Role of lncRNAs in Helicobacter pylori and Epstein-Barr virus associated gastric cancers.

Helicobacter pylori infection is a risk factor for the development of gastric cancer (GC), and the role of co-infection with viruses, such as Epstein-Barr virus, in carcinogenesis cannot be ignored. Furthermore, it is now known that genetic factors such as long non-coding RNAs (lncRNAs) are involved in many diseases, including GC. On the other side, they can also be used as therapeutic goals. Modified lncRNAs can cause aberrant expression of genes encoding proximal proteins, which are essential for the development of carcinoma. In this review, we present the most recent studies on lncRNAs in GC, concentrating on their roles in H. pylori and EBV infections, and discuss some of the molecular mechanisms of these GC-related pathogens. There was also a discussion of the research gaps and future perspectives.

The emerging role of LncRNA AWPPH in multiple cancers: a review study.

Long non-coding RNAs (lncRNAs) are transcribed RNA molecules longer than 200 nucleotides in length that have no protein-coding potential. They are able to react with DNA, RNA, and protein. Hence they involve in regulating gene expression at the epigenetic, transcriptional, post-transcriptional, and translational levels. LncRNAs have been proven to play an important role in human malignancies and prognostic outcomes. In this review, we will comprehensively and functionally discuss the role of a novel identified lncRNA, namely lncRNA WAPPH located on human chromosome 2q13, in various cancers. Increasing research studies have shown that lncRNA AWPPH is deregulated in different malignancies, including breast cancer, gastric cancer, colorectal cancer, ovarian cancer, bladder cancer, leukemia, and others. LncRNA WAPPH serves as an oncogene in tumorigenesis and the development of cancer. Moreover, lncRNA AWPPH is involved in numerous biological processes of solid and blood cancers. Taken together, based on our scrutiny analysis, lncRNA AWPPH can be regarded as a putative biomarker for diagnosis or therapeutic target in human malignancies.

Cloning, purification and characterization of human dentine matrix protein 1(DMP1).

Introduction: Human teeth are composed mainly of dentin, formed by the odontoblasts. Dentin matrix protein 1 (DMP1) is one of odontoblast differentiation's most important growth factors. Human DMP1 has yet to be completely identified or studied. This study aimed to clone and characterize human DMP1. Materials and methods: The DMP1 gene sequence was prepared and cloned by transfection of human 293 cells. Results: The recombinant DMP1 was purified and characterized. Conclusion: The results suggested its future use in dental tissue regeneration and tissue engineering.

Status of Crimean-Congo haemorrhagic fever virus in ticks in Iran: A systematic review with meta-analysis.

Crimean-Congo haemorrhagic fever (CCHF) is a re-emerging viral haemorrhagic fever causing outbreaks in Iran in the last 15 years. In this systematic review and meta-analysis, the status of Crimean-Congo haemorrhagic fever virus (CCHFV) in ticks would be evaluated. PubMed, Google Scholar and Web of Science were searched for peer-reviewed original papers published between 2000 and 1 July 2022. We included papers that evaluated the prevalence of CCHFV in individual ticks using reverse transcription polymerase chain reaction (RT-PCR). The pooled prevalence of CCHFV was 6.0% (95% confidence interval [CI]: 4.5-7.9%), with heterogeneity (I2 = 82.706; P < 0.0001). The prevalence of CCHFV was higher related to regions with above sea level of 1001-1500m (6.4%; 95% CI: 4.3-9.5%), an average temperature of ≤15 °C (8.3%; 95% CI: 5.6-12.0%), latitude of ≥36° (8.1%; 95% CI: 5.2-12.3%), an annual rainfall of 101-300 mm (9.8%; 95% CI: 6.1-15.4%) and humidity of ≥61% (10.2%; 95% CI: 5.1-19.3%). Due to the importance of CCHF, it is better to do new epidemiologic studies on ticks by related organizations and adjacent regions of some provinces in which human cases have been previously reported.

An estimation of global Aeromonas infection prevalence in children with diarrhoea: a systematic review and meta-analysis.

OBJECTIVES: Diarrhoea is the most commonly related disease caused by Aeromonas. To improve knowledge on prevalence, this systematic review and meta-analysis was performed to evaluate the global prevalence of Aeromonas in children with diarrhoea worldwide. METHODS: We systematically searched PubMed, Google scholar, Wiley Online Library, ScienceDirect, and Web of sciences to identify all cross-sectional published papers between 2000 and 10 July 2022. After initial scrutinizing, 31 papers reporting the prevalence of Aeromonas in children with diarrhoea were found to be adequate for meta-analysis. The statistical study was accompanied by using random effects models. RESULTS: A total of 5660 identified papers, 31 cross-sectional studies encompassing 38,663 participants were included in the meta-analysis. The pooled prevalence of Aeromonas in children with diarrhoea worldwide was 4.2% (95% CI 3.1-5.6%). In the subgroup analysis, the highest prevalence was seen among children in Upper middle-income countries with pooled prevalence of 5.1% (95% CI 2.8-9.2%). The prevalence of Aeromonas in children with diarrhoea was higher in countries with populations of over 100 million people (9.4%; 95% CI 5.6-15.3%), and water and sanitation quality score of less than 25% (8.8%; 95% CI 5.2-14.4%). Additionally, Cumulative Forest Plot showed a decreasing trend in the prevalence of Aeromonas infection in children with diarrhoea over time (P = 0.0001). CONCLUSION: The results of this study showed a better comprehension of Aeromonas prevalence in children with diarrhoea on a global scale. As well as our findings showed that much work is still required to decline the burden of bacterial diarrhoea in countries with high populations, low-level income, and unsanitary water.

Gene network analysis of oxaliplatin-resistant colorectal cancer to target a crucial gene using chitosan/hyaluronic acid/protamine polyplexes containing CRISPR-Cas9.

Colorectal cancer (CRC) treatment is dramatically hampered by resistance to oxaliplatin alone or in the combination of irinotecan or 5-fluorouracil and leucovorin. This study aims to design and assess Chitosan/Hyaluronic Acid/Protamine sulfate (CS/HA/PS) polyplexes loaded with CRISPR plasmid for targeting a key gene in cancer drug resistance. Here, recent findings were considered to validate oxaliplatin-resistant CRC-related genes and systems biology approaches employed to detect the critical gene. The polyplexes were characterized according to particle size, zeta potential, and stability. Moreover, carrier toxicity and transfection efficiency were assessed on oxaliplatin-resistant HT-29 cells. The post-transfection evaluations were performed to confirm gene disruption-mediated CRISPR. Eventually, excision cross complementation group 1(ERCC1), a crucial member of the nucleotide excision repair pathway, was selected to be targeted using CRISPR/Cas9 to reverse oxaliplatin resistance in HT-29 cells. CS/HA/PS polyplexes containing CRISPR/Cas9 plasmid exhibited negligible toxicity and comparable transfection efficiency with Lipofectamine™. Following the efficient gene delivery, sequences in CRISPR/Cas9 target sites were altered, ERCC1 was downregulated, and drug sensitivity was successfully restored in oxaliplatin-resistant cells. Findings indicate that CS/HA/PS/CRISPR polyplexes provide a potential strategy for delivering cargo and targeting oxaliplatin resistance-related gene to manipulate drug resistance as a rising concern in cancer therapeutic approaches.

Smart redox-sensitive micelles based on chitosan for dasatinib delivery in suppressing inflammatory diseases.

Dasatinib (DAS) exhibits anti-inflammatory effects by retrieving the balance between inflammatory and anti-inflammatory cytokines secreted by macrophages. The aim of this study was the development of redox-responsive micelles with the potential of passive targeting and on-demand drug release for DAS delivery to macrophages. For this purpose, two molecular weights of chitosan (CHIT) were conjugated to DAS at different molar ratios using 3,3'-dithiodipropionic anhydride (DTDPA) as disulfide bond containing linker to synthesize a series of CHIT-S-S-DAS amphiphilic conjugates. Micelles obtained by the sonication method had particle sizes of 129.3-172.2 nm, zeta potentials of +17.5 to +20.9 mV, drug contents of 0.90-7.20 %, CMC values of 35.3-96.6 µg/ml, and exhibited redox-responsive in vitro drug release. Optimized micelles were non-toxic and dramatically more efficient than non-redox responsive micelles in reducing TNF-α and IL-6 and increasing IL-10 secretion from LPS-stimulated RAW264.7 cells. Furthermore, the redox-responsive micelles were able to reduce the mice paw edema, reduce the plasma levels of pro-inflammatory cytokines and increase plasma level of IL-10, considerably more than free DAS and non-redox responsive micelles in carrageenan-induced mice paw edema model of inflammation.

Ocular delivery of sunitinib-loaded nanoparticles doped in tragacanthic acid hydrogel in treatment of diabetic retinopathy in rats.

OBJECTIVE: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus. This study aimed to compare the effect of sunitinib-loaded poly (glycerol sebacate) (PGS)/gelatin nanoparticles doped in an injectable hydrogel with bevacizumab as a standard treatment of DR. METHODS: The shear-sensitive hydrogel was prepared based on tragacanthic acid (TA) cross-linked with sodium acetate. DR was induced in rats by streptozotocin (STZ), and the animals were injected intravitreally a single dose of 20 µL sunitinib solution in three different concentrations (12.5, 25, and 50 µg/mL), sunitinib-loaded nanoparticles in hydrogel (413 µg/mL) and bevacizumab solution (6.25 mg/mL). The efficacy of the treatments was studied by histological and immunohisitological tests, angiogenesis, and optical coherence tomography (OCT). Vascular endothelial growth factor (VEGF) concentration was measured in the retina. RESULTS: The results revealed that 20 µL of sunitinib with the concentration of 25 µg/mL was effective in DR without any disruption in the retina or any other side effects. This dose was considered the therapeutic dose for nanoparticles. Sunitinib loaded PGS/gelatin nanoparticles that were incorporated in the injectable hydrogel were as effective as bevacizumab in controlling DR. Although sunitinib solution reduced VEGF production and neovascularization in the retina compared to the negative control group, it was not as suitable as the nanoparticles. TA-based hydrogel showed no toxicity on the normal retina, and the angiography and histologic studies confirmed the VEGF results.' CONCLUSIONS: Sunitinib nanoparticles doped in TA hydrogel may be an appropriate substitution of bevacizumab in the treatment of DR.

Rational design of a new variant of Reteplase with optimized physicochemical profile and large-scale production in Escherichia coli.

Structural engineering of the recombinant thrombolytic drug, Reteplase, and its cost-effective production are important goals in the pharmaceutical industry. In this study, a single-point mutant of the protein was rationally designed and evaluated in terms of physicochemical characteristics, enzymatic activity, as well as large-scale production settings. An accurate homology model of Reteplase was used as the input to appropriate tools to identify the aggregation-prone sites, while considering the structural stability. Selected variants underwent extensive molecular dynamic simulations (total 540 ns) to assess their solvation profile and their thermal stability. The Reteplase-fibrin interaction was investigated by docking. The best variant was expressed in E. coli, and Box-Behnken design was used through response surface methodology to optimize its expression conditions. M72R mutant demonstrated appropriate stability, enhanced enzymatic activity (p < 0.05), and strengthened binding to fibrin, compared to the wild type. The optimal conditions for the variant's production in a bioreactor was shown to be 37 ºC, induction with 0.5 mM IPTG, for 2 h of incubation. Under these conditions, the final amount of the produced enzyme was increased by about 23 mg/L compared to the wild type, with an increase in the enzymatic activity by about 2 IU/mL. This study thus offered a new Reteplase variant with nearly all favorable properties, except solubility. The impact of temperature and incubation time on its large-scale production were underlined as well.

Co-Expression of Chaperones for Improvement of Soluble Expression and Purification of An Anti-HER2 scFv in Escherichia Coli.

Background: Single-chain fragment variable (scFv) is one of the most commonly used antibody fragments. They offer some advantages over full-length antibodies, including better penetration to target tissues. However, their functional production has been a challenge for manufacturers due to the potential misfolding and formation of inclusion bodies. Here we evaluated the soluble expression and purification of molecular chaperone co-expression. Materials and Methods: E. coli BL21(DE3) cells were co-transformed with the mixture of plasmids pKJE7 and pET22b-scFv by the electroporation method. First, L-arabinose was added to induce the expression of molecular chaperones, and then IPTG was used as an inducer to start the expression of anti-HER2 scFv. The effect of cultivation temperature and IPTG concentration on soluble expression of the protein with or without chaperones was evaluated. The soluble expressed protein was subjected to native purification using the Ni-NTA affinity column. Results: SDS-PAGE analysis confirmed the successful co-expression of anti-HER2-scFv and DnaK/DnaJ/GrpE chaperones. Co-expression with chaperones and low-temperature cultivation synergistically improved the soluble expression of anti-HER2 scFv. Co-expression with chaperone also exhibited an approximately four-fold increase in the final yield of purified soluble protein. Conclusion: The combination of co-expression with chaperones and low temperature presented in this work may be useful for the improvement of commercial production of other scFvs in E. coli as functionally bioactive and soluble form.

Bioprocess optimization of interferon ß-1-a in Pichia pastoris and its improved inhibitory effect against hepatocellular carcinoma cells

Interferon-ß-1a (INF-ß-1a) has gained significant attention due to its emerging applications in the treatment of different human diseases. Therefore, many researchers have attempted to produce it in large quantities and also in a biologically active form using different expression systems. In the present study, we aimed to improve the expression level of INF-ß-1a by Pichia pastoris using optimization of culture conditions. The codon-optimized INF-ß- 1a gene was cloned into pPICZαA plasmid under the control of alcohol oxidase I (AOX1) promoter. The protein expression was induced using different concentrations of methanol at different pHs and temperatures. The biological activity of produced protein was evaluated by anti-proliferative assay. The ideal culture conditions for the expression of INF-ß-1a by P. pastoris were found to be induction with 2% methanol at pH 7.0 culture medium at 30 C which yielded a concentration of 15.5 mg/L INF-ß-1a in a shake flask. Our results indicate that differences in glycosylation pattern could result in different biological activities as INF- ß-1a produced by P. pastoris could significantly more reduce the cell viability of HepG-2 cells, a hepatocellular carcinoma cell line, than a commercially available form of this protein produced by CHO

A retrospective cross-sectional survey on nosocomial bacterial infections and their antimicrobial susceptibility patterns in hospitalized patients in northwest of Iran.

OBJECTIVE: Nosocomial infections (NIs) are known as one of the remarkable problems in all countries. This study is aimed to estimate the prevalence rate of nosocomial bacterial agents with antimicrobial susceptibility pattern in hospitalized patients. This study was conducted from April 2017 to September 2018, on 4029 hospitalized patients. We set out to recognize the commonest bacterial infections and antimicrobial susceptibility patterns of nosocomial infection. RESULTS: Of the 4029 patients, 509 (12.6%) of them were culture positive. Of these Escherichia coli (E. coli) (98.3%) and Staphylococcus epidermidis (S. epidermidis) (37.5%) were the most abundant bacterial identified in the urinary tract and bloodstream cultures respectively, Moreover, Acinetobacter spp. (100%) and Pseudomonas aeruginosa (22.2%) were the most abundant organisms detected in the respiratory system. According to susceptibility testing results, 370 (80.5%) and 264 (57.3%) in Gram-negatives and 44 (91.7%) and 35 (72.9%) in gram positives isolated strains were classified as multidrug-resistant (MDR) and extensive drug-resistant (XDR) strain respectively. On account of the high prevalence of MDR and XDR bacterial species, there is a pressing need for the expansion of new strategies on antibiotic supervision and infection control to introduce new guideline on empirical antibiotic therapy.

Relationship between Sphk1/S1P and microRNAs in human cancers.

Sphingosine kinases type 1 (SphK1) is a key enzyme in the phosphorylation of sphingosine to sphingosine 1-phosphate (S1P). Different abnormalities in SphK1 functions may correspond with poor prognosis in various cancers. Additionally, upregulated SphK1/S1P could promote cancer cell proliferation, angiogenesis, mobility, invasion, and metastasis. MicroRNAs as conserved small noncoding RNAs play major roles in cancer initiation, progression, metastasis, etc. Their posttranscriptionally mechanisms could affect the development of cancer growth or tumorigenesis suppression. The growing number of studies has described that various microRNAs can be regulated by SphK1, and its expression level can also be regulated by microRNAs. In this review, the relationship of SphK1 and microRNA functions and their interaction in human malignancies have been discussed. Based on them novel treatment strategies can be introduced.

Design and production of new chimeric reteplase with enhanced fibrin affinity: a theoretical and experimental study.

Plasminogen activators (PAs) are widely used for treatment of disorders caused by clot formation. Fibrin specific PAs are safe drugs from this group because of reducing the incidence of hemorrhage. The newer generation of PAs like tenecteplase, reteplase and desmoteplase were designed with the aim of achieving desirable properties such as improving specificity and affinity to fibrin and increasing half-life. Protein engineering and using of theoretical methods can help to rational and reliable design of new PAs with a set of favorable properties. In the present study, two new chimeric reteplase named M1-chr and M2-chr were designed with the aim of enhancing fibrin affinity also some potential properties include of increasing resistance to plasminogen activator inhibitor-1 and decreasing neurotoxicity. So, finger domain of desmoteplase was added to reteplase as a high fibrin specific domain. Some other point mutations were considering to achieve other mentioned properties. Three dimensional structure of wild-type reteplase and mutants were created by homology modeling and were evaluated by molecular dynamic simulation. Then, mutants docked to fibrin by HADDOCK web tools. Result of theoretical section verified the stability of mutants' structures. Also showed better interaction between M1-chr with fibrin than M2-chr. Wild-type and mutants were produced in bacterial expression system. Experimental assessment showed both mutants have appropriate enzymatic activity also 1.9-fold fibrin binding ability compared to wild-type. Therefore, this study offers new thrombolytic drugs with desirable properties specially enhanced fibrin affinity so they can represent a promising future in cost-effective production of favorable thrombolytic drugs.Communicated by Ramaswamy H. Sarma.

Optimization of solvent media to solubilize TEV protease using response surface method.

BACKGROUND AND PURPOSE: Tobacco etch virus (TEV) protease, a 27 KDa protein, consists of the catalytic domain of nuclear inclusion a (NIa) protein produced by Tobacco etch virus. Because of its unique sequence, TEV protease is used for purging fusion tags from proteins. It also has many advantages such as stability and activity in a board range of temperature and pH and overproduction in Escherichia coli and these benefits make this protease valuable. Despite all these benefits, TEV protease has problems like low solubility (less than 1 mg/mL). There are methods for enhancing protein solubility and in this study, the effect of additives during cell lysis was studied. EXPERIMENTAL APPROACH: Eleven different additives that made twelve different lysis buffers were used and their effect on TEV protease solubility analyzed by Plackett-Burman and response surface methodology methods. FINDINGS / RESULTS: Three best effective additives on TEV solubility (L-proline, sodium selenite, and CuCl2) were selected according to software analysis and the best concentration of them was applied to optimize TEV protease solubility. CONCLUSION AND IMPLICATIONS: The obtained results provided the composition of an optimum solvent for obtaining soluble TEV protease.

Prevalence of Occult Hepatitis B Virus Infection in Hemodialysis Patients Using Nested PCR.

BACKGROUND: Occult hepatitis B infection (OBI) is defined as the lack of detectable HBsAg in serum, despite the presence of intrahepatic viral DNA, and low levels of covalently closed circular DNA (cccDNA). Since the hemodialysis patients are at a greater disadvantage if they are a carrier of Hep B, as it can lead to OBI this study was designed to determine the prevalence of OBI in hemodialysis patients residing in Zanjan, Iran. METHODS: We conducted an anti-HBc test (ELISA) on 166 HBsAg negative hemodialysis patient samples. OBI was evaluated using seropositive (anti-HBc and/or anti-HBs) and seronegative (anti-HBc and anti-HBs) using nested PCR. RESULTS: Out of the total hemodialysis patients sampled, the study consisted of 58.4% male and 41.6% female participants. The age of the study group ranged from 58.89±15.49, and had received approximately 28.27±27.43 years of dialysis. Additionally, 5.4% of patients had a history of blood transfusions, while 58.4% were vaccinated against the hepatitis B virus (HBV). Moreover, 23.5% patients were anti-HBc positive, while 76.5% patients tested negative. Lastly, 66.3% of the patients were positive for anti-HBs, whereas 33.7% were negative for anti-HBs. Overall, the study revealed that the prevalence of OBI was 6%, and HBV DNA was detected in 2.1% of individuals who were vaccinated against hepatitis B (p < 0.01). CONCLUSION: Though no significant difference between the prevalence of OBI to the patients' age, sex, duration of dialysis, or history of blood transfusion was identified, however, a strong correlation between the prevalence of OBI to HBV vaccination was found.

Rational design of a new mutant of tobacco etch virus protease in order to increase the in vitro solubility.

BACKGROUND AND PURPOSE: Tobacco etch virus (TEV) protease is a protease with high sequence specificity which is useful for the cleavage of fusion proteins. A major limitation of this enzyme is its relatively poor solubility. This study aimed to investigate the effects of some suggested mutations by online tools and molecular dynamics simulation to improve the solubility of TEV protease in vitro. EXPERIMENTAL APPROACH: We designed a rational multi-stage process to determine the solubilizing mutations of TEV protease. At the first stage, all the possible mutations were predicted using online tools such as PoPMuSiC and Eris servers, in which five mutations include N23F, N23L, Q74L, Q74V, and Q74I were suggested for further studies. In the next step, the three dimensional structure of the wild type (WT) and the best mutations were subjected to molecular dynamic simulations to evaluate the dynamic behaviour of the obtained structures. The selected mutation was introduced into the structure using site-directed mutagenesis and expressed in Escherichia coli BL21DE3. After purification, solubility and activity of the purified mutant and WT-TEV proteases were assayed. FINDINGS /RESULTS: By considering the analysis of various factors such as structural and solubility properties, one mutant, N23F, was selected for in vitro studies which led to a 1.5 times increase in the solubility compared to the WT while its activity was decreased somewhat. CONCLUSION AND IMPLICATIONS: We propose N23F mutation, according to computational and experimental analyses for TEV proteases which resulted in a 150% increase in solubility compared to the WT.

Investigation of Supercharging as A Strategy to Enhance the Solubility and Plasminogen Cleavage Activity of Reteplase.

BACKGROUND: Reteplase, the recombinant form of tissue plasminogen activator, is a thrombolytic drug with outstanding characteristics, while demonstrating limited solubility and reduced plasminogen activation. Previously, we in silico designed a variant of Reteplase with positively supercharged surface, which showed promising stability, solubility and activity. This study was devoted to evaluation of the utility of supercharging technique for enhancing these characteristics in Reteplase. OBJECTIVE: To test the hypothesis that reinforced surface charge of a rationally-designed Reteplase variant will not compromise its stability, will increase its solubility, and will enhance its plasminogen cleavage activity. MATERIALS AND METHODS: Supercharged Reteplase coding sequence was cloned in pDest527 vector and expressed in E. coli BL21 (DE3). The expressed protein was extracted by cell disruption. Inclusion bodies were solubilized using guanidine hydrochloride, followed by dialysis for protein refolding. After confirmation with SDS-PAGE and western blotting, extracted proteins were assayed for solubility and tested for bioactivity. RESULTS: SDS-PAGE and western blot analysis confirmed the successful expression of Reteplase. Western blot experiments showed most of Reteplase expressed in the insoluble form. Plasminogen cleavage assay showed significantly higher activity of the supercharged variant than the wild type protein (P < 0.001). The stability of the supercharged variant was also comparable to the wild type. CONCLUSION: Our findings, i.e. the contribution of the surface supercharging technique to retained stability, enhanced plasminogen cleavage activity, while inefficiently changed solubility of Reteplase, contain implications for future designs of soluble variants of this fibrinolytic protein drug.

Shear sensitive injectable hydrogels of cross-linked tragacanthic acid for ocular drug delivery: Rheological and biological evaluation.

Drug delivery to posterior segment of eye has always been challenging. The aim of the present study was to provide a novel injectable, shear sensitive hydrogel based on tragacanthic acid (TA) with three kinds of acetate salts as cross-linker. Rheological properties by strain and shear stress sweep measurements and also dynamic rheological experiments including frequency and time sweep measurements were studied. Biological studies comprising, cell culture, Draize test on rabbit eyes and histopathological tests were done. The results showed the optimized hydrogel was biocompatible, injectable and owning acceptable firmness in rest state after injection. Healing time of the hydrogel was 46 s and was shear-sensitive. It showed no cytotoxicity on HUVEC cells. No allergic reaction was seen in Draize test and histological examination showed integrity of the retinal layers with no evidence of pathological changes, such as deformations, degeneration, or inflammation. TA hydrogel is promising in ocular drug delivery.