Construction of a three-component regulatory network of transcribed ultraconserved regions for the identification of prognostic biomarkers in gastric cancer

Altered expression and functional roles of the transcribed ultraconserved regions (T-UCRs), as genomic sequences with 100% conservation between the genomes of human, mouse, and rat, in the pathophysiology of neoplasms has already been investigated. Nevertheless, the relevance of the functions for T-UCRs in gastric cancer (GC) is still the subject of inquiry. In the current study, we first used a genome-wide profiling approach to analyze the expression of T-UCRs in GC patients. Then, we constructed a three-component regulatory network and investigated potential diagnostic and prognostic values of the T-UCRs. The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset was used as a resource for the RNA-sequencing data. FeatureCounts was utilized to quantify the number of reads mapped to each T-UCR. Differential expression analysis was then conducted using DESeq2. In the following, interactions between T-UCRs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were combined into a three-component network. Enrichment analyses were performed and a protein–protein interaction (PPI) network was constructed. The R Survival package was utilized to identify survival-related significantly differentially expressed T-UCRs (DET-UCRs). Using an in-house cohort of GC tissues, expression of two DET-UCRs was furthermore experimentally verified. Our results showed that several T-UCRs were dysregulated in TCGA-STAD tumoral samples compared to nontumoral counterparts. The three-component network was constructed which composed of DET-UCRs, miRNAs, and mRNAs nodes. Functional enrichment and PPI network analyses revealed important enriched signaling pathways and gene ontologies such as “pathway in cancer” and regulation of cell proliferation and apoptosis. Five T-UCRs were significantly correlated with the overall survival of GC patients. While no expression of uc.232 was observed in our in-house cohort of GC tissues, uc.343 showed an increased expression, although not statistically significant, in gastric tumoral tissues. The constructed three-component regulatory network of T-UCRs in GC presents a comprehensive understanding of the underlying gene expression regulation processes involved in tumor development and can serve as a basis to investigate potential prognostic biomarkers and therapeutic targets.     

High Bone Mass in Mice Lacking Cx37 Because of Defective Osteoclast Differentiation

Connexin (Cx) proteins are essential for cell differentiation, function, and survival in all tissues with Cx43 being the most studied in bone. We now report that Cx37, another member of the connexin family of proteins, is expressed in osteoclasts, osteoblasts, and osteocytes. Mice with global deletion of Cx37 (Cx37^−/−) exhibit higher bone mineral density, cancellous bone volume, and mechanical strength compared with wild type littermates. Osteoclast number and surface are significantly lower in bone of Cx37^−/− mice. In contrast, osteoblast number and surface and bone formation rate in bones from Cx37^−/− mice are unchanged. Moreover, markers of osteoblast activity ex vivo and in vivo are similar to those of Cx37^+/+ littermates. sRANKL/M-CSF treatment of nonadherent Cx37^−/− bone marrow cells rendered a 5-fold lower level of osteoclast differentiation compared with Cx37^+/+ cell cultures. Further, Cx37^−/− osteoclasts are smaller and have fewer nuclei per cell. Expression of RANK, TRAP, cathepsin K, calcitonin receptor, matrix metalloproteinase 9, NFATc1, DC-STAMP, ATP6v0d1, and CD44, markers of osteoclast number, fusion, or activity, is lower in Cx37^−/− osteoclasts compared with controls. In addition, nonadherent bone marrow cells from Cx37^−/− mice exhibit higher levels of markers for osteoclast precursors, suggesting altered osteoclast differentiation. The reduction of osteoclast differentiation is associated with activation of Notch signaling. We conclude that Cx37 is required for osteoclast differentiation and fusion, and its absence leads to arrested osteoclast maturation and high bone mass in mice. These findings demonstrate a previously unrecognized role of Cx37 in bone homeostasis that is not compensated for by Cx43 in vivo.     

The single source preparation of rod-like mercury sulfide nanostructures via hydrothermal method

High-quality and high-yield rod-like HgS dendrites with cubic structure was synthesized by a wet chemical route, without using any surfactant and organic solvents at 180 °C for 5 h, by using Hg(NO₃)₂·H₂O and thioglycolic acid (TGA) as starting reagents. The obtained HgS with different morphologies and sized were characterized by Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray analysis (EDX), and X-ray diffraction (XRD). The effects of reaction parameters, such as temperature, precursor concentration and reaction time on the morphology and particle size of products were investigated. Our experimental results showed that temperature reaction played key role in the final morphology of HgS. The morphology of HgS nanostructures could be changed from rod-like dendrites to nanoparticles by only decreased temperature reaction to 110 °C. In the present study the possible mechanism of HgS nanoparticles growth to dendrites in the aqueous solution was also discussed and the optical properties rod-like HgS dendrites were investigated by ultraviolet-visible (UV-Vis) spectroscopy.     

Molecular Dynamics Study of the Human Beta-defensins 2 and 3 Chimeric Peptides with the Cell Membrane Model of Pseudomonas aeruginosa

International Journal of Peptide Research and Therapeutics - Pseudomonas aeruginosa is a unique microorganism among the antibiotic-resistant microbial pathogens. Among the various therapeutic...     

An epitopic approach to designing and characterization of a multiple antigenic polypeptide against Botulinum neurotoxins A and E

Botulinum neurotoxin (BoNT) serotypes A, B and E are most frequently associated with human botulism. Recombinant vaccines against BoNTs are usually based on one or more domain(s) of the toxin molecule. In this study, we investigate a new-designed multiple antigenic polypeptide for serotypes A and E (MAP/AE), containing two linear epitopes from each serotype. A synthetic gene was used to express the recombinant MAP/AE, in E. coli. Anti-MAP/AE antibodies were produced by injecting the purified MAP/AE to Balb/C mice. The interactivity of these antibodies and BoNT/A and E has been shown by ELISA. High titers of anti-MAP/AE antibodies were detected in mice sera. The anti-MAP/AE antibody titer is clearly detectable even at 25,600 dilution level. The anti-MAP/AE antibodies bound to both BoNT/A and BoNT/E holotoxin molecules. Neutralization ability of the antibodies for both toxin serotypes was determined, by an inhibitory ELISA assay. Results are suggestive of the feasibility of this epitope targeting strategy to develop novel multivalent recombinant vaccines against BoNTs.     

Glutathione S-transferase genetic polymorphisms (GSTM1, GSTT1 and GSTO2) in three Iranian populations

Genetic polymorphisms in genes encoding glutathione S-transferases M1 (GSTM1; a member of class mu), T1 (GSTT1; a member of class theta) and O2 (GSTO2; a member of class omega) have been defined previously. Studies have revealed that there were significant differences between populations for allelic frequencies of GSTT1, GSTM1 and GSTO2 N412D polymorphisms. To get more insight into the genetic structure of Iranian populations the present study was done on Iranian Georgians living in Frydoonshahr (Isfahan province) and two Persian populations who living in Shiraz (Fars province) and Frydoonshahr. Study subjects consisted of 401 unrelated healthy individuals. From these 121 were Georgians. The remaining subjects were Persians from either Frydoonshahr (n = 34) or Shiraz (n = 246). The genetic polymorphism of GSTT1, GSTM1 and GSTO2 N412D was detected by PCR-based method. The frequency of GSTT1 null genotype in Georgian and Persians of Frydoonshahr and Shiraz was 15.7, 35.2 and 24.8%, respectively. There was significant difference between these populations for the distributions of the GSTT1 genotypes (χ² = 7.00, df = 2, P = 0.030). No significant difference was observed between these populations for polymorphisms of GSTM1 (χ² = 1.682, df = 2, P = 0.431) and GSTO N142D (χ² = 4.622, df = 4, P = 0.328). The prevalence of GSTT1 null genotype in Iranian Georgians showed significant difference with Persians and other Asian countries, but it seems to be similar with the frequency which was reported from European populations.     

Renal function and risk factors of moderate to severe chronic kidney disease in Golestan Province, northeast of Iran

Introduction

The incidence of end-stage renal disease is increasing worldwide. Earlier studies reported high prevalence rates of obesity and hypertension, two major risk factors of chronic kidney disease (CKD), in Golestan Province, Iran. We aimed to investigate prevalence of moderate to severe CKD and its risk factors in the region.

Methods

Questionnaire data and blood samples were collected from 3591 participants (≥18 years old) from the general population. Based on serum creatinine levels, glomerular filtration rate (GFR) was estimated.

Results

High body mass index (BMI) was common: 35.0% of participants were overweight (BMI 25–29.9) and 24.5% were obese (BMI ≥30). Prevalence of CKD stages 3 to 5 (CKD–S3-5), i.e., GFR <60 mL/min/1.73 m², was 4.6%. The odds ratio (OR) and 95% confidence interval (95% CI) for the risk of CKD–S3-5 associated with every year increase in age was 1.13 (1.11–1.15). Men were at lower risk of CKD–S3-5 than women (OR = 0.28; 95% CI 0.18–0.45). Obesity (OR = 1.78; 95% CI 1.04–3.05) and self-reported diabetes (OR = 1.70; 95% CI 1.00–2.86), hypertension (OR = 3.16; 95% CI 2.02–4.95), ischemic heart disease (OR = 2.73; 95% CI 1.55–4.81), and myocardial infarction (OR = 2.69; 95% CI 1.14–6.32) were associated with increased risk of CKD–S3-5 in the models adjusted for age and sex. The association persisted for self-reported hypertension even after adjustments for BMI and history of diabetes (OR = 2.85; 95% CI 1.77–4.59).

Conclusion

A considerable proportion of inhabitants in Golestan have CKD–S3-5. Screening of individuals with major risk factors of CKD, in order to early detection and treatment of impaired renal function, may be plausible. Further studies on optimal risk prediction of future end-stage renal disease and effectiveness of any screening program are warranted.     

Sulfonamide-1,2,4-triazole derivatives as antifungal and antibacterial agents: synthesis, biological evaluation, lipophilicity, and conformational studies

A series of 10 new 5-[2-(substituted sulfamoyl)-4,5-dimethoxy-benzyl]-4aryl-s-triazole-3-thiones were synthesized and evaluated for in vitro antifungal and antibacterial activity. All compounds tested showed significant antifungal activity against all the micromycetes, compared to the commercial fungicide bifonazole. Differences in their activity depend on the substitution of different reactive groups. More specifically, best antifungal activity among synthetic analogues was shown with N-dimethylsulfamoyl group. All the compounds tested against bacteria showed the same activity as the commercial agent streptomycin, except for Enterobacter cloacce and Salmonella species. Chloramphenicol showed lower bactericidal effect than the synthetic compounds. Furthermore, it is apparent that different compounds reacted in different ways against bacteria. Gram (-) bacteria seem to be more sensitive to these compounds than Gram (+) species. An effort was made to correlate the above-mentioned differences in activity with lipophilicity studies. Furthermore, molecular modeling was used to obtain the main conformational features of this class of molecules for future structure-activity relationship studies.     

Role of MutS homolog 2 (MSH2) in intestinal myofibroblast proliferation during Crohn's disease stricture formation

Tissue remodeling and mesenchymal cell accumulation accompanies chronic inflammatory disorders involving joints, lung, vasculature, and bowel. Chronic inflammation may alter DNA-mismatch repair (MMR) systems in mesenchymal cells, but is not defined in Crohn's disease (CD) and its associated intestinal remodeling and stricture formation. We determined whether DNA-MMR alteration plays a role in the pathogenesis of CD tissue remodeling. Control and CD bowel tissues were used to generate primary cultures of muscularis mucosa myofibroblasts, which were assessed directly or following stimulation with TNF-alpha/LPS or H2O2. MutS homolog (MSH)2, MSH3, and MSH6 expression in tissues and myofibroblasts was determined. Immunohistochemical staining revealed an increased expression of MSH2 in CD muscularis mucosa and submucosal tissues compared with controls or uninvolved CD tissue, and MSH2 expression was increased in CD myofibroblasts compared with control cells. TNF-alpha/LPS and H2O2 further enhanced MSH2 expression in both control and CD cells, which were decreased by simvastatin. There were no significant changes in MSH3 and MSH6 expression. Proliferating cell nuclear antigen and Ki67 staining of CD tissue revealed increased proliferation in the muscularis mucosa and submucosa of chronically inflamed tissues, and enhanced proliferation was seen in CD myofibroblasts compared with controls. Simvastatin reversed the effects of inflammatory stress on the DNA-MMR and inhibited proliferation of control and CD myofibroblasts. Gene silencing with MSH2 siRNA selectively decreased CD myofibroblast proliferation. These data demonstrate a potential role for MSH2 in the pathogenesis of nonneoplastic mesenchymal cell accumulation and intestinal remodeling in CD chronic inflammation.     

Cytokine response following transthoracic and transhiatal esophagectomy in patients with esophageal cancer

Curative esophageal resection is usually performed using either a transthoracic (TT) or transhiatal (TH) approach. Forty patients with esophageal squamous cell carcinoma who underwent esophagectomies (24 TT and 16 TH), 12 patients who underwent surgery for gastric cancer, and 16 healthy individuals were enrolled in this study. Blood samples were taken from the patients, pre- and post-surgery. The levels of synthesis of T-helper 1 and 2 cytokines were assessed in vitro in the presence of mitogen. Our initial data indicated that at admission, 24 h before surgery, blood cells from both groups of esophageal cancer patients produced significantly lower levels of the Th1 cytokines, IFN-gamma and IL-2 than those from cells of healthy donors. Cells collected from gastric cancer patients prior to surgery produced intermediate levels of IFN-gamma and IL-2: significantly lower than healthy donors, and slightly more (non-significant) than esophageal cancer patients. These results contrast with those for the production of Th2 cytokines prior to surgery, which did not differ significantly between any groups: either the esophageal or gastric cancer patients, or healthy donors. Th1 and Th2 cytokine production was then studied using blood cells collected seven days after surgery. Cells from both groups of esophageal cancer patients, undergoing either TT or TH surgery, produced significantly lower levels of the Th1 cytokines, IFN-gamma and IL-2 than those from cells of gastric cancer patients who had undergone surgery. Postoperative and preoperative production was compared. For patients who had undergone TT esophageal resection, we observed that the post-operative production of IL-2, IL-5 and IL-13 was significantly lower than the pre-operative production of those cytokines. Such reduced post-operative compared to pre-operative production was only significant in patients who had undergone TT esophagectomy. A similar, but non-significant trend was observed in patients who had undergone either TH esophagectomy, or gastrectomy. The results indicate that digestive tract cancer patients, both esophageal and gastric, have (prior to surgery), a significantly reduced, basal, mitogen-induced production of Th1 but not of Th2 cytokine. Post-operatively, a significantly reduced production of Th1 and Th2 cytokines, except for IFN-gamma, was observed only in patients who had undergone surgical esophageal resection using the TT method.