Investigating Associations between HLA-DR Genotype, H. pylori Infection, and Anti-CagA IgA Seropositivity in a Turkish Gastritis Cohort.

Helicobacter pylori (H. pylori) is associated with gastric inflammation and mucosal antibodies against its cytotoxin-associated gene A (CagA) are protective. Vaccine-elicited immunity against H. pylori requires MHC class II expression, indicating that CD4+ T cells are protective. We hypothesized that the HLA-DR genotypes in human populations include protective alleles that more effectively bind immunogenic CagA peptide fragments and susceptible alleles with an impaired capacity to present CagA peptides. We recruited patients (n = 170) admitted for gastroendoscopy procedures and performed high-resolution HLA-DRB1 typing. Serum anti-CagA IgA levels were analyzed by ELISA (23.2% positive) and H. pylori classified as positive or negative in gastric mucosal tissue slides (72.9% positive). Pearson Chi-square analysis revealed that H. pylori infection was significantly increased in DRB1*11:04-positive individuals (p = 0.027). Anti-CagA IgA was significantly decreased in DRB1*11:04 positive individuals (p = 0.041). In contrast, anti-CagA IgA was significantly increased in DRB1*03:01 positive individuals (p = 0.030). For these HLA-DRB1 alleles of interest, we utilized two in silico prediction methods to compare their capacity to present CagA peptides. Both methods predicted increased numbers of peptides for DRB1*03:01 than DRB1*11:04. In addition, both alleles preferred distinctively different CagA 15mer peptide sequences for high affinity binding. These observations suggest that DRB1*11:04 is a susceptible genotype with impaired CagA immunity, whereas DRB1*03:01 is a protective genotype that promotes enhanced CagA immunity.

Investigating associations between HLA DQA1 ~ DQB1 haplotypes, H. pylori infection, metaplasia, and anti-CagA IgA seropositivity in a Turkish gastritis cohort.

Helicobacter pylori was reported as an important cause of gastritis, and gastric ulcers and CagA oncoprotein-producing H. pylori subgroups were blamed to increase the severity of gastritis. Disparities were reported in that the presence of serum anti-CagA IgA was not parallel with CagA-positive H. pylori cohabitation. We hypothesized that the HLA-DQA1 ~ DQB1 haplotypes in human populations include protective haplotypes that more effectively present immunogenic CagA peptides and susceptible haplotypes with an impaired capacity to present CagA peptides. We recruited patients (n = 201) admitted for gastroendoscopy procedures and performed high-resolution HLA-DQA1 and DQB1 typing. Serum anti-CagA IgA levels were analyzed by ELISA (23.0% positive), and H. pylori was classified as positive or negative in gastric mucosal tissue slides (72.6% positive). The HLA DQA1*05:05 allele (29.1%) and HLA DQB1*03:01 allele (32.8%) were found at the highest frequency among gastritis patients of Turkish descent. In HLA DQA1*05:05 ~ DQB1*03:01 double homozygous (7.3%) and heterozygous (40.7%) haplotype carriers, the presence of anti-CagA IgA decreased dramatically, the presence of H. pylori increased, and the presence of metaplasia followed a decreasing trend. The DQ protein encoded by HLA DQA1*05:05-DQ*03:01 showed a low binding affinity to the CagA peptide when binding capacity was analyzed by the NetMHCIIPan 4.0 prediction method. In conclusion, HLA DQA1 ~ DQB1 polymorphisms are crucial as host defense mechanisms against CagA H. pylori since antigen binding capacity plays a crucial role in anti-CagA IgA production.

Modifying inter-cistronic sequence significantly enhances IRES dependent second gene expression in bicistronic vector: Construction of optimised cassette for gene therapy of familial hypercholesterolemia.

Internal ribosome entry site (IRES) sequences have become a valuable tool in the construction of gene transfer and therapeutic vectors for multi-cistronic gene expression from a single mRNA transcript. The optimal conditions for effective use of this sequence to construct a functional expression vector are not precisely defined but it is generally assumed that the internal ribosome entry site dependent expression of the second gene in such as cassette is less efficient than the cap-dependent expression of the first gene. Mainly tailoring inter-cistronic sequence significantly enhances IRES dependent second gene expression in bicistronic vector further in construction of optimised cassette for gene therapy of familial hypercholesterolemia. We tailored the size of the inter-cistronic spacer sequence at the 5' region of the internal ribosome entry site sequence using sequential deletions and demonstrated that the expression of the 3' gene can be significantly increased to similar levels as the cap-dependent expression of the 5' gene. Maximum expression efficiency of the downstream gene was obtained when the spacer is composed of 18-141 base pairs. In this case a single mRNA transcriptional unit containing both the first and the second Cistron was detected. Whilst constructs with spacer sequences of 216 bp or longer generate a single transcriptional unit containing only the first Cistron. This suggests that long spacers may affect transcription termination. When the spacer is 188 bp, both transcripts were produced simultaneously in most transfected cells, while a fraction of them expressed only the first but not the second gene. Expression analyses of vectors containing optimised cassettes clearly confirm that efficiency of gene transfer and biological activity of the expressed transgenic proteins in the transduced cells can be achieved. Furthermore, Computational analysis was carried out by molecular dynamics (MD) simulation to determine the most emerges as viable containing specific binding site and bridging of 5' and 3' ends involving direct RNA-RNA contacts and RNA-protein interactions. These results provide a mechanistic basis for translation stimulation and RNA resembling for the synergistic stimulation of cap-dependent translation.

Comparison of absorbed irrigation fluid volumes during retrograde intrarenal surgery and percutaneous nephrolithotomy for the treatment of kidney stones larger than 2 cm.

PURPOSE: Irrigation-induced increase in intrarenal pressure is of concern because it may cause infection due to increased pyelovenous and pyelolymphatic absorption. This study is the first to compare prospectively the absorbed fluid volumes during percutaneous nephrolithotomy (PCNL) and retrograde intrarenal surgery (RIRS) for stones larger than 2 cm. MATERIALS AND METHODS: General anesthesia was applied to all patients. Isotonic solution containing 1 % ethanol was used as irrigation fluid. Venous blood ethanol concentration was first measured with the start of irrigation and thereafter every 15 min until the patients left the recovery room. Absorbed fluid volumes were measured using the blood ethanol concentrations. Duration of irrigation, irrigated fluid volume, stone size and grade of hydronephrosis were also recorded. RESULTS: A total of 60 patients were included the study. Fluid absorption occurred in all patients. Minimum and maximum ranges of fluid absorption were 20-573 mL for RIRS and 13-364 mL for PCNL. The increase in fluid absorbed volume was observed as a result of the given amount of irrigating fluid used in the PCNL group. Also prolongation of operation led to a significant increase in absorption in the PCNL group. Increase in body mass index, stone size, and hydronephrosis did not affect fluid absorption significantly in either of the two operation techniques in correlation analyzes. CONCLUSION: Both RIRS and PCNL are conducted under high pressure and can be accompanied potential complications such as SIRS. The fluid absorption confirmed in our study should be taken into consideration during RIRS and PCNL.

Importance of Delphian Lymph Node Evaluation in Autoimmune Thyroiditis: Fact or Fiction?

BACKGROUND: Our main objective was to evaluate the association between autoimmune thyroiditis and the Delphian lymph node during different stages of thyroiditis. MATERIAL/METHODS: The relationships between the ultrasonography (US) results of thyroiditis and characteristics of the Delphian lymph node in different stages of AT were evaluated. Thyroid hormone and antibody levels were assessed. A total of 126 patients were divided into four groups according to the thyroid US findings: Group 1: control cases; Group 2: indeterminate cases; Group 3: established thyroiditis cases; Group 4: advanced-late stage thyroiditis cases. Indeterminate cases attended a 1-year follow-up, and the cases with a sonographic finding matching thyroiditis formed Group 2. RESULTS: The rate of Delphian lymph node presence in Group 4 was significantly higher than in Groups 1 and 2 (p<0.01). In addition, its presence was significantly higher in Group 3 than in Group 1 (p<0.05). Although there was a difference in Delphian lymph node presence between Groups 2 and 3, it was not significant (p=0.052), nor was there a significant difference between Groups 1 and 2 (p>0.05). Both the long and short axis measurements were significantly higher in Groups 2, 3, and 4 compared to those in the control group. However, the same increase was not observed in the long/short axis ratio. CONCLUSIONS: Both the presence and dimensions of the Delphian lymph node were highly correlated with the progress of autoimmune thyroiditis. Evaluating the Delphian lymph nodes might prevent missing a diagnosis of autoimmune thyroiditis.

Importance of sonographic paratracheal lymph node evaluationin early autoimmune thyroiditis.

BACKGROUND/AIM: To review the sonographic views of paratracheal lymph nodes (PLNs) in the diagnosis and during different stages of autoimmune thyroiditis. MATERIALS AND METHODS: Features of the PLNs (left and right), thyroid sonography, and laboratory data were investigated in 126 cases. Patients were divided into three groups by using thyroid sonographic criteria in the literature (group 1: control, group 2: early-stage/indeterminate, group 3: definite thyroiditis). Indeterminate patients were followed up for 1 year and included as indeterminate/early-stage thyroiditis patients. RESULTS: Percentage of right and left PLN was 13.3% and 46.2% in control cases, 21.2% and 80% in early-stage/indeterminate cases, and 41.3% and 88.5% in definite thyroiditis cases. Significant among-group differences were evident in terms of right and left PLNs presence (Pearson chi-squared test, P = 0.011 and P = 0.001). CONCLUSION: Careful and thorough review of the PLNs can ensure diagnosis of autoimmune thyroiditis even in cases of early stage of the disease and prevent false-negative diagnoses.

The involvement of IL-10, IL-6, IFN-gamma, TNF-alpha and TGF-beta gene polymorphisms among Turkish lung cancer patients.

Several genes encoding different cytokines may play crucial roles in host susceptibility to lung cancer, since cytokine production capacity varies among individuals and depends on cytokine gene polymorphisms. The association between cytokine gene polymorphisms with primary lung carcinoma was investigated. DNA samples were obtained from a Turkish population of 44 patients with primary lung cancer, and 59 healthy control subjects. All genotyping (IFN-gamma, TGF-beta1, TNF-alpha, IL-6 and IL-10) experiments were performed using sequence-specific primers (SSP)-PCR. When compared to the healthy controls, the frequencies of high/intermediate producing genotypes of IL-10 and low producing genotype of TNF-alpha were significantly more common in the patient group. It is noteworthy that lung cancer patients with the TGF-beta T/T genotype in codon 10 had statistically longer survival compared to those having the C/C genotype (Kaplan-Meier survival function test, log rank significance = 0.014). These results suggest that IL-10, TNF-alpha and TGF-beta1 gene polymorphisms may affect host susceptibility to lung cancer and the outcome of the patients.

Higher serum nitrate levels are associated with poor survival in lung cancer patients.

OBJECTIVES: Angiogenic factors induce tumour growth and angiogenesis which leads to tumour metastasis and a poor survival rate. This study aimed to assess the possible roles of nitric oxide (NO) and vascular endothelial growth factor-A (VEGF-A) in the overall survival of patients with late stage lung cancer. DESIGN AND METHODS: The study was carried out with primary lung carcinoma patients (n=31) and healthy controls (n=15). Pre- and post-cisplatin-based chemotherapy serum nitrite/nitrate levels were measured as nitrite after enzymatic conversion followed by Griess reaction and serum VEGF-A analysis was performed using ELISA. After patient follow-up, survival rates were calculated by using the Kaplan-Meier method [Dudek et al. Cancer Invest 2005; 23(3):193-200]. RESULTS: The serum nitrite/nitrate and VEGF-A levels of lung cancer patients and the control group were 93.7+/-48.9 and 63.7+/-32.2 microM (p=0.018), and 620+/-491 and 255+/-157 pg/mL (p=0.001), respectively. High nitrite/nitrate (>67.2 microM) concentration had statistically significant effects on overall survival (Cox analysis, p=0.026). The overall survival of the lung cancer patients with higher serum nitrate concentrations was significantly less than the ones with lower serum nitrite/nitrate (Kaplan-Meier survival functions test, log rank significance=0.0007). CONCLUSION: Our results suggest that having a high serum nitrite/nitrate concentration is a strong indicator of poor survival for late stage lung cancer patients. However, this conclusion deserves to be elucidated further by using a larger sample size.

Chronic black tea administration protects plasma proteins, plasma, liver and kidney lipids against oxidation.

BACKGROUND: Black tea is known to have protective effects against plasma lipid and lipoprotein oxidation, but its influence on lipid peroxidation in tissue has been less studied. The effect of oral black tea consumption on protein oxidation has also not been demonstrated. The present study investigated the antioxidant effects of oral black tea consumption. MATERIAL/METHODS: Male Sprague-Dawley rats were fed a regular murine chow diet. The controls were supplied with water ad libitum, while the black tea group received aqueous black tea extract as the sole source of liquids. At the end of the ten-week experimental period, intestinal brush border, liver and kidney reduced-glutathione concentrations were evaluated as an index of cellular antioxidant defence. Plasma and tissue malondialdehyde concentrations and plasma protein carbonyl content were measured to evaluate lipid peroxidation and protein oxidation, respectively. RESULTS: The plasma malondialdehyde and protein carbonyl contents of rats consuming the black tea were significantly less than in controls. Similarly, liver and kidney malondialdehyde concentrations were significantly lower in the experimental group, while jejunoileal mucosa were not affected. Ten weeks of black tea administration caused significantly higher reduced-glutathione levels in the kidneys of black tea-administered rats, and a significant negative correlation was observed between kidney malondialdehyde and glutathione concentrations. CONCLUSIONS: These findings provide evidence that long term black tea supplementation is capable of protecting both plasma proteins and plasma lipids from oxidative injury, and demonstrate that chronic black tea administration protects both liver and kidney tissues - but not the jejunoileal mucosa - against oxidation.

Interference by anti-cancer chemotherapeutic agents in the MTT-tumor chemosensitivity assay.

BACKGROUND: One of the major goals of oncology is to predict the response of patients with cancer to chemotherapeutic agents by employing laboratory methods variously called 'tumor chemosensitivity assays', 'drug response assays', or 'drug sensitivity assays', in vitro. The MTT assay is one of the methods used to predict the drug response in malignancies. However, it may suffer from interference by the anticancer drugs with the MTT assay. METHODS: The MTT assay, a colorimetric viability assay, was checked in a cell-free system in terms of its possible chemical interactions with 22 different anticancer drugs. RESULTS: It was found that epirubicine, paclitaxel, doxetaxel, and cisplatin caused a relatively significant increase in absorbance values, resulting in the MTT assay giving rise to false results (untrue increase in viability) although most of the drugs tested did not seem to cause any significant change. CONCLUSIONS: It was concluded that before employing the MTT assay, drugs (or any kind of substances) to be included in the assay should be checked first in terms of possible chemical interactions with MTT, otherwise it may be impossible to evaluate the MTT viability assay results correctly.