Autoimmunity-related LINC01934 and AP002954.4 lncRNA polymorphisms may be effective in pediatric celiac disease: a case-control study.

OBJECTIVE: Various studies have reported that certain long non-coding RNA levels are unusually low in the intestines of celiac disease patients, suggesting that this may be associated with the inflammation observed in celiac disease. Despite these studies, the research aimed at uncovering the potential role of long non-coding RNAs in the pathogenesis of autoimmune diseases like celiac disease remains insufficient. Therefore, in this study, we plan to assess long non-coding RNA polymorphisms associated with autoimmunity in children diagnosed with celiac disease according to the European Society for Paediatric Gastroenterology Hepatology and Nutrition criteria. METHODS: DNA was isolated from paraffin tissue samples of 88 pediatric celiac disease patients and 74 healthy pediatric individuals. Single-nucleotide polymorphism genotyping of five long non-coding RNA polymorphisms associated with autoimmunity (LINC01934-rs1018326, IL18RAP-rs917997, AP002954.4-rs10892258, UQCRC2P1-rs6441961, and HCG14 rs3135316) was conducted using the TaqMan single-nucleotide polymorphism genotyping assays with the LightCycler 480. RESULTS: In our study, the genotypic and allelic frequency distribution of LINC01934-rs1018326 and AP002954.4-rs10892258 polymorphisms was found to be statistically significant in the comparison between the two groups (p<0.05). According to the multiple genetic model analyses, the LINC01934-rs1018326 polymorphism was observed to confer a 1.14-fold risk in the recessive model and a 1.2-fold risk in the additive model for pediatric celiac disease. Similarly, the AP002954.4-rs10892258 polymorphism was found to pose a 1.40-fold risk in the dominant model and a 1.7-fold risk in the additive model. CONCLUSION: Our study results draw attention to the LINC01934-rs1018326 and AP002954.4-rs10892258 polymorphisms in celiac disease and suggest that these polymorphisms may be associated with inflammation in autoimmune diseases like celiac disease.

Variation Analysis in Premenopausal and Postmenopausal Breast Cancer Cases.

Menopausal status affects the prognoses and consequences of breast cancer. Therefore, this retrospective study aimed to reveal the molecular variation profile differences in breast cancer patients according to their menopausal status, with the hypothesis that the molecular variation profiles will be different at premenopausal and postmenopausal ages. Breast cancer patients (n = 254) who underwent molecular subtyping and QIAseq Human Breast Cancer NGS Panel screening between 2018 and 2022 were evaluated retrospectively. Their menopausal status was defined by age, and those aged 50 years and above were considered postmenopausal. Of the subjects, 58.66% (n = 149) were premenopausal and 41.34% (n = 105) were postmenopausal. The mean age at the time of diagnosis for all patients was 49.31 ± 11.19 years, with respective values of 42.11 ± 5.51 and 59.54 ± 9.01 years for the premenopausal and postmenopausal groups, respectively (p = 0.000). Among premenopausal patients, the percentages of patients in BCa subtypes (luminal A, luminal B-HER2(-), luminal B-HER2(+), HER2 positive, and triple-negative) were determined to be 34.90%, 8.05%, 26.17%, 10.74%, and 20.13%, respectively, while in the postmenopausal group, these values were 39.05%, 16.19%, 24.76%, 6.67%, and 13.33%, respectively (p > 0.05). Considering menopausal status, the distribution of hormone receptors in premenopausal patients was ER(+)/PgR(+) 63.76%, ER(-)/PgR(-) 23.49%, ER(+)/PgR(-) 10.74%, and ER(-)/PgR(+) 2.01%, respectively, while in postmenopausal women, this distribution was observed to be 74.29%, 23.81%, 1.90% and 0.00% in the same order (p = 0.008). The most frequently mutated gene was TP53 in 130 patients (51.18%), followed by PIK3CA in 85 patients (33.46%), BRCA2 and NF1 in 56 patients (22.05%), PTEN in 54 patients (21.26%), and ATR and CHEK2 in 53 patients (20.87%). TP53, PIK3CA, NF1, BRCA2, PTEN, and CHEK2 mutations were more frequently observed in premenopausal patients, while TP53, PIK3CA, BRCA2, BRCA1, and ATR mutations in postmenopausal patients. These findings contribute to a deeper understanding of the underlying causes of breast cancer with respect to menopausal status. This study is the first from Turkey that reflects the molecular subtyping and somatic mutation profiles of breast cancer patients according to menopausal status.

An effective treatment approach of liposomally encapsulated metformin in colon cancer.

Metformin is a drug that is widely used in the treatment of type-2 diabetes and its anticarcinogenic effect has been detected in many studies since the 2000s. Metformin has a short half-life and poor biocompatibility, which limits the activity of the drug. As a solution to this situation, our study aimed to increase the anticarcinogenic effects and reduce the side effects of metformin in colon cancer by liposomal encapsulation. For this purpose, in our study, liposome production was carried out using the thin film hydration method. The amount of metformin loaded in liposomes was determined by a standard absorbance curve at 237 nm. Size distributions and membrane zeta potentials of the liposomes were evaluated with Malvern Zetasizer ZS90. Transmission electron microscopy was performed by staining the liposomes negatively with uranyl acetate. Cultured HT-29 cells were treated with liposomal metformin or free metformin at concentrations of 0, 10, 20, and 40 mM for 24 and 48 h. At the end of the treatment period, cell viability was evaluated by CellTiter-Glo luminescent cell viability test. The anticarcinogenic effects of liposomal and free metformin on HT-29 cells were compared. As a result, liposome encapsulated metformin treatment for 24 h was more effective on HT-29 cells at 20- and 40-mM concentrations causing significantly greater decrease in the IC-50 dose compared to the free metformin. The result suggests that liposomal encapsulated metformin may offer a promising approach to increase the efficacy of the drug in the treatment of colon cancer.

Evaluation of New Generation Sequencing (NGS)-Based Somatic Gene Variations and Real-Time Polymerase Chain Reaction (PCR)-Based Gene Fusions in Elderly and Young Acute Leukemia Patients: A Retrospective View.

Malignant diseases occurring in elderly patients follow a different course from younger patients and show different genetic structures. Therefore, in this retrospective study, the somatic gene variant profile and fusion gene profiles of elderly and young acute leukemia patients were determined to draw attention to the existing genetic difference, and the results were compared. In this study, the records of 204 acute leukemia patients aged 18+ who were referred to the Molecular Pathology Laboratory from the Hematology Clinic between 2018 and 2022 were reviewed retrospectively. Fusion gene detection in patients was performed with the HemaVision®-28Q Panel. The NGS Myeloid Neoplasms Panel was conducted using the MiniSEQ NGS platform according to the manufacturer's protocol. When all cases are evaluated together, the most frequently diagnosed acute leukemia is acute myeloid leukemia (85.8%). Both groups had a similar fusion gene profile; however, the fusion burden was higher in the elderly group. When the groups were evaluated in terms of somatic gene variations, there were differences between the groups, and the variation load was higher in the elderly group. Considering the different somatic gene variation profiles, it is understood that the genetic structure of tumor cells is different in elderly patients compared to young cases.

Link Between Obsessive-Compulsive Disorder and ApoE Gene Polymorphisms.

Objective: Many researchers have considered obsessive compulsive disorder (OCD) to be a neurodegenerative disease just like Alzheimer's disease (AD). The most studied gene in neurodegenerative diseases is apolipoprotein E (ApoE) gene, and ApoE ɛ4 allele in particular. Although a small number of studies have explored the relationship between ApoE gene polymorphisms and OCD, the link between age at onset of OCD, its subtypes and ApoE gene polymorphisms has not been revealed so far. For this purpose, in our study, the relationship of ApoE gene polymorphisms with age at onset of OCD and its subtypes has been investigated to reveal their neurodegenerative connections. Patients and Methods: ApoE gene polymorphisms of 64 OCD and 28 healthy cases were studied using a LightCycler480 real-time PCR platform. Results: A statistically significant difference was found between groups of patients with early- and late-onset OCD in terms of age (p = 0.03), educational level (p = 0.00) and marital status (p = 0.002). ApoE ɛ4ɛ4 genotype, the prevalence of which is below 2% in healthy individuals, was not detected in our control groups; however, it was identified in 5.1% of our OCD cases. Correlation analysis revealed the presence of a potentially significant link between the hoarding obsession and presence of the ɛ4ɛ4 genotype. A significant correlation was detected between the presence of the ɛ3ɛ3 allele, the symmetry obsession and associated ordering compulsion in patients with OCD (p<0.005). Conclusion: The ApoE gene polymorphism profile and age of onset in OCD patients may play critical roles in the development process of neurodegenerative characteristics of the disease. The small number of cases and the inability to perform brain imaging in patients to detect the neurodegenerative link in OCD are limitations of our study. In this respect, we suggest conduction of further studies with a greater number of patients who will also undergo brain imaging studies. In addition, OCD patients have other genes associated with neurodegenerative diseases that can be screened.

Association between chronic tinnitus and brain-derived neurotrophic factor antisense RNA polymorphisms linked to the Val66Met polymorphism in BDNF.

Tinnitus is the sound heard in the ear or head of a person in the absence of external stimuli. Its etiopathogenesis is still not fully understood and the etiological causes responsible for tinnitus are quite variable. Brain-derived neurotrophic factor (BDNF) is one of the key neurotrophic factors in the growth, differentiation, and survival of neurons and in the developing auditory pathway, including the inner ear sensory epithelium. The regulation of BDNF gene is known to be managed by BDNF antisense (BDNF-AS) gene. BDNF-AS is located downstream of the BDNF gene and transcribes a long non-coding RNA. Inhibition of BDNF-AS upregulates BDNF mRNA, which increases protein levels and stimulates neuronal development and differentiation. Thus, BDNF and BDNF-AS both may play roles in the auditory pathway. Polymorphisms in both genes may have impact on hearing performance. A link was suggested between tinnitus and BDNF Val66Met polymorphism. However, there is no study questioning the relationship of tinnitus with BDNF-AS polymorphisms linked with BDNF Val66Met polymorphism. Therefore, this study aimed to scrutinize the role of BDNF-AS polymorphisms showing linkage with the BDNF Val66Met polymorphism in the course of tinnitus pathophysiology. Six BDNF-AS polymorphisms were analyzed on the tinnitus patients (n = 85) and the control subjects (n = 60) by Fluidigm Real-Time PCR using the Fluidigm Biomark microfluidic platform. When BDNF-AS polymorphisms were compared between the groups in terms of genotype and gender distribution, statistically significant differences were detected in rs925946, rs1519480, and rs10767658, polymorphisms (p less than 0.05). When the polymorphisms were compared by the duration of tinnitus, significant differences were found in rs925946, rs1488830, rs1519480, and rs10767658 polymorphisms (p less than 0.05). According to genetic inheritance model analysis, 2.33 and 1.53-fold risks were found for the rs10767658 polymorphism in the recessive and the additive models, respectively. For the rs1519480 polymorphism, a 2.25 fold risk was observed in the additive model. For the rs925946 polymorphism, 2.44 fold protective effect in dominant model, and 0.62 fold risk was found in the additive model. In conclusion, four of the polymorphisms in BDNF-AS gene (rs955946, rs1488830, rs1519480, and rs10767658) are potential gene loci that may play a role in the auditory pathway and affect auditory performance.

Relationship between villous atrophy and Wnt pathway gene expressions in pediatric celiac patients.

OBJECTIVE: Celiac disease is an autoimmune disease characterized by an abnormal immune response occurring in the small intestine linked to consumption of food containing gluten in individuals with a genetic predisposition. Dysregulation of Wnt signal transduction plays a role in the pathogenesis of many diseases including autoimmune diseases like celiac disease. In this study, the correlation of Wnt pathway gene expressions with each other and the correlation with clinical data were researched in pediatric celiac disease cases grouped according to the Marsh classification. METHODS: Gene expression levels of FZD8, DVL2, LRP5, RHOA, CCND2, CXADR, and NFATC1, which are involved in the Wnt pathway, were determined using quantitative real-time polymerase chain reaction in 40 celiac disease and 30 healthy individuals. RESULTS: All cases with the short height symptom were observed to be in Marsh 3b\3c groups (p=0.03). The gene expressions of DVL2, CCND2, and NFATC1 were high in the Marsh 3b group, and these genes showed positive correlation with each other (p=0.002). LRP5 and CXADR gene expressions were lower in the Marsh 3b group compared to other Marsh groups, and these genes showed a positive correlation with each other (p=0.003). CCND2 gene expression was associated with Marsh 3b group, diarrhea, and vomiting symptoms. DVL2 gene expression was correlated with Marsh 2 group and constipation symptom (p<0.05). CONCLUSION: Wnt signaling in the early stages of the disease of Marsh 1-2 involves high expression of LRP5 and CXADR genes, while expression of these two genes reduces, and DVL2, CCND2, and NFATC1 gene expressions clearly increase with a transduction variation observed from Marsh 3a stage when villous atrophy begins to form. It appears that the Wnt pathway may contribute to disease progression through expression changes.

Serotonin, ghrelin, and motilin gene/receptor/transporter polymorphisms in childhood functional constipation.

OBJECTIVE: Functional constipation is the most common form of constipation, and its exact aetiology is still unclear. However, it is known that deficiencies in hormonal factors cause constipation by changing physiological mechanisms. Motilin, ghrelin, serotonin acetylcholine, nitric oxide, and vasoactive intestinal polypeptide are factors that play a role in colon motility. There are a limited number of studies in the literature where hormone levels and gene polymorphisms of serotonin and motilin are examined. Our study aimed to investigate the role of motilin, ghrelin, and serotonin gene/receptor/transporter polymorphisms in constipation pathogenesis in patients diagnosed with functional constipation according to the Rome 4 criteria. METHODS: Sociodemographic data, symptom duration, accompanying findings, the presence of constipation in the family, Rome 4 criteria, and clinical findings according to Bristol scale of 200 cases (100 constipated patients and 100 healthy control) who applied to Istanbul Haseki Training and Research Hospital, Pediatric Gastroenterology Outpatient Clinic, between March and September 2019 (6-month period) were recorded. Polymorphisms of motilin-MLN (rs2281820), serotonin receptor-HTR3A (rs1062613), serotonin transporter-5-HTT (rs1042173), ghrelin-GHRL (rs27647), and ghrelin receptor-GHSR (rs572169) were detected by real-time PCR. RESULTS: There was no difference between the two groups in terms of sociodemographic characteristics. Notably, 40% of the constipated group had a family history of constipation. The number of patients who started to have constipation under 24 months was 78, and the number of patients who started to have constipation after 24 months was 22. There was no significant difference between constipation and control groups in terms of genotype and allele frequencies in MLN, HTR3A, 5-HTT, GHRL, and GHSR polymorphisms (p<0.05). Considering only the constipated group, the rates of gene polymorphism were similar among those with/without a positive family history of constipation, constipation onset age, those with/without fissures, those with/without skin tag, and those with type 1/type 2 stool types according to the Bristol stool scale. CONCLUSION: Our study results showed that gene polymorphisms of these three hormones may not be related to constipation in children.

Serotonin, ghrelin, and motilin gene/receptor/transporter polymorphisms in childhood functional constipation

SUMMARY OBJECTIVE: Functional constipation is the most common form of constipation, and its exact aetiology is still unclear. However, it is known that deficiencies in hormonal factors cause constipation by changing physiological mechanisms. Motilin, ghrelin, serotonin acetylcholine, nitric oxide, and vasoactive intestinal polypeptide are factors that play a role in colon motility. There are a limited number of studies in the literature where hormone levels and gene polymorphisms of serotonin and motilin are examined. Our study aimed to investigate the role of motilin, ghrelin, and serotonin gene/receptor/transporter polymorphisms in constipation pathogenesis in patients diagnosed with functional constipation according to the Rome 4 criteria. METHODS: Sociodemographic data, symptom duration, accompanying findings, the presence of constipation in the family, Rome 4 criteria, and clinical findings according to Bristol scale of 200 cases (100 constipated patients and 100 healthy control) who applied to Istanbul Haseki Training and Research Hospital, Pediatric Gastroenterology Outpatient Clinic, between March and September 2019 (6-month period) were recorded. Polymorphisms of motilin-MLN (rs2281820), serotonin receptor-HTR3A (rs1062613), serotonin transporter-5-HTT (rs1042173), ghrelin-GHRL (rs27647), and ghrelin receptor-GHSR (rs572169) were detected by real-time PCR. RESULTS: There was no difference between the two groups in terms of sociodemographic characteristics. Notably, 40% of the constipated group had a family history of constipation. The number of patients who started to have constipation under 24 months was 78, and the number of patients who started to have constipation after 24 months was 22. There was no significant difference between constipation and control groups in terms of genotype and allele frequencies in MLN, HTR3A, 5-HTT, GHRL, and GHSR polymorphisms (p<0.05). Considering only the constipated group, the rates of gene polymorphism were similar among those with/without a positive family history of constipation, constipation onset age, those with/without fissures, those with/without skin tag, and those with type 1/type 2 stool types according to the Bristol stool scale. CONCLUSION: Our study results showed that gene polymorphisms of these three hormones may not be related to constipation in children.

Overexpressions of RHOA, CSNK1A1, DVL2, FZD8, and LRP5 genes enhance gastric cancer development in the presence of Helicobacter pylori.

BACKGROUND AND STUDY AIMS: Intestinal metaplasia (IM), and Helicobacter pylori (HP) infection can be shown as risk factors in the development of gastric cancer (GC). WNT signaling pathway plays a critical role in carcinogenesis. However, the literature studies are limited on the significance of this pathway for the transition from IM to GC. PATIENTS AND METHODS: We aimed to investigate the importance of the genes of WNT signaling pathways diagnostic and prognostic markers in the presence and absence of HP in conversion from IM to GC. 104 patients, (GC group n = 35, IM group n = 45, control group n = 25) were included in this case-control study. Expression of genes in WNT signalling were searched in study groups with qRT-PCR array and qRT-PCR method. Data were analysed using PCR array data analysis software. RESULTS: Statistically significant overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes was detected in the GC and IM groups compared to the control group (p < 0.05). Statistically significant overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes was observed in patients with metastatic GC compared to patients with GC without metastasis (p < 0.05). It was found that the RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes were statistically significantly over-expressed in diffuse GC patients compared to non-diffuse GC patients (p < 0.05). Statistically significant overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes was detected in HP positive IM patients compared to HP negative IM patients (p < 0.05). CONCLUSION: Overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes in IM may suggest that these genes are important markers in the development of IM and inflammation with HP. In addition, these genes are linked to tumor burden in the GC group. Consequently, we can conclude that these genes are poor prognosis biomarkers for GC and have the potential to be used as markers for future treatment monitoring.

Relationship between villous atrophy and Wnt pathway gene expressions in pediatric celiac patients

SUMMARY OBJECTIVE: Celiac disease is an autoimmune disease characterized by an abnormal immune response occurring in the small intestine linked to consumption of food containing gluten in individuals with a genetic predisposition. Dysregulation of Wnt signal transduction plays a role in the pathogenesis of many diseases including autoimmune diseases like celiac disease. In this study, the correlation of Wnt pathway gene expressions with each other and the correlation with clinical data were researched in pediatric celiac disease cases grouped according to the Marsh classification. METHODS: Gene expression levels of FZD8, DVL2, LRP5, RHOA, CCND2, CXADR, and NFATC1, which are involved in the Wnt pathway, were determined using quantitative real-time polymerase chain reaction in 40 celiac disease and 30 healthy individuals. RESULTS: All cases with the short height symptom were observed to be in Marsh 3b/3c groups (p=0.03). The gene expressions of DVL2, CCND2, and NFATC1 were high in the Marsh 3b group, and these genes showed positive correlation with each other (p=0.002). LRP5 and CXADR gene expressions were lower in the Marsh 3b group compared to other Marsh groups, and these genes showed a positive correlation with each other (p=0.003). CCND2 gene expression was associated with Marsh 3b group, diarrhea, and vomiting symptoms. DVL2 gene expression was correlated with Marsh 2 group and constipation symptom (p<0.05). CONCLUSION: Wnt signaling in the early stages of the disease of Marsh 1-2 involves high expression of LRP5 and CXADR genes, while expression of these two genes reduces, and DVL2, CCND2, and NFATC1 gene expressions clearly increase with a transduction variation observed from Marsh 3a stage when villous atrophy begins to form. It appears that the Wnt pathway may contribute to disease progression through expression changes.

Link between obsessive-compulsive disorder and polymorphisms in HDAC genes

Objective: Recently, epigenetic mechanisms related to histone modifications including histone deacetylation (HDAC) have been emphasized in psychiatric diseases. Few studies have investigated the relationship of HDAC gene variations to psychiatric diseases, but these gene variations have never been studied in obsessive-compulsive disorder (OCD). The present case-control study aimed to compare symptomatology with HDAC gene variations in patients with OCD. Methods: Illumina next-generation sequencing of six HDAC genes (HDAC2,3,4,9,10,11) was performed on DNA samples isolated from 200 Turkish subjects recruited from routine clinical practice. Twenty-seven single nucleotide polymorphism (SNPs) in six HDAC genes were scanned with the LightSNiP method. Results: New variants, all previously unreported in the literature, were identified in the HDAC4, HDAC10, and HDAC11 genes. When control and OCD patient groups were compared, a statistically significant difference was found in HDAC2 rs13212283, HDAC4 rs1063639, and HDAC10 rs1555048 in terms of genotype distribution (p < 0.05). In addition, in the OCD group, a statistically significant relationship was found between some obsessions/compulsions and HDAC2, HDAC3, and HDAC4 polymorphisms (p < 0.05). Conclusions: Our study shows that the HDAC2, HDAC3, HDAC4, and HDAC10 genes may play a role in the pathogenesis of OCD.

Link between obsessive-compulsive disorder and polymorphisms in HDAC genes.

OBJECTIVE: Recently, epigenetic mechanisms related to histone modifications including histone deacetylation (HDAC) have been emphasized in psychiatric diseases. Few studies have investigated the relationship of HDAC gene variations to psychiatric diseases, but these gene variations have never been studied in obsessive-compulsive disorder (OCD). The present case-control study aimed to compare symptomatology with HDAC gene variations in patients with OCD. METHODS: Illumina next-generation sequencing of six HDAC genes (HDAC2,3,4,9,10,11) was performed on DNA samples isolated from 200 Turkish subjects recruited from routine clinical practice. Twenty-seven single nucleotide polymorphism (SNPs) in six HDAC genes were scanned with the LightSNiP method. RESULTS: New variants, all previously unreported in the literature, were identified in the HDAC4, HDAC10, and HDAC11 genes. When control and OCD patient groups were compared, a statistically significant difference was found in HDAC2 rs13212283, HDAC4 rs1063639, and HDAC10 rs1555048 in terms of genotype distribution (p < 0.05). In addition, in the OCD group, a statistically significant relationship was found between some obsessions/compulsions and HDAC2, HDAC3, and HDAC4 polymorphisms (p < 0.05). CONCLUSIONS: Our study shows that the HDAC2, HDAC3, HDAC4, and HDAC10 genes may play a role in the pathogenesis of OCD.

The role of microRNAs in corneal neovascularization and its relation to VEGF.

PURPOSE: This study aimed to investigate the changes in the level of miRNA associated with Vascular Endothelial Growth Factor (VEGF) in corneal neovascularization (CNV), to elucidate the process of CNV formation and, thus, to prepare the ground for further experimental, and clinical studies together with drug treatments. METHODS: Twelve male Wistar-Albino rats were randomly divided into two groups of six, and two corneas of each rat were used. In all groups, CNV was generated by silver nitrate sticks. At the end of the study, rats were sacrificed by cervical dislocation under ether anaesthesia, and then, their corneas were removed. The expression levels of VEGF and miRNA in corneas were determined by qRT-PCR array and qRT-PCR. Data analysis was performed using web-based software named PCR array data. RESULTS: When the corneal samples of rats with CNV were compared to those of the control rats, it was found that a statistically significant difference was present regarding the VEGF level (p < 0.05) with the fold-regulation value> 2. According to the under- and over-expression data in miRNA PCR Array findings of both groups, statistically significant differences were found regarding nine genes with Fold-regulation value <-2 and Fold-regulation value> 2 (p < 0.05). When the corneal samples of the rats with CNV were compared to those of the control rats, statistically significant over-expressions (Fold-regulation value> 2) of rno-miR-21_2, rno-miR-126_1 and rno-miR-150_1 genes were found (p = 0.002443, p = 0.030146, p = 0.000348, respectively). In the same comparison, rno-miR-184_1 gene showed statistically significant under-expression with a Fold-regulation value <-2 (p = 0.006428). Also, in the comparison of the two groups, the fold regulation value of the rno-miR-31_1 gene was found to be close to - g and statistically significantly under-expressed (p = 0.005082). CONCLUSION: The over-expressions of rno-miR-21_2, rno-miR-126_1, and rno-miR-150_1 genes, and the under-expression of rno-miR-184_1 gene were thought to could play roles in the formation process of CNV by regulation of VEGF-A and through modulation of angiogenesis.

Chronic tinnitus and BDNF/GDNF CpG promoter methylations: a case-control study.

Brain-derived neurotrophic factor (BDNF) and Glial-derived neurotrophic factor (GDNF) are neurotrophic factors that play key roles in the auditory pathway. While the relationship between serum levels and polymorphisms of BDNF/GDNF and chronic tinnitus is emphasized in the literature, there is no study showing the link between the promoter methylations of these genes and tinnitus. For this purpose, the relationship between chronic tinnitus and peripheral blood derived BDNF/GDNF promoter methylations was investigated to identify their role in the pathophysiology of tinnitus. In this case-control study, we examined the possible effects of BDNF/GDNF methylations in the blood samples of patients with tinnitus complaints for more than 3 months. Sixty tinnitus subjects between the ages of 18-55 and 50 healthy control subjects in the same age group who were free of any otorhinolaryngology and systemic disease were selected for examination. Methylation of total 12 CpG sites in BDNF and GDNF promoter regions were determined by the bisulfite-pyrosequencing method. Statistically significant differences were detected between BDNF CpG6 and GDNF CpG3-5-6 methylation ratios in the comparison of control group and the chronic tinnitus patients (P = 0.002, 0.0005, 0.00003, and 0.0029, respectively). To our knowledge, this is the first study in the literature investigating the relationship between chronic tinnitus and peripheral blood derived BDNF/GDNF promoter methylations. It is believed that the current results might be supported by investigating the relationships between BDNF/GDNF methylations and genotypes in future research using higher sample sizes.

Roles of 5,10-methylenetetrahydrofolate reductase C677T and A1298C polymorphisms in early- and late-onset obsessive-compulsive disorder.

BACKGROUND: The C677T and A1298C mutations of 5,10-methylenetetrahydrofolate reductase (MTHFR) have been linked with conditions such as depression, bipolar disorder, and schizophrenia, but there are not clear the relationship between MTHFR polymorphisms and obsessive-compulsive disorder (OCD). AIM: The current study was planned to investigate the link between the MTHFR polymorphisms and OCD in patients to reveal any potential correlations that may be used as a novel marker in diagnosis of people who are in high-risk group of developing OCD. MATERIALS AND METHODS: Blood samples from 64 highly characterized symptomatic cases and 64 gender- and age-matched control participants were analyzed for MTHFR C677T and A1298C gene variants. The MTHFR gene polymorphisms were detected through real-time polymerase chain reaction, followed by melting curve analysis. The results were tested with analysis of variance test and the differences with P < 0.05 were reported as statistically significant. RESULTS: A statistically significant difference in age, education level, and marital status was found in the comparison of all groups in sociodemographic findings (P = 0.004, P = 0.001, and P = 0.001, respectively). A statistically significant difference was found in the comparison of the tic story of early- and late-onset OCD patients (P = 0.002). There was no significant difference in the genotype frequencies and allele distributions of MTHFR polymorphisms between the patients and controls (P > 0.05). CONCLUSION: The results suggest that MTHFR polymorphisms are unlikely to play a major role in the pathogenesis of OCD. Further studies are needed in biochemical data on folate metabolism to clarify the effect of the MTHFR polymorphisms in OCD pathophysiology.

Expression profiles of histone modification genes in gastric cancer progression.

Gastric cancer (GC) development can be attributed to several risk factors including atrophic gastritis (AG), intestinal metaplasia (IM), and the presence of Helicobacter pylori (HP). Also, histone modification is an epigenetic mechanism that plays a pivotal role in GC carcinogenesis. In this preliminary study, we aimed to describe the expression profiles of histone modification in the AG, IM, and GC patient groups. A total of 80 patients with AG (n = 27), IM (n = 25), and GC (n = 28) with an additional 20 control subjects were included in the study. Expression profiles of three histone phosphorylation genes (PAK1, NEK6, and AURKA) and five histone deacetylation genes (HDACs 1, 2, 3, 5, and 7) were examined based on the results of Real Time qPCR method. It was observed that AURKA and HDAC2 genes were significantly overexpressed in all groups compared to the control (P < 0.05). In GC patients, overexpression of HDAC2 gene was detected in the absence of metastasis, and overexpression of AURKA, HDAC2, and NEK6 genes was detected in the presence of metastasis. When cancer involvements were compared, significant overexpression of the HDAC2 gene was noted in overall and corpus involvements (P < 0.05). In addition, overexpression of AURKA, NEK6, HDAC1, and HDAC2 genes and underexpression of HDAC5 gene were detected in the antrum involvement (P < 0.05). In conclusion, decreased expression of HDAC5 in GC is reported for the first time in this study, while supporting the existing literature in AURKA, NEK6, HDAC1, and HDAC2 up regulations during GC development.

Boron intake, osteocalcin polymorphism and serum level in postmenopausal osteoporosis.

The relationship between daily boron intake and osteocalcin-mediated osteoporosis was studied in boron-exposed postmenopausal women. It is known that boron and osteocalcin are important in bone metabolism, however the effect of boron in bone metabolism has not been fully discovered. The study was performed on 53 postmenopausal women aged 55-60 living in parts of Balikesir, Turkey, where the subjects are naturally exposed to high (≥1 mg/L) or low (<1 mg/L) boron concentration in drinking water. 24-h urine samples were collected from all participants and creatinine clearance was detected. Boron intake levels of the subjects whose clearance levels were between 80-124 mL/min were measured by inductively coupled plasma-optical emission spectrometry (ICP-OES) in urine samples. Serum osteocalcin levels of the subjects were measured by osteocalcin enzyme-linked immunosorbent assay (ELISA) kit. Osteocalcin polymorphism rs1800247 was detected using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Serum osteocalcin levels in boron-exposed postmenopausal women were significantly higher than that of control group (P ≤ 0.05) and the correlation between the serum osteocalcin level and rs1800247 polymorphism was not significant in both groups (P > 0.05). The differences in the distribution of osteocalcin genotypes and alleles in postmenopausal women were not significant between the boron exposed and the control groups (P > 0.05). Serum osteocalcin level in the CC genotype was significantly higher compared to the TC genotype in boron-exposed group (P ≤ 0.05). Our study suggests that daily boron intake of 1 mg/L may affect bone metabolism in postmenopausal women positively.

Evidence of associations between brain-derived neurotrophic factor (BDNF) serum levels and gene polymorphisms with tinnitus.

BACKGROUND: Brain-derived neurotrophic factor (BDNF) gene polymorphisms are associated with abnormalities in regulation of BDNF secretion. Studies also linked BDNF polymorphisms with changes in brainstem auditory-evoked response test results. Furthermore, BDNF levels are reduced in tinnitus, psychiatric disorders, depression, dysthymic disorder that may be associated with stress, conversion disorder, and suicide attempts due to crises of life. For this purpose, we investigated whether there is any role of BDNF changes in the pathophysiology of tinnitus. MATERIALS AND METHODS: In this study, we examined the possible effects of BDNF variants in individuals diagnosed with tinnitus for more than 3 months. Fifty-two tinnitus subjects between the ages of 18 and 55, and 42 years healthy control subjects in the same age group, who were free of any otorhinolaryngology and systemic disease, were selected for examination. The intensity of tinnitus and depression was measured using the tinnitus handicap inventory, and the differential diagnosis of psychiatric diagnoses made using the Structured Clinical Interview for Fourth Edition of Mental Disorders. BDNF gene polymorphism was analyzed in the genomic deoxyribonucleic acid (DNA) samples extracted from the venous blood, and the serum levels of BDNF were measured. One-way analysis of variance and Chi-squared tests were applied. RESULTS: Serum BDNF level was found lower in the tinnitus patients than controls, and it appeared that there is no correlation between BDNF gene polymorphism and tinnitus. CONCLUSIONS: This study suggests neurotrophic factors such as BDNF may have a role in tinnitus etiology. Future studies with larger sample size may be required to further confirm our results.

Biological effects of tolerable level chronic boron intake on transcription factors.

The mechanism of boron effect on human transcription and translation has not been fully understood. In the current study it was aimed to reveal the role of boron on the expression of certain transcription factors that play key roles in many cellular pathways on human subjects chronically exposed to low amounts of boron. The boron concentrations in drinking water samples were 1.57±0.06mg/l for boron group while the corresponding value for the control group was 0.016±0.002mg/l. RNA isolation was performed using PAX gene RNA kit on the blood samples from the subjects. The RNA was then reverse transcribed into cDNA and analyzed using the Human Transcription Factors RT2 Profiler™ PCR Arrays. While the boron amount in urine was detected as 3.56±1.47mg/day in the boron group, it was 0.72±0.30mg/day in the control group. Daily boron intake of the boron and control groups were calculated to be 6.98±3.39 and 1.18±0.41mg/day, respectively. The expression levels of the transcription factor genes were compared between the boron and control groups and no statistically significant difference was detected (P>0.05). The data suggest that boron intake at 6.98±3.39mg/day, which is the dose at which beneficial effects might be seen, does not result in toxicity at molecular level since the expression levels of transcription factors are not changed. Although boron intake over this level will seem to increase RNA synthesis, further examination of the topic is needed using new molecular epidemiological data.