the highest portion of good-quality miRNA molecules, which was also confirmed by gene-specific real-time PCR experiments.

Interaction of HLA-DRB1*03 and smoking for the development of anti-Jo-1 antibodies in adult idiopathic inflammatory myopathies: a European-wide case study.

OBJECTIVES: HLA-DRB1*03 is strongly associated with anti-Jo-1-positive idiopathic inflammatory myopathies (IIM) and there is now increasing evidence that Jo-1 antigen is preferentially expressed in lung tissue. This study examined whether smoking was associated with the development of anti-Jo-1 antibodies in HLA-DRB1*03-positive IIM. METHODS: IIM cases were selected with concurrent information regarding HLA-DRB1 status, smoking history and anti-Jo-1 antibody status. DNA was genotyped at DRB1 using a commercial sequence-specific oligonucleotide kit. Anti-Jo-1 antibody status was established using a line blot assay or immunoprecipitation. RESULTS: 557 Caucasian IIM patients were recruited from Hungary (181), UK (99), Sweden (94) and Czech Republic (183). Smoking frequency was increased in anti-Jo-1-positive IIM cases, and reached statistical significance in Hungarian IIM (45% Jo-1-positive vs 17% Jo-1-negative, OR 3.94, 95% CI 1.53 to 9.89, p<0.0001). A strong association between HLA-DRB1*03 and anti-Jo-1 status was observed across all four cohorts (DRB1*03 frequency: 74% Jo-1-positive vs 35% Jo-1-negative, OR 5.55, 95% CI 3.42 to 9.14, p<0.0001). The frequency of HLA-DRB1*03 was increased in smokers. The frequency of anti-Jo-1 was increased in DRB1*03-positive smokers vs DRB1*03-negative non-smokers (42% vs 8%, OR 7.75, 95% CI 4.21 to 14.28, p<0.0001) and DRB1*03-positive non-smokers (42% vs 31%, p=0.08). In DRB1*03-negative patients, anti-Jo-1 status between smokers and non-smokers was not significantly different. No significant interaction was noted between smoking and DRB1*03 status using anti-Jo-1 as the outcome measure. CONCLUSION: Smoking appears to be associated with an increased risk of possession of anti-Jo-1 in HLA-DRB1*03-positive IIM cases. The authors hypothesise that an interaction between HLA-DRB1*03 and smoking may prime the development of anti-Jo-1 antibodies.

HLA DRB1, DQB1 and insulin promoter VNTR polymorphisms: interactions and the association with adult-onset diabetes mellitus in Czech patients.

Both the human leucocyte antigen (HLA) DRB1 and the HLA DQB1 gene loci play a role in the development and progression of autoimmune diabetes mellitus (T1DM). Similarly, the insulin promoter variable number tandem repeats (INS-VNTR) polymorphism is also involved in the pathogenesis of diabetes mellitus (DM). We studied the association between each of these polymorphisms and DM diagnosed in patients older than age 35 years. Furthermore, we analysed possible interactions between HLA DRB1/DQB1 and INS-VNTR polymorphisms. Based on C-peptide and GADA levels we were able to distinguish three types of diabetes: T1DM, latent autoimmune diabetes in adults (LADA) and T2DM. INS-VNTR was genotyped indirectly by typing INS-23HphI A/T polymorphism. The genotype and allele frequencies of INS-23HphI did not differ between each of the diabetic groups and group of healthy subjects. We did, however, observe an association between the INS-23HphI alleles, genotypes and C-peptide secretion in all diabetic patients: A allele frequency was 86.2% in the C-peptide-negative group vs. 65.4% in the C-peptide-positive group (P(corr.) < 0.005); AA genotype was found to be 72.4% in the C-peptide-negative group vs. 42.6% in the C-peptide-positive groups (P(corr.) < 0.01). The HLA genotyping revealed a significantly higher frequency of HLA DRB1*03 allele in both T1DM and LADA groups when compared to healthy subjects: T1DM (25.7%) vs. control group (10.15%), odds ratio (OR) = 3.06, P < 0.05; LADA (27.6%) vs. control (10.15%), OR = 3.37, P < 0.01. The simultaneous presence of both HLA DRB1*04 and INS-23HphI AA genotype was detected in 37.5% of the T1DM group compared to only 9.2% of the healthy individuals group (OR = 5.9, P(corr.) < 0.007). We summarize that in the Central Bohemian population of the Czech Republic, the INS-23HphI A allele appears to be associated with a decrease in pancreatic beta cell secretory activity. HLA genotyping points to at least a partial difference in mechanism, which leads to T1DM and LADA development as well as a more diverse genetic predisposition in juvenile- and adult-onset diabetes. The simultaneous effect of HLA and INS-VNTR alleles/genotypes predispose individuals to an increased risk of diabetes development.

KCNJ11 E23K polymorphism and diabetes mellitus with adult onset in Czech patients.

In this work, we studied the association of the E23K polymorphism of the Kir6.2 ATP-sensitive potassium channels in 212 Czech patients with diabetes mellitus who were diagnosed after the age of 35. Patients were classified into T1DM, LADA and T2DM groups based on C-peptide and GADA levels. Carriers of the predisposing Kir6.2 E23K K allele showed no increased risk of either type of diabetes mellitus development. On the other hand, we found a correlation between E23K SNP of the KCNJ11 gene and C-peptide levels, which may be considered a measure of pancreatic beta-cell activity, although this correlation was not statistically significant. In conclusion, we failed to confirm the Kir6.2 E23K as a genetic marker for T1DM, LADA and T2DM in the Central Bohemian population of the Czech Republic.

Polymorphism of interleukin-18 promoter influences the onset of kidney graft function after transplantation.

It has been well recognized that the promoter polymorphisms of interleukin-18 (IL-18) influence the level of cytokine expression. In our previously published data, we showed constitutive IL-18 expression in the epithelium of renal distal tubules in patients after kidney transplantation and significantly elevated IL-18 expression during acute rejection. In this study, we evaluated the clinical significance of two functional promoter polymorphisms of the IL-18 gene at positions -607 A/C (rs1946518) and -137 C/G (rs187238) in patients after kidney transplantation and looked for associations with the onset of graft function and the incidence of rejection episodes. Promoter polymorphisms in 124 patients and 103 unrelated controls were evaluated by sequence-specific primer polymerase chain reaction and the allele, genotype and haplotype frequencies were statistically correlated. We found a statistically different distribution of the allele frequency of -607 A/C polymorphism between patients with immediate or delayed onset of kidney graft function. Data showed that the C allele, which contributes to higher IL-18 expression, is more frequent in patients with delayed onset of function (P = 0.03, odds ratio = 1.93; 95% confidence interval = 1.15-3.25). A/C single nucleotide polymorphisms of the IL-18 promoter at position -607 may influence the onset of early kidney allograft function.

Association of MHC class I chain related gene-A microsatellite polymorphism with the susceptibility to T1DM and LADA in Czech adult patients.

The results in this study suggest that microsatellite polymorphism within the transmembrane region of MIC-A gene is associated with genetic susceptibility to adult-onset of type 1 diabetes mellitus (T1DM), MIC-A5.1 allele, corrected P = 0.001, whereas it is not associated with latent autoimmune diabetes in adults (LADA) in Czech population. According to our findings, we can hypothesize that adult-onset T1DM and LADA may have partly different immunogenetic aetiopathogenesis.

The frequency of alleles of the Pro12Ala polymorphism in PPARgamma2 is different between healthy controls and patients with type 2 diabetes.

The aim of this initial case-control study was to determine the association between common Pro12Ala polymorphism in the PPARgamma2 gene and type 2 diabetes in the Czech Republic. Furthermore, the effect of this polymorphism on phenotypic characteristics and on levels of lipids (total cholesterol, HDL-cholesterol, LDL-cholesterol and triglycerides) was studied. One hundred thirty-three patients with type 2 diabetes and 97 control subjects were investigated. PCR and RFLP analysis were used for identification of individual genotypes. In the group of patients, three samples (2.26%) were identified as homozygous for the Ala/Ala genotype and 99 samples (74.44%) were homozygotes for the Pro/Pro genotype. Thirty-one samples (23.31%) were identified as Pro12Ala heterozygous. In the control group, six samples (6.19%) were homozygous for the Ala/Ala genotype and 61 samples (62.89%) were homozygotes for the Pro/Pro genotype. Thirty samples (30.93%) were identified as Pro12Ala heterozygous. The allele frequency for the Ala allele was lower in the type 2 diabetic group than in the control group (13.91% vs. 21.43%, P = 0.022). There was no difference (at P < 0.05) between the phenotypic characteristics (BMI, sex) studied in the group of patients according to the Pro12Ala genotype. There was no significant effect of the Pro12Ala polymorphism on lipid levels.

[Genetic risk factors in autoimmune diabetes mellitus, their significance and function]. / Genetické rizikové faktory autoimunitného diabetes mellitus, ich význam a funkcia.

Autoimmune diabetes mellitus is characterized by selective destruction of beta pancreatic cells and by cellular infiltration with T- (particularly Th1) and B-lymphocytes. The marker of autoimmunity is the presence of autoantibodies (ICA, IAA, GADab, IA2ab). Etiology of the autoimmune process is still unknown. It is suggested that the pathogenesis is activated by genetic and environmental factors. Individual predisposition can influence also the onset and progression of the disease. The most important genetic risk factors of autoimmune diabetes mellitus are the HLA class II alleles (DQB1*0302, 0201; DRB1*0301, 0401; DQA1*0301, 0501) and the risk alleles of INS-VNTR of the promoter region. Recent studies have shown various genetic risk factors for the autoimmune diabetes mellitus. Individual predispositions belong to the genetic polymorphisms in cytokine genes (IL-10, IL-12, IL-18) and the microsatellite polymorphism of MHC class I chain-related gene A (MIC-A).

Fluorescence-based automated fragment analysis of microsatellite polymorphism within the transmembrane region of the MIC-A gene.

MHC class I chain-related genes (MIC) are located within the MHC class I region of chromosome 6. Sequence analysis of the MIC-A gene showed a trinucleotide repeat (GCT) microsatellite polymorphism within the transmembrane region. So far, six alleles of the exon 5 of the MIC-A gene, which consist of 4, 5, 6, 9 and 10 repetitions of GCT, or five repetitions of GCT with an additional nucleotide insertion (GGCT), have been identified. Recent works support the findings that MIC-A is associated with several autoimmune diseases. In our work we present a modification of a method used for microsatellite polymorphism detection within the transmembrane region of the MIC-A gene. It is the ALFexpress fluorescence-based automated fragment analysis. We also present the frequencies of MIC-A exon 5 alleles found in the Czech population. We have identified five alleles of the transmembrane region of MIC-A, which comprise 4, 5, 6 and 9 repetitions or five repetitions with an additional nucleotide insertion. The most frequent allele was A5.1 (59.3%) and the less frequent was the allele A5 (20.0%). No A7, A8 or A10 alleles were identified.

Enhancement of rat islet tolerance with bone marrow transplantation using a non-myeloablative procedure II: failure despite the presence of lymphocyte microchimerism in the fully allogeneic Lewis/Brown-Norway model.

Transplantation of donor bone marrow cells (BMTx) has been proven to be capable of including allogeneic transplant tolerance. In our previous experiments we reported the positive effect of BMTx together with short-term tacrolimus/hydrocortisone therapy on pancreatic islet survival in recipients haploidentical with donors. In this project we used the same transplant protocol to further investigate this effect in a fully mean histocompatibility system-mismatched model. Lewis male rats and Brown-Norway female rats were used as donors and recipients, respectively. Diabetic animals were treated according to four different protocols. Recipients in group I (n = 12) underwent islet transplantation (ITx) only. Group II (n = 12) and group III (n = 11) included animals treated for 52 days with tacrolimus (0.5 mg/kg) and hydrocortisone (2 mg/kg). Diabetes was induced by intravenously applied streptozocin (50 mg/kg). Seven days later islets were injected intrahepatically through the portal vein. In addition, rats in group III underwent BMTx on day 10. In group IV (n = 6) tacrolimus therapy, ITx and BMTx were used according to the previously published protocol of Ricordi et al. After more than 120 days, cumulative survival rates were 56% and 64% for recipients in groups II and III, respectively (p > 0.05). All animals in group I became hyperglycemic by day 11 following transplantation. Despite positive detection of lymphocyte microchimerism, we did not observe improved survival of allogeneic islets in animals treated with BMTx. Surprisingly, better islet survival was not found in group IV either (survival rate at 100 days: 33%). We conclude that demonstration of lymphocyte microchimerism, as detected by a sensitive polymerase chain reaction method, did not improve allogeneic islet survival in vivo and was not able to block mixed lymphocyte reaction in vitro. Whether a larger amount of transplanted hematopoietic cells could induce tolerance in this model remains to be evaluated.

HLA in Czech adult patients with autoimmune diabetes mellitus: comparison with Czech children with type 1 diabetes and patients with type 2 diabetes.

Type 1 diabetes results from an autoimmune insulitis, associated with HLA class II alleles. The evidence about HLA allele association is not clear in patients diagnosed after 35 years of age. In this study we have analyzed HLA alleles of DQB1 and DRB1 genes by sequence specific primer (SSP)-PCR technique in adult patients with disease onset after 35 years of age. Two hundred and eighty-one patients were divided into three groups according to the insulin therapy, the level of C peptide (CP), and GAD antibodies (anti-GAD). Group 1 (type 1 diabetes in adults) was characterized by CP less than 200 pmol/L and anti-GAD more or less than 50 ng/mL (n = 80). All of them had insulin therapy within 6 months after diagnosis. Group 2 latent autoimmune diabetes mellitus in adults (LADA) was defined by a minimum 6-month-long phase after diagnosis without insulin therapy, and was characterized by CP more than 200 pmol/L and anti-GAD more than 50 ng/mL (n = 70). Group 3 (type 2 diabetes) was characterized by CP more than 200 pmol/L and anti-GAD less than 50 ng/mL (n = 131). None ever had insulin therapy. In group 1, there was increased frequency of DRB1*04 (45.0% vs. controls 14.1%, OR = 5.0, P < 0.0005) and DQB1*0302 alleles (43.3% vs. controls 11.1%, OR = 6.1, P < 0.00005). There was increased frequency of DRB1*03 and DQB1*0201, and decreased frequency of DQB1*0602 (3.3% vs. controls 20.2%), but it was not significant. In group 2, there was a significantly increased frequency of DRB1*03 only (50.0% vs. controls 21.2%, OR = 3.7, P < 0.05). Compared with children with type 1 diabetes and adults with type 2 diabetes (group 3), we conclude that the presence of predisposing DQB1 alleles in adults with type 1 diabetes decreases with the age, probably due to environmental factors. Only the DRB1*03, but not the DQB1 gene, becomes the main predisposing allele in LADA patients. These findings suggest that the presence of HLA-DQB1*0302 identifies patients at high risk of requiring insulin treatment. Type 1 diabetes mellitus (DM) in children or adults may have partly different immunogenetic etiopathogenesis than LADA.

[Methods for identification of HLA antigen polymorphisms]. / Metódy na identifikáciu polymorfizmu HLA antigénov.

The HLA complex is the most polymorphic genetic system in man yet known. The variability of the HLA antigens is given by the presence of many alleles of the HLA genes. Requirements for compatibility of HLA antigens in organ and bone marrow transplantations, and also in the determination of genetic risk factors in autoimmune diseases evoke strong pressure on progress in HLA typing methods, mainly for increasing their sensitivity and resolution. For typing of the HLA antigens there are used cellular, serological, biochemical and DNA methods. For HLA class I typing there following tests are used: cytotoxic test (serological), CML (cellular), 1D--IEF (biochemical), RFLP, SSO, SSP--PCR, and SBT (DNA methods). For HLA class II typing, cytotoxic test (cellular), MLC (serological), RFLP, SSO, SSP--PCR, and SBT (DNA methods) are used. DNA methods represent the modern trend in the area of HLA typing and it will probably replace larger part of other HLA typing techniques. In our article, we describe the principles of methods that are used for HLA typing.