Molecular and in silico analyses of SYN III gene variants in autism spectrum disorder.

BACKGROUND: Defects in neurotransmission and synaptogenesis are noteworthy in the pathogenesis of ASD. Synapsin III (SYN III) is defined as a synaptic vesicle protein that plays an important role in synaptogenesis and regulation of neurotransmitter release and neurite outgrowth. Therefore, SYN III may associate with many neurodevelopmental diseases, including ASD. AIM: The aim of this study was to investigate whether the SYN III gene -631 C > G (rs133946) and -196 G > A (rs133945) polymorphisms are associated with susceptibility to ASD. METHODS: SYN III variants and the risk of ASD were investigated in 26 healthy children and 24 ASD children. SYN III gene variants were genotyped by PCR-RFLP methods. The differences in genotype and allele frequencies between the ASD and control groups were calculated using the chi-square (χ2). We analysed the SYN III gene using web-based tools. RESULTS: Our results suggest that the presence of the AA genotype of the SYN III -196 G > A (rs133945) polymorphism affects the characteristics and development of ASD in children (p = 0.012). SYN III -631 C > G (rs133946) polymorphism was not associated with ASD (p = 0.524). We have shown the prediction of gene-gene interaction that SYN III is co-expressed with 17 genes, physical interaction with 3 genes, and co-localization with 12 genes. The importance of different genes (SYN I, II, III, GABRD, NOS1AP, GNAO1) for ASD pathogenesis was revealed by GO analysis. CONCLUSION: Considering the role of SYN III and related genes, especially in the synaptic vesicle pathway and neurotransmission, its effect on ASD can be further investigated.

miR-181a-5p is a potential candidate epigenetic biomarker in multiple sclerosis.

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by demyelination and axonal degeneration. Abnormal expression of microRNAs (miRNAs) plays an important role in MS pathology. In this cohort study, differential expression of the four miRNAs (hsa-miR-155-5p, hsa-miR-9-5p, hsa-miR-181a-5p, and hsa-miR-125b-5p) was investigated in 69 individuals, including 39 MS patients (relapsing-remitting MS (RRMS), n = 27; secondary progressive MS (SPMS), n = 12) and 30 healthy controls. In silico analyses revealed possible genes and pathways specific to miRNAs. Peripheral blood miRNA expressions were detected by quantitative real-time PCR (qPCR). hsa-miR-181a-5p was downregulated and associated with increased MS risk (P = 0.012). The other three miRNAs were upregulated and not associated with MS (P < 0.05). The area under the curve (AUC) is 0.779. In silico analyses showed that hsa-miR-181a-5p may participate in MS pathology by targeting MAP2K1, CREB1, ATXN1, and ATXN3 genes in inflammation and neurodegeneration pathways. The circulatory hsa-miR-181a-5p can regulate target genes, reversing the mechanisms involved in MS pathologies such as protein uptake and processing, cell proliferation and survival, inflammation, and neurodegeneration. Thus, this miRNA could be used as an epigenomic-guided diagnostic tool and for therapeutic purpose.

Prodynorphin (PDYN) gene polymorphisms in Turkish patients with methamphetamine use disorder, changes in PDYN serum levels in withdrawal and the relationship between PDYN, temperament and depression.

Aim of the study is to compare prodynorphin (PDYN) rs1997794, rs1022563, rs6045819, rs2235749 polymorphisms in individuals with methamphetamine use disorder (MD) to that of healthy controls (HC), and to investigate the differences in serum PDYN levels in methamphetamine withdrawal. It is also aimed to explore the temperament characteristics and depression and their relationship with PDYN polymorphisms and PDYN serum levels in MD group. PDYN gene and serum levels were studied in 134 patients with MD and 97 HC. Patients with MD were administered Beck Depression Inventory (BDI) and Temperament Evaluation of Memphis, Pisa, Paris and San Diego Autoquestionnaire (TEMPS-A). For rs1022563 polymorphism, TT and CT genotype frequency and T allele frequency were significantly higher in the MD group than the frequencies in HC. It was found that rs2235749 polymorphism AA genotype was associated with increased risk of MD. PDYN rs1997794 CT genotypes had significantly higher scores of TEMPS-A irritable than CC genotypes and PDYN rs1022563 CC genotypes had significantly higher scores of TEMPS-A irritable than TT genotypes. PDYN levels among persons with MD were significantly higher than among the HC group when the withdrawal level increased and withdrawal symptoms improved. During the period in which the withdrawal level increased, there was a negative correlation between PDYN level and BDI and a positive relationship between PDYN level and TEMPS-A hyperthymic. It may be beneficial to screen temperament characteristics associated with increased risk of addiction in patients with MD and develop interventions based on temperament characteristics and the effects of PDYN.

In Vitro Effects of Propofol on Cytotoxic, Apoptotic and PI3K-Akt Signaling Pathway Genes on Brain Cancer Cells.

AIM: The study aimed to determine the cytotoxic and apoptotic effect of propofol on glioma cells. BACKGROUND: Propofol [2,6-diisopropylphenol] is a commonly used intravenous anesthetic. Propofol is known to have a mechanism of action on the PI3K-AKT pathway. OBJECTIVE: This study aimed to evaluate the effect of propofol on the proliferation and apoptosis of human glioma cells, as well as to investigate changes in expression levels of the PI3K-AKT signaling pathway genes. MATERIALS AND METHODS: The cytotoxic effect of propofol on the U-87 MG cell line was determined by WST-1 method. Annexin V-FITC and Mitoprobe JC-1 assay were used to measure apoptosis by flow cytometry. The expression levels of genes in the PI3K-AKT signaling pathway were investigated by qRT-PCR. RESULTS: We have shown that propofol induced apoptosis in U-87 MG cells by 17.1 fold compared to the untreated control. Furthermore, significant differences were found in the expression levels of the PI3K-AKT signaling pathway genes. CONCLUSION: As a result of our study, it was found that propofol caused differences in expression levels of PI3K-AKT signaling pathway genes and it was suggested that these differences may be related to apoptosis induction.

The role of Wnt pathway antagonists in early-stage lung adenocarcinoma.

PURPOSE: We aimed to examine the expression levels of the genes encoding adenomatous polyposis coli (APC) 1, APC-2, Dickkopf related protein (DKK)-1, DKK-3, secreted frizzled-related protein (SFRP)-2, SFRP-4, and SFRP-5, which play roles in the Wnt signaling pathway, in lung adenocarcinoma and adjacent normal lung tissues and to evaluate their relationships with clinicopathologic factors. MATERIALS AND METHODS: The expression levels of genes in formalin-fixed paraffin-embedded samples of tumor tissue and adjacent intact lung tissue from 57 patients who underwent surgery for lung adenocarcinoma between 2011 and 2018 were determined by real-time PCR analysis. RESULTS: The expression levels of the DKK-1 in tumor tissue, especially in stage I-II tumor tissue, were significantly suppressed compared to those in normal tissue (p < 0.025). Whereas DKK-1 expression was suppressed in the tumor tissue of patients with early-stage lung adenocarcinoma, expression of the SFRP-5 in these patients was significantly higher in tumor tissue than in normal tissue (p < 0.039). CONCLUSION: In our study, opposing regulation was found between the SFRP-5 and DKK-1, which are known to be extracellular antagonists of the Wnt signaling pathway. The SFRP-5 was found to have an oncogenic role in adenocarcinoma development. Studies of the opposing regulation between these genes in early-stage lung adenocarcinoma may shed light on the mechanisms associated with the development of carcinogenesis. The relationships or interactions of these genes may serve as potential therapeutic targets.

Extracellular Matrix Protein 1 Gene Mutation in Turkish Patients with Lipoid Proteinosis.

BACKGROUND: Lipoid proteinosis (LP) is a rare autosomal recessive genodermatosis characterized by mucocutaneous lesions and hoarseness of voice that develop in early childhood. LP is caused by mutation in the extracellular matrix protein 1 (ECM1) gene, which is located on 1q21.2. AIMS: This study aimed to present the profile of ECM1 gene mutations and to identify possible novel mutations specific to Turkey. MATERIALS AND METHODS: The ECM1 gene mutations of 19 LP patients from five families were evaluated using DNA isolated from peripheral blood samples. All ten exons in the ECM1 gene region were amplified by polymerase chain reaction (PCR). The PCR products were analyzed using a DNA sequencing analyzer. The results of DNA sequencing were analyzed with bioinformatics methods. RESULTS: of the 19 LP patients evaluated in our study, we detected defects in exon 6 (c.507delT, 658T>G), exon 9 (157C>T, 727C>T), and exon 10 (c.93_94delGCinsTT) of the ECM1 gene. CONCLUSIONS: Our results indicate that defects in exons 6, 9, and 10 of the ECM1 gene were responsible for LP in our country. The identification of these pathogenic mutations is valuable because it facilitates early diagnosis and genetic counseling.

Molecular investigation of staphylococcal cassette chromosome mec types and genotypic relations of methicillin-resistant staphylococci isolated from before and after hospital exposed students.

Background: Reservoir of methicillin resistance genes called staphylococcal cassette chromosome mec (SCCmec), plasmids and genomic characterisations of isolates have been widely investigated in epidemiologic research. However, the extent to which these organisms are transported by patients or hospital staff is not entirely clear. Aim: This study aims to investigate the molecular relatedness and plasmid profiles of MR staphylococci isolated from nursing students before and after hospital training, to find out the possible source. Materials and Methods: This study examined 39 methicillin-resistant (MR) staphylococci and 2 inducible clindamycin-resistant, methicillin-susceptible Staphylococcus aureus. Specimens were collected before and after 4 months of hospital training from the hands and nares of 75 nursing students. A polymerase chain reaction technique was used to confirm the existence of mecA gene and identify SCCmec types; total DNA was digested by SmaI endonuclease restriction to monitorise clonal relatedness by pulsed-field gel electrophoresis (PFGE); plasmid profiles were monitorised on agarose gel. Results: All 39 isolates tested positive for mecA; SCCmec type III was observed most frequently. Interestingly, in one isolate of Staphylococcus epidermidis, four different types of SCCmec elements were observed. There were 23 different types of plasmids, whose sizes ranged from 1.4 to 46.0 kb. After PFGE dendogram analysis, two strains were classified as indistinguishable; six were closely related. Most of the isolates obtained after hospital training showed clonal similarity and seven had multiple SCCmec elements require further investigation for the possible mechanism. Conclusion: Most of the isolates obtained after hospital training showed clonal similarity and seven had multiple SCCmec elements require further investigation for the possible mechanism.

The Role of Forkhead Box Class O3A and SIRT1 Gene Variants in Early-Onset Psoriasis.

BACKGROUND: Psoriasis is a chronic inflammatory skin disorder, which is characterized by a heightened immunological response. Although the immunogenetics of this chronic inflammatory disorder is poorly understood, its expression is known to be dependent on proinflammatory cytokines. It is known that two distinct subtypes of chronic plaque psoriasis: Early-onset psoriasis (EOP) before the age of 40 years and late-onset psoriasis after the age of 40 years. Forkhead box class O3A (FOXO3A) is a transcription factor, which plays an important role in cell-cycle regulation, apoptosis, oxidative stress, and DNA repair. The silent information regulator (SIRT) is thought to have a role in skin disorders, including psoriasis, that are characterized by hyperproliferation and inflammation. AIM: The aim of this study was to investigate FOXO3A and SIRT1 gene polymorphisms in EOP. METHODS: The study group consisted of 142 EOP patients and 123 unrelated healthy controls. FOXO3A polymorphisms were determined using the polymerase chain reaction (PCR)-restriction fragment length polymorphism method. SIRT1 gene polymorphisms were determined by PCR-confronting two-pair primers methods. RESULTS: The FOXO3A rs4946936 and SIRT1 rs7069102 gene polymorphisms were positively correlated with EOP and disease severity. The GG genotype frequency of SIRT1 rs7069102 gene polymorphisms was increased in severe EOP. The CC frequency of FOXO3A rs4946936 was increased in EOP with nail disorders. CONCLUSION: The rs7069102 gene polymorphism of SIRT1 and rs4946936 polymorphism of FOXO3A are associated with early onset psoriasis; this may be responsible for increased keratinocyte proliferation in the pathogenesis of psoriasis and disease severity.

Sirtuin gene polymorphisms are associated with chronic obstructive pulmonary disease in patients in Mugla province.

INTRODUCTION: Chronic obstructive pulmonary disease (COPD) is an irreversible progressive chronic inflammatory disease that causes shortness of breath in consequence of a decrease in pulmonary functions. The pulmonary inflammatory pathogenesis is multifactorial. We have too little up-to-date information about the relation between COPD and genetics. In our study, the relation with the SIRT1 gene's mononucleotide polymorphisms (SNP) rs7895833, rs7069102 and rs2273773 was analyzed through various laboratory data. MATERIAL AND METHODS: One hundred COPD patients from the archive records of the Chest Diseases Department of Mugla Sitki Kocman University Medical Faculty were included in the study. A control group was constituted from 100 healthy individuals who live in the same geographical region. The SIRT1 genotypes for these patients were determined using polymerase chain reaction (PCR) and confronting two-pair primers (CTPP) methods. The SIRT1 gene polymorphisms rs7895833, rs7069102 and rs2273773 were analyzed. GG, AG, AA genotypes and G and A alleles of rs7895833, TT, TC, CC genotypes and T and C alleles of rs2273773, and CC, CG, GG genotypes and C and G alleles of rs7069102 were examined. The data in both groups were compared. CONCLUSIONS: A significant difference between GG, AG and AA genotypes of rs7895833 was found. Especially, the AG genotype was observed more in the group with COPD, with a significant difference. A significant difference between TT, TC and CC genotypes of rs2273773 was found. There was a significant difference between two groups with regards to C and G alleles of rs7069102. A significant difference was not found between the groups with regards to G and A alleles of rs7895833. A difference was not found for both groups between T and C alleles of rs2273773. It shows that these polymorphisms of the SIRT1 gene may be associated with COPD.

Genetic variants of synaptic vesicle and presynaptic plasma membrane proteins in idiopathic generalized epilepsy.

BACKGROUND: The aim of this study was to analyze the role of the genetic variants of two synaptic vesicle proteins (VAMP2 and Synaptotagmin XI) and two presynaptic plasma membrane proteins (Syntaxin 1A and SNAP-25) in patients with idiopathic generalized epilepsy (IGE). METHOD: Eighty-five patients with IGE and 93 healthy subjects were included in the study. We analyzed the functional polymorphisms of VAMP2, Synaptotagmin XI, Syntaxin 1A and SNAP-25 genes with polymerase chain reaction and restriction fragment length polymorphism methods. RESULTS: In the patients with IGE, significant differences alleles and genotypes of 26 bp Ins/Del polymorphism of the VAMP2 gene and the 33-bp promoter region of Synaptotagmin XI were observed, however no associaton was found regarding Intron 7 rs1569061 of Syntaxin 1A gene, MnlI rs3746544 and DdeI rs1051312 polymorphisms of SNAP-25 gene compared with healthy subjects. Carriers of the C allele of Synaptotagmin XI had worse measures compared with the T allele of Synaptotagmin XI. In the haplotype analysis, the frequency of the T alleles of rs1569061 and of the C alleles of the 33-bp promoter region of Synaptotagmin XI was found to be significantly higher in patients with IGE as compared with the healthy subjects. CONCLUSION: The genetic variations of VAMP2, Synaptotagmin XI might be indication of the relationship between these genes and IGE.

A Study of the Impact of Death Receptor 4 (DR4) Gene Polymorphisms in Alzheimer's Disease.

BACKGROUND: Excessive apoptosis is believed to play a role in many degenerative and non-degenerative neurological diseases including Alzheimer's disease (AD). Much recent data suggest that apoptotic mechanisms may represent the missing link between Aß deposition and proteolysis of tau protein. However, there is emerging evidence that apoptotic mechanisms may play a role in Alzheimer's Disease pathogenesis in the absence of overt apoptosis. TNF-related apoptosis inducing ligand receptor 1 (Death Receptor 4, DR4) might impair the apoptotic signal transduction and lead to dysregulation of the homeostasis between cell survival and cell death. AIMS: The aim of our study was to further investigate the relationship between genetic variants of DR4 and Alzheimer's Disease. STUDY DESIGN: Case control study. METHODS: Sixty-eight patients with AD were included in the study. The control group comprised 72 subjects without signs of neurodegenerative diseases, as evidenced by the examination.DNA was extracted from whole blood using the salting-out procedure. Genotypes were identified by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR-RFLP) products. RESULTS: We observed significant differences in the genotypic distribution of the rs6557634 polymorphism in AD patients compared with controls (p<0.05); our data suggest that the GA genotype in rs6557634 could be protective against AD (p<0.05). However, there were no significant differences between AD patients and control groups in terms of the DR4 rs20575 polymorphism (p>0.05) and the DR4 rs20576 polymorphism (p>0.05). According to haplotype analysis of the DR4 gene for rs6557634, rs20575 and rs20576 polymorphisms, GCA and GCC haplotypes might be a risk factor for AD. Also, we have shown that ACA, GGC and GGA haplotypes might be protective factors against AD. CONCLUSION: The present results indicate for the first time the possible contribution of the DR4 gene rs6557634, rs20575, rs20576 polymorphisms in Alzheimer's Disease, which may influence susceptibility to Alzheimer's Disease.

Cytokine polymorphism in patients with migraine: some suggestive clues of migraine and inflammation.

OBJECTIVE: There are contrasting results obtained in migraineurs concerning the levels and the role of both pro-inflammatory and anti-inflammatory cytokines. In this study, the association of the occurrence and clinical characteristics of migraine with the polymorphisms of tumor necrosis factor alpha (TNF-alpha) -308 G/A (rs1800629), interleukin-1alpha (IL-1alpha) +4845 G/T (rs17561), IL-1beta+3953 C/T (rs1143634) and interleukin-1 receptor antagonist variable number tandem repeat (IL-1RA VNTR) genes were studied. We also investigated the genetic linkage between these genes. DESIGN, SETTING, PATIENTS: Sixty-seven patients with migraine without aura (MwoA) and 96 unrelated, age- and sex-matched migraine-free, healthy control subjects from the same geographic area were investigated. RESULTS: We observed significant differences in the genotypic distribution of the TNF-alpha-308 G/A and IL-1beta+3953 C/T polymorphism for migraineurs compared with controls (P = 0.004). Frequency of the TNF-alpha-308 GG genotype was higher in the control group than MwoA group (82.1% vs 55.2%). Differences in the distribution of the allele frequencies were also observed, being the TNF-alpha-308 G allele overrepresented in control group and TNF-alpha-308 A allele in MwoA group. In addition, there was a significant increase of the IL-1beta+3953 T allele in MwoA cases compared with controls (P = 0.004). CONCLUSIONS: In conclusion, the present results indicate the possible contribution of TNF-alpha and IL-1beta gene polymorphisms to migraine headache generation in MwoA patients.