Hypermethylation of tumor suppressor genes in gastric cancer: associations with demographic and clinicopathological characteristics

Background: Gastric cancer (GC) is one of the most common cancers worldwide. Despite the declining prevalence in Western countries, it is still a major health problem in Turkey and Asian countries. In the current study, we investigated the hypermethylation status of 25 TSGs in GC. Furthermore, the association between hypermethylation status of these TSGs and some demographic and clinicopathological characteristics were investigated.Methods: Formalin-fixed paraffin-embedded tissue samples obtained from 27 patients with GC and genomic DNA isolated from these tissues. To compare the methylation status of 25 TSGs, methylation-specific multiplex ligation-dependent probe amplification (MS–MLPA) technique was used. Results were evaluated in terms of age, gender, positive lymph node status, lymphovascular invasion, perineural invasion, mortality and five-years of survival, retrospectively.Results: Tumor suppressor gene hypermethylation was detected 16 (59.3%) of 27 GC tissues. Patients with hypermethylation-detected and patients with no hypermethylation-detected in their TSGs were classified as group 1 and group 2, respectively. The mean age of group 1 was 66.38±7.43 and the mean age of group 2 was found as 58.18±11.12 (p= 0.03). Hypermethylation was detected in 12 of 25 TSGs in patients with GC. Hypermethylation was detected as 51.8% for WT1, 40.7% for ESR1, 18.5% for CDH13, 14.8% for MSH6 and CD44, 7.4% for TP73 and PAX5 genes in the tumor tissues of patients with GC. Mean positive lymph node number was 8.81±5.38 in group 1 and 4.81±3.21 in group 2 (p= 0.037). Lymphovascular invasion, perineural invasion, mortality and five-years of mean survival were not statistically different between group 1 and group 2 (p>0.05 for all comparisons).Conclusions: Hypermethylation frequency of certain tumor suppressor genes may increase with advancing age and with positive lymph nodes in gastric cancer patients.

Investigating the effect of ribavirin treatment on genetic mutations in Crimean-Congo haemorrhagic fever virus (CCHFV) through next-generation sequencing.

Crimean-Congo haemorrhagic fever (CCHF) is the most widespread tick-borne viral haemorrhagic fever affecting humans, and yet a licensed drug against the virus (CCHFV) is still not available. While several studies have suggested the efficacy of ribavirin against CCHFV, current literature remains inconclusive. In this study, we have utilised next-generation sequencing to investigate the mutagenic effect of ribavirin on the CCHFV genome during clinical disease. Samples collected from CCHF patients receiving ribavirin treatment or supportive care only at Sivas Cumhuriyet University Hospital, Turkey, were analysed. By comparing the frequency of mutations in each group, we found little evidence of an overall mutagenic effect. This suggests that ribavirin, administered at the acute stages of CCHFV infection (at the World Health Organization-recommended dose) is unable to induce lethal mutagenesis that would cause an extinction event in the CCHFV population and reduce viremia

Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection.

Crimean-Congo hemorrhagic fever (CCHF) caused by CCHF virus (CCHFV) is one of the epidemic-prone diseases prioritized by the World Health Organisation as public health emergency with an urgent need for accelerated research. The trajectory of host response against CCHFV is multifarious and remains unknown. Here, we reported the temporal spectrum of pathogenesis following the CCHFV infection using genome-wide blood transcriptomics analysis followed by advanced systems biology analysis, temporal immune-pathogenic alterations, and context-specific progressive and postinfection genome-scale metabolic models (GSMM) on samples collected during the acute (T0), early convalescent (T1), and convalescent-phase (T2). The interplay between the retinoic acid-inducible gene-I-like/nucleotide-binding oligomerization domain-like receptor and tumor necrosis factor signaling governed the trajectory of antiviral immune responses. The rearrangement of intracellular metabolic fluxes toward the amino acid metabolism and metabolic shift toward oxidative phosphorylation and fatty acid oxidation during acute CCHFV infection determine the pathogenicity. The upregulation of the tricarboxylic acid cycle during CCHFV infection, compared to the noninfected healthy control and between the severity groups, indicated an increased energy demand and cellular stress. The upregulation of glycolysis and pyruvate metabolism potentiated energy generation through alternative pathways associated with the severity of the infection. The downregulation of metabolic processes at the convalescent phase identified by blood cell transcriptomics and single-cell type proteomics of five immune cells (CD4+ and CD8+ T cells, CD14+ monocytes, B cells, and NK cells) potentially leads to metabolic rewiring through the recovery due to hyperactivity during the acute phase leading to post-viral fatigue syndrome

Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.

The pathogenesis and host-viral interactions of the Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) are convoluted and not well evaluated. Application of the multi-omics system biology approaches, including biological network analysis in elucidating the complex host-viral response, interrogates the viral pathogenesis. The present study aimed to fingerprint the system-level alterations during acute CCHFV-infection and the cellular immune responses during productive CCHFV-replication in vitro. We used system-wide network-based system biology analysis of peripheral blood mononuclear cells (PBMCs) from a longitudinal cohort of CCHF patients during the acute phase of infection and after one year of recovery (convalescent phase) followed by untargeted quantitative proteomics analysis of the most permissive CCHFV-infected Huh7 and SW13 cells. In the RNAseq analysis of the PBMCs, comparing the acute and convalescent-phase, we observed system-level host's metabolic reprogramming towards central carbon and energy metabolism (CCEM) with distinct upregulation of oxidative phosphorylation (OXPHOS) during CCHFV-infection. Upon application of network-based system biology methods, negative coordination of the biological signaling systems like FOXO/Notch axis and Akt/mTOR/HIF-1 signaling with metabolic pathways during CCHFV-infection were observed. The temporal quantitative proteomics in Huh7 showed a dynamic change in the CCEM over time and concordant with the cross-sectional proteomics in SW13 cells. By blocking the two key CCEM pathways, glycolysis and glutaminolysis, viral replication was inhibited in vitro. Activation of key interferon stimulating genes during infection suggested the role of type I and II interferon-mediated antiviral mechanisms both at the system level and during progressive replication

SDF-1/CXCL12 and CXCR4 gene variants, and elevated serum SDF-1 levels are associated with preeclampsia

Objective: We aimed to compare the frequencies of stromal cell-derived factor-1 (SDF-1) 3′A and CXCR4 single-nucleotide polymorphisms (SNPs) and serum SDF-1 levels in patients with preeclampsia (PE). Methods: In total, 89 women with PE and 89 control women were included in the study. Genotyping was done by polymerase chain reaction-restriction fragment length polymorphism method. Enzyme-linked immunosorbent assay method was used to measure serum SDF-1 level. Results: For SDF-1 3′A SNP, the frequency of GA genotype, total number of GA and AA genotypes, and the A allele frequency was higher in PE patients than controls (p = 0.04, 0.023, and 0.029, respectively). For CXCR4 SNP, the frequency of CT genotype, total number of CT and TT genotypes, and the T allele frequency were higher in PE patients than controls (p = 0.04, 0.006, and 0.005, respectively). SDF-1 serum level was detected higher in preeclamptic women compared with controls (p = 0.001). In PE patients, there was no significant association between serum SDF-1 levels and genotypes of SDF-1 3′A SNP. SDF-1 level was significantly higher in patients bearing CXCR4 CT genotype than CC genotype (p = 0.001). Furthermore, SDF-1 levels in patients bearing CT+TT genotype were found higher than that of patients with CC genotypes (p = 0.001). Conclusion: Results of our study suggest that SDF-1 3′A and CXCR4 polymorphisms and elevated serum SDF-1 levels may have a role in the development of PE

Prevalence of Fabry Disease in Familial Mediterranean Fever Patients from Central Anatolia of Turkey

WOS: 000379533500009PubMed ID: 27105876Fabry disease (FD) is a progressive, X-linked inherited disorder of glycosphingolipid metabolism due to deficient or absent lysosomal alpha-galactosidase A (AGALA) activity. FD and familial Mediterranean fever (FMF) have typical clinical similarities, and both diseases may progress to end-stage renal diseases. In this study, we aimed to determine the prevalence of FD in patients with FMF from Central Anatolia of Turkey. The study group consisted of 177 FMF patients, followed up by the Adult and Pediatric Nephrology Clinic of Cumhuriyet University Hospital. Screening for AGALA activity was performed by the dry blood spot method. Mutation analysis for GLA gene was carried out for patients having an AGALA enzyme activity value lower than the normal reference value. Low AGALA activity was detected in 23 (13 %) patients. Heterozygous GLA gene mutation c.[937G > T] p.[D313Y] was detected in one female patient (0.56 %). The patient was a 53-year-old female with proteinuria and who had undergone left nephrectomy; her glomerular filtration rate (GFR) by scintigraphy was found to be 70 ml/min. She had M694V mutation and no clinical manifestation of FD. In our study, the prevalence rate of FD was found as 0.56 % in FMF patients. The similarities between the symptoms of FMF and FD might lead to a diagnostic dilemma in physicians at countries where FMF is observed frequently. Although the prevalence of FD is rare, physicians should keep in mind that FD has an ambiguous symptomology pattern of FMF

Quality of Life of Individuals with Bipolar Disorder and Schizophrenia

Introduction: Quality of life (QoL) is a concept defined as a subjective perception of one's position in life and is negatively affected in many psychiatric illnesses such as bipolar disorder (BD) and schizophrenia (SCZ). It is hypothesized that therapeutic approaches based on QoL can increase the patient's adherence to treatment and contribute to a satisfactory life. This study aimed to compare the QoL of individuals having BD and schizophrenia with that of healthy controls (HCs) and to investigate the impact of the state of remission on QoL.Method: The World Health Organization QoL Scale-Short Form (WHOQOL-Bref) was administered to individuals with BD (n=124) and SCZ (n=74) and to HCs (n=81) to evaluate QoL. The WHOQOL-Bref subscale and total scores were compared between the groups using multifactor analysis of covariance (MANCOVA) by considering age and education level as the covariates. Then, the patient groups were compared using MANCOVA based on the state of remission by taking age, level of education, and Global Assessment of Functioning scores as the covariates. The relationship between clinical features and QoL scores was evaluated using correlation analysis, and linear regression analysis was applied for the variables that were found to be significant.Results: It was found that individuals with SCZ or BD had lower WHOQOL-Bref psychological, social, and total scores than HCs. Those with SCZ additionally had lower physical and environmental subscale scores than HCs. Furthermore, those with SCZ had lower WHOQOL-Bref physical, psychological, social, and total scores than individuals with BD. There was no significant difference in WHOQOL-Bref scores between individuals with BD and SCZ in the remission period. WHOQOL-Bref physical, psychological, and total scores were found to be significantly lower in unremitted BD patients when compared with remitted BD patients. Unremitted BD patients were found to have significantly lower WHOQOL-Bref psychological, environmental, and total scale scores than unremitted SCZ patients. Conclusion: It can be concluded that the QoL of individuals with BD is between that of healthy individuals and those with SCZ. However, unremitted BD patients have lower QoL than unremitted SCZ patients. Both patient groups display similar features during remission. Identifying the similarities and differences in terms of QoL in both patient groups is of great importance to develop the best type of treatment for the patients

IDENTIFICATION OF AN IMPORTANT FACTOR INVOLVED IN CCHFV INFECTION

Despite intensive research, much of the molecular pathogenesis of CCHFV is still unknown. Genome-wide screening methods (particularly CRISPR/Cas9-based screens and insertional mutagenesis in haploid cell systems) have facilitated and accelerated the identification and characterization of host genes involved in infectious diseases. Combining haploid cells with genome saturating chemical mutagenesis using N-Ethyl-N-nitrosourea, we have developed an unbiased screening system that interrogates single nucleotide variants for their relevance in viral infections. To identify host factors involved in CCHFV infections, we performed resistant screens with a viral RNA replication competent vesicular stomatitis virus, pseudotyped with the glycoproteins of the CCHFV (VSV-CCHF_G). Resistant clones were individually selected, expanded and rescreened using the infectious CCHFV IbAr10200 laboratory strain. Subsequently, whole exome sequencing was conducted on the resistant clones. Three clones showing nearly 100% resistance to CCHFV displayed mutations in the gene encoding for protein we named X. Through the use of knocked out haploid and diploid cells as well as soluble form of this protein on VSV-CCHF_G, CCHFV IbAr 10200 and CCHFV isolate, we showed that this protein is important for CCHFV infection. These data were then confirmed in vivo, in a mice model. By using an unbiaised screening system, our study identified an important factor involved for CCHFV cell entry and infection