Screening the critical protein subnetwork to delineate potential mechanisms and protective agents associated with arsenic-induced cutaneous squamous cell carcinoma: A toxicogenomic study

Recent studies show that complex mechanisms are involved in arsenic-induced malignant transformation of cells. This study aimed to decipher molecular mechanisms associated with arsenic-induced cutaneous squamous cell carcinoma (cSCC) and suggest potential protective factors. RNA-seq-based differentially expressed genes between arsenic-exposed human keratinocytes (HaCaT) and controls were used to construct a protein-protein interaction (PPI) network and discover critical subnetwork-based mechanisms. Protective compounds against arsenic toxicity were determined and their target interactions in the core sub-network were identified by the comparative toxicogenomic database (CTD). The binding affinity between the effective factor and target was calculated by molecular docking. A total of 15 key proteins were screened out as critical arsenic-responsive subnetwork (FN1, IL-1A, CCN2, PECAM1, FGF5, EDN1, FGF1, PXDN, DNAJB9, XBP1, ERN1, PDIA4, DNAJB11, FOS, PDIA6) and 7 effective protective agents were identified (folic acid, quercetin, zinc, acetylcysteine, methionine, catechin, selenium). The GeneMANIA predicted detailed interactions of the subnetwork and revealed terms related to unfolded protein response as the main processes. FN1, IL1A and CCN2, as top significant genes, had good docking affinity with folic acid and quercetin, as selected key compounds. Integration of gene expression and protein-protein interaction related to arsenic exposure in cSCC explored the potential mechanisms and protective agents.

Therapeutic Potential of Resveratrol and Atorvastatin Following High-Fat Diet Uptake-Induced Nonalcoholic Fatty Liver Disease by Targeting Genes Involved in Cholesterol Metabolism and miR33

The present study was designed to evaluate the effects of resveratrol, atorvastatin, and a combination of resveratrol and atorvastatin on expression levels of genes involved in the cholesterol metabolic pathway in the fatty liver of C57/BL6 mice. A high-fat diet was used to induce fatty liver in C57/BL6 mice treated with resveratrol, atorvastatin, or a combination of resveratrol and atorvastatin. Pathological and biochemical studies were performed. In addition, hepatic gene expressions of ATP-binding cassette transporter A1 (ABCA1), ABCG1, liver X receptor (LXR)α, scavenger receptor B1 (SR-B1), low-density lipoprotein receptor (LDLR), and miR33 were evaluated by the real-time PCR method, and the Western blot method was used to measure the ABCA1, ABCG1, and LXRα protein levels. Resveratrol and atorvastatin reduced fat accumulation in the liver of mice with fatty liver, and this effect was correlated with decreased blood glucose levels, triglyceride, cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol blood levels compared with the positive control (PC) group. In contrast to the animals of the PC group, fatty liver groups that received resveratrol and atorvastatin had a significant effect on the mRNA levels of the ABCA1, ABCG1, LXRα, SR-B1, LDLR, and miR33 genes. Moreover, resveratrol and atorvastatin administration elevated ABCA1 and ABCG1 and reduced LXRα protein expression. Obtained results showed that resveratrol and atorvastatin combination therapy can improve nonalcoholic fatty liver disease by targeting genes involved in cholesterol metabolism and miR33.

Metabolomic study of serum in patients with invasive ductal breast carcinoma with LC-MS/MS approach

BACKGROUND

Invasive ductal carcinoma (IDC) is the most common type of breast cancer so its early detection can lead to a significant decrease in mortality rate. However, prognostic factors for IDC are not adequate and we need novel markers for the treatment of different individuals. Although positron emission tomography and magnetic resonance imaging techniques are available, they are based on morphological features that do not provide any clue for molecular events accompanying cancer progression. In recent years, "omics" approaches have been extensively developed to propose novel molecular signatures of cancers as putative biomarkers, especially in biofluids. Therefore, a mass spectrometry-based metabolomics investigation was performed to find some putative metabolite markers of IDC and potential metabolites with prognostic value related to the estrogen receptor, progesterone receptor, lymphovascular invasion, and human epidermal growth factor receptor 2.

METHODS

An untargeted metabolomics study of IDC patients was performed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The multivariate principal component analysis by XCMS online built a model that could separate the study groups and define the significantly altered m/z parameters. The most important biological pathways were also identified by pathway enrichment analysis.

RESULTS

The results showed that the significantly altered metabolites in IDC serum samples mostly belonged to amino acids and lipids. The most important involved pathways included arginine and proline metabolism, glycerophospholipid metabolism, and phenylalanine, tyrosine, and tryptophan biosynthesis.

CONCLUSIONS

Significantly altered metabolites in IDC serum samples compared to healthy controls could lead to the development of metabolite-based potential biomarkers after confirmation with other methods and in large cohorts.

Metformin reduces lipid accumulation in HepG2 cells via downregulation of miR-33b

INTRODUCTION

Here, we aimed to investigate whether the beneficial effects of metformin on lipid accumulation is mediated through regulation of miR-33b.

METHODS

The expression of the genes and miRNAs and protein levels were evaluated using real-time PCR and western blot, respectively. To investigate the potential role of miR-33b in lipid accumulation, the mimic of the miR-33b was transfected into HepG2 cells.

RESULTS

We found that metformin reduces high glucose-induced lipid accumulation in HepG2 cells through inhibiting of SREBP1c and FAS and increasing the expression of CPT1 and CROT. Overexpression of miR-33b significantly prevented the decreasing effect of metformin on lipid content and intra and extra triglyceride levels. Importantly, miR-33b mimic inhibited the increasing effects of metformin on the expression of CPT1 and CROT.

CONCLUSION

These findings suggest that metformin attenuates high glucose-induced lipid accumulation in HepG2 cell by downregulating the expression of miR-33b.

Serum cortisol concentration and COVID-19 severity: a systematic review and meta-analysis

The novel COVID-19 outbreak is a major health threat to human beings with multiorgan injuries. However, its endocrine system manifestations are much less studied. In this study, we aimed to reassess the available findings on the association between cortisol level and severity of COVID-19 infection. We conducted a systematic search on Medline/PubMed, Scopus, Web of Science, and Cochrane Library databases. To pool data, a random-effects model was performed depending on the heterogeneity among studies. Sensitivity analysis was also carried out by removing each study systematically. In addition, subgroup and meta-regression analyses were performed depending on the presence of the variables of sex and age. Subsequently, 11 studies (5 observational studies and 6 case reports) were included in the meta-analysis. Pooled analysis on the observational studies showed significantly higher levels of cortisol in patients with severe COVID-19 in comparison with those with mild-to-moderate COVID-19 (standardized mean difference: 1.48 µg/dL; 95% CI (0.51 to 2.46); p=0.003). Assessment of the results of case reports revealed that the patients with severe COVID-19 demonstrated higher cortisol levels than the patients with mild-to-moderate COVID-19. No publication bias was observed using the Begg’s (p=0.08) and Egger’s tests (p=0.09). Meta-regression illustrated a significant correlation between cortisol levels with sex. The serum cortisol level seems to be higher in patients with severe COVID-19 infection. This finding could be helpful to detect patients with poor prognosis at early stages of the disease, although age and sex may modify this level.

Mass Spectrometry-Based Proteomics Research to Fight COVID-19: An Expert Review on Hopes and Challenges

The COVID-19 pandemic caused by the severe acute respiratory syndrome (SARS)-CoV-2 infection is a systemic disease and a major planetary health burden. While SARS-CoV-2 impacts host biology extensively, our knowledge of these alterations from a systems perspective remains incomplete. Moreover, there is currently only a limited description of this systemic disease. For precision diagnosis and treatment of SARS-CoV-2, multiomics technologies and systems science research offer significant prospects. This expert review offers a critical analysis of the prospects and challenges of the emerging mass spectrometry-based proteomics approaches to the study of COVID-19 as seen through a systems medicine lens. We also discuss the ways in which proteomics is poised to offer hope for diagnostics and therapeutics innovation on SARS-CoV-2 infection as the disease transitions from a pandemic to an endemic disease, and thus further challenging the health systems and services worldwide in the coming decade. Proteomics is an important high-throughput technology platform to achieve a functional overview of the ways in which COVID-19 changes host biology, and hence, can help identify possible points of entry for innovation in medicines and vaccines, among others.

Molecular pathways involved in COVID-19 and potential pathway-based therapeutic targets

Deciphering the molecular downstream consequences of severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 infection is important for a greater understanding of the disease and treatment planning. Furthermore, greater understanding of the underlying mechanisms of diagnostic and therapeutic strategies can help in the development of vaccines and drugs against COVID-19. At present, the molecular mechanisms of SARS-CoV-2 in the host cells are not sufficiently comprehended. Some of the mechanisms are proposed considering the existing similarities between SARS-CoV-2 and the other members of the β-CoVs, and others are explained based on studies advanced in the structure and function of SARS-CoV-2. In this review, we endeavored to map the possible mechanisms of the host response following SARS-CoV-2 infection and surveyed current research conducted by in vitro, in vivo and human observations, as well as existing suggestions. We addressed the specific signaling events that can cause cytokine storm and demonstrated three forms of cell death signaling following virus infection, including apoptosis, pyroptosis, and necroptosis. Given the elicited signaling pathways, we introduced possible pathway-based therapeutic targets; ADAM17 was especially highlighted as one of the most important elements of several signaling pathways involved in the immunopathogenesis of COVID-19. We also provided the possible drug candidates against these targets. Moreover, the cytokine-cytokine receptor interaction pathway was found as one of the important cross-talk pathways through a pathway-pathway interaction analysis for SARS-CoV-2 infection.

Discovery of Novel Pyruvate Kinase Inhibitors Against Leishmania major Among FDA Approved Drugs Through System Biology and Molecular Docking Approach

Objectives

Leishmaniasis is one of the common forms of neglected parasitic diseases that cause a worldwide disease burden without any effective therapeutic strategy. Control of the disease currently relies on chemotherapy because most of the available drugs have toxic side-effects and drug-resistant strains have emerged. Therefore, the development of new therapeutic strategies to treat patients for leishmaniasis has become a priority. The first step in drug discovery is to identify an effective drug target by methods such as system biology. Protein kinases are a promising drug target for different diseases. Due to lack of a functional krebs cycle in Leishmania species, they use glycolysis as the only source of ATP generation. Pyruvate kinase is the enzyme involved in the last step of glycolysis and considered as essential enzyme for the Leishmania survival.

Materials and Methods

This study sought to discover FDA approved compounds against the leishmanial pyruvate kinase protein. Our approach involved using quantitative proteomics, protein interaction networks and docking to detect new drug targets and potent inhibitors.

Results

Pyruvate kinase was determined as the potential drug target based on protein network analysis. The docking studies suggested trametinib and irinotecan with high binding energies of -10.4 and -10.3 kcal/mol, respectively, as the potential chemotherapeutic agents against L. major.

Conclusion

This study demonstrated the importance of integrating protein network analysis and molecular docking to identify new anti-leishmanial drugs. These potential inhibitors constitute novel drug candidates that should be tested in vitro and in vivo to determine their potential as an alternative chemotherapy in the treatment of leishmaniasis.

Increased the circulating levels of malondialdehyde in patients with obstructive sleep apnea: a systematic review and meta-analysis

PURPOSE

Obstructive sleep apnea (OSA) is a prevalent sleep disorder associated with increased risk of cardiovascular disease. Several studies have demonstrated elevated oxidative stress in patients with OSA. This oxidative stress is a direct inducer of lipid peroxidation. Malondialdehyde (MDA), a robust marker of lipid peroxidation, has been evaluated in patients with OSA but results have been inconsistent. The present systematic review and meta-analysis was performed to quantify the circulating levels of MDA in patients with OSA compared to controls.

METHODS

Search was performed in data bases of PubMed, Scopus, EMBASE, Web of Science, and Cochrane library, to find out those studies that measured MDA in patients with OSA compared to controls.

RESULTS

The search produced 563 records and after removing duplicates, 383 records remained. Screening by title and abstract and the evaluation of the full text resulted in the selection of 14 articles, which were included in the meta-analysis. Pooled analysis demonstrated higher levels of MDA in the patients compared to the controls (SMD (95% CI): 1.18 (0.68, 1.68), p < 0.0001).

CONCLUSION

The results of this meta-analysis demonstrated considerable elevation of MDA in patients with OSA compared to controls. The meta-analysis also indicated a positive association of MDA levels with the degree of severity of OSA. These results suggest a state of increased lipid peroxidation in patients with OSA.

Identification of differential protein expression and putative drug target in metacyclic stage of Leishmania major and Leishmania tropica: A quantitative proteomics and computational view

Cutaneous leishmaniasis (CL) is an infectious disease that commonly caused by Leishmania (L.) major and L.tropica. Recently there has been a growing interest in proteomics analysis on Leishmania for drug target discovery. Therefore, we aimed to distinguish proteins which might be characteristic for each of the species from those shared by both to the detection of drug targets, which may become helpful for designing new drugs for CL. To identify differences in protein profiles of L. major and L. tropica, we conducted a Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) analysis. Totally 67 differentially expressed proteins (DEPs) (fold change> 2 and p < 0.05) were identified between species. Of these, 42 and 25 proteins were up-regulated in L. major and L. tropica, respectively. Several enriched GO terms were identified via biological process of up-regulated proteins. Furthermore, the small molecule metabolic process and translation were detected as significant biological processes for up-regulated proteins in L. major, while translation was identified for L. tropica. Also, KEGG analysis has revealed glycolysis/gluconeogenesis and translation as the top pathways in the proteins up-regulated in L. major and L. tropica, respectively. Finally glycosomal malate dehydrogenase was identified as putative drug target using network and homology analyses. The DEPs between the species are essential in host-pathogen interactions and parasite survival in the macrophage. Furthermore, L. major and L. tropica possibly uses different pathogenicity mechanisms that leads to anthroponotic or zoonotic CL. Our results may help in the drug discovery and chemotherapeutic interventions.

Effect of Metformin on Circulating Levels of Inflammatory Markers in Patients With Type 2 Diabetes: A Systematic Review and Meta-analysis of Randomized Controlled Trials

BACKGROUND

Emerging evidence indicates that metformin has anti-inflammatory effect; however, the results differ concerning randomized controlled trails of the effect of metformin on inflammatory markers in type 2 diabetes (T2D) patients.

OBJECTIVE

This study reassessed the data on the effect of metformin treatment on inflammatory markers in T2D patients through a systematic review and meta-analysis.

METHODS

A systematic search was performed in the PubMed, ISI Web of Science, EMBASE, Cochrane Library and Scopus databases to collect relevant published data up to September 2020. Data of each study was combined using random-effects model. Subgroup analysis was performed based on subgroups of the treatment duration, dose and target population.

RESULTS

Thirteen RCTs including 1776 participants with T2D were analyzed. Although CRP levels significantly decreased [SMD: -0.76 mg/L; 95% CI (-1.48, -0.049); P = 0.036] in patients with T2D following metformin treatment, circulating levels of TNF-α [SMD: -0.17 pg/mL; 95% CI (-0.55, 0.20); P = 0.37] and IL-6 [SMD: -0.06 pg/mL; 95% CI (-0.38, 0.25); P = 0.69] were insignificant after metformin treatment. Compared to treatment duration of less than 24 weeks, longer treatment duration (more than 24 weeks) was associated with reduced level of CRP.

RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE

Based on available evidence from RCTs in this meta-analysis, metformin decreased CRP level. However, strategies for the treatment of inflammation should focus on metformin in patients with T2D.

CONCLUSION

The present study evidences that therapy with metformin can reduce CRP level significantly in T2D patients compared to other inflammatory markers.

Prognostic value of microRNA-125a/b family in patients with gastric cancer: a meta-analysis

AIM

This meta-analysis was designed to reassess the prognostic and clinicopathologic values of the microRNA-125 family in GC patients.

BACKGROUND

The miR-125 family (including miR-125a, miR-125b) has been reported as being pivotal prognostic biomarkers of gastric cancer (GC). However, there is controversy about the role of the miR-125 family in predicting the progression of GC.

METHODS

The miR-125 family (including miR-125a, miR-125b) has been reported as being pivotal prognostic biomarkers of gastric cancer (GC). However, there is controversy about the role of the miR-125 family in predicting the progression of GC.

RESULTS

The electronic databases of PubMed, ISI Web of Science, Scopus, and Cochrane Library were systematically searched for relevant studies. Overall survival (OS) rate as the primary outcome from each study was extracted. The overall hazard ratio (HR or survival rate in patients with GC) and odds ratio (OR) with 95% confidence interval (CI) was calculated to evaluate the association between miR-125 family expression and prognosis and susceptibility to gastric cancer. The quality of evidence was evaluated using the Newcastle-Ottava Scale (NOS). The extracted data was combined based on the random-effects model.

CONCLUSION

The low expression of miR-125 family predicts poor OS in GC patients. Thus, the miR-125 family may be helpful as a potential biomarker for the prognosis of gastric cancer.

Effect of rosiglitazone on circulating malondialdehyde (MDA) level in diabetes based on a systematic review and meta-analysis of eight clinical trials

Patients with type 2 diabetes have high levels of malondialdehyde (MDA), and clinical data suggest a reducing effect of rosiglitazone (RSG) on the level of MDA in these patients. However, the results of available studies on the level of MDA in RSG-treated patients are not univocal. This meta-analysis aimed to assess the impact of RSG on the level of MDA. We performed a comprehensive search of PubMed, the Institute for Scientific Information Web of Science, Embase, Scopus, and Cochrane Library for related controlled trials until July 2020. Eligible studies were selected based on the inclusion criteria. Extracted data from each study were combined using a random-effects model. Sensitivity and subgroup analyses were conducted to explore potential heterogeneity. Eight trials with 456 subjects met the inclusion criteria. The results significantly showed the reducing effect of RSG on circulating MDA level (−0.47 μmol/mL; 95% CI −0.93 to −0.01; p=0.04; I2=82.1%; p heterogeneity=0.00) in individuals with T2D. No publication bias was observed with Begg’s rank correlation (p=0.71) and Egger’s linear regression (p=0.52) tests. Subgroup analyses showed that an intervention dose of 8 mg/day in serum samples was found to have a reducing effect on the level of MDA (−0.56 μmol/mL; 95% CI −0.98 to −0.14; p=0.008; I2=11.4%; p heterogeneity=0.32). Random-effects meta-regression did not show any significant association between the level of MDA and potential confounders including RSG dose, treatment duration, and sex. In conclusion, we found a significant reduction in MDA concentration in subjects with T2D who received a dose of 8 mg of RSG daily.

Circulating levels of CTRP3 in patients with type 2 diabetes mellitus compared to controls: A systematic review and meta-analysis

Growing evidence suggests that adipokines may be therapeutic targets for cardiometabolic diseases such as type 2 diabetes mellitus (T2DM). C1q TNF Related Protein 3 (CTRP3) is a newly discovered adipokine which shares properties with adiponectin. The literature about the association between circulating levels of CTRP3 and T2DM has been conflicting. The present study reassessed the data on circulating CTRP3 levels in T2DM patients compared to controls through a systematic review and meta-analysis. A literature search was performed in Medline, Embase, Scopus, and Web of science to identify studies that measured circulating CTRP3 levels in T2DM patients and controls. The search identified 124 studies of which 59 were screened for title and abstract and 13 were subsequently screened at the full text stage and 12 studies included into the meta-analysis. Subgroup analyses, depending on the presence of T2DM complications, matching for BMI, age, and cut off value of fasting blood sugar and HOMA-IR, were performed. The results show that circulating CTRP3 levels are negatively associated with T2DM status (SMD: -0.837; 95% CI: (-1.656 to -0.017); p = 0.045). No publication bias was identified using the Begg's rank correlation and Egger's linear regression tests (P = 1 and P = 0.44, respectively). Meta-regression demonstrated significant association between CRTP3 levels with BMI (slope: 0.11; 95% CI: 0.04-0.19; p = 0.001) and sex (slope: -0.07; 95% CI: -0.12 to -0.01; p = 0.008). The present systematic review and meta-analysis evidences a negative association between circulating level of CTRP3 and T2DM status. BMI and sex may modify this association.

Stage-Specific Differential Gene Expression of Glutathione Peroxidase in Leishmania Major and Leishmania Tropica

BACKGROUND

Leishmania (L) major and L. tropica are the etiological agents of cutaneous leishmaniosis. Leishmania species cause a board spectrum of phenotypes. A small number of genes are differentially expressed between them that have likely an important role in the disease phenotype. Procyclic and metacyclic are two morphological promastigote forms of Leishmania that express different genes. The glutathione peroxidase is an important antioxidant enzyme that essential in parasite protection against oxidative stress and parasite survival. This study aimed to compare glutathione peroxidase (TDPX) gene expression in procyclic and metacyclic and also interspecies in Iranian isolates of L. major and L. tropica.

METHODS

The samples were cultured in Novy-Nicolle-Mc Neal medium to obtain the promastigotes and identified using PCR-RFLP technique. They were then grown in RPMI1640 media for mass cultivation. The expression level of TDPX gene was compared by Real-time PCR.

RESULTS

By comparison of expression level, up-regulation of TDPX gene was observed (5.37 and 2.29 folds) in L. major and L. tropica metacyclic compared to their procyclic, respectively. Moreover, there was no significant difference between procyclic forms of isolates, while 3.05 folds up-regulation in metacyclic was detected in L. major compared L. tropica.

CONCLUSION

Our data provide a foundation for identifying infectivity and high survival related factors in the Leishmania spp. In addition, the results improve our understanding of the molecular basis of metacyclogenesis and development of new potential targets to control or treatment and also, to the identification of species-specific factors contributing to virulence and pathogenicity in the host cells.

Association between circulating visfatin and pre-eclampsia: a systematic review and meta-analysis

OBJECTIVE

Pre-eclampsia (PE) is a serious pregnancy status characterized by high blood pressure. Although visfatin is usually associated with PE. Observational studies evaluating the relationship between circulating visfatin and pre-eclampsia have reported inconsistent results. We conducted this systematic review and meta-analysis to summarize published data on the association between visfatin and pre-eclampsia.

METHODS

Electronic databases PubMed, ISI web of science, EMBASE, Scopus and the Cochrane library were comprehensively searched for selection of eligible studies until January 5, 2020. A random-effects model and the generic inverse variance method were used for quantitative data synthesis. The assessment of study quality was performed using the e Newcastle-Ottawa scale and the Agency for Healthcare Research and Quality. Sensitivity analyses and prespecified subgroup were conducted to evaluate potential heterogeneity. Random-effects meta-regression was conducted to assess the impact of potential confounders on the estimated effect sizes. The protocol for this study was registered in PROSPERO (No. CRD42018105861) in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA).

RESULTS

Thirteen studies comprising a total of 536 subjects were included in this meta-analysis. We observed that the pre-eclampsia risk is associated with a statistically significant elevation of visfatin level [SMD (1.33 µg/l) (95% CI 0.37, 2.2) p = .007]. No significant publication bias was observed in the meta-analysis. Subgroup and sensitivity analyses indicated that the pooled effects size were affected by systolic blood pressure [SMD (1.82 µg/l) 95% CI (0.94, 2.7), p < .05], gestational age [SMD (2.01 µg/l) 95% CI (0.57, 3.4), p = .006], body mass index [SMD (1.6 µg/l) 95% CI (0.37, 3), p < .05] and pregnancy trimesters[SMD (2.3 µg/l) 95% CI (0.95, 3.7), p = .001]. Random-effects meta-regression showed a significant association of visfatin level with potential confounders including systolic blood pressure, gestational age and birth weight at delivery of pre-eclampsia patients.

CONCLUSIONS

Collectively, our data revealed that the increase of visfatin level can be associated with the risk of pre-eclampsia. However, further studies on pre-eclampsia populations are warranted for corroboration of our findings.

Integrated Bioinformatics Analysis of mRNAs and miRNAs Identified Potential Biomarkers of Oral Squamous Cell Carcinoma

Background: Oral cancer is a frequently encountered neoplasm of the head and neck region, being the eighth most common type of human malignancy worldwide. Despite improvement in its control, morbidity and mortality, rates have improved little in the past decades. The present investigations about gene interaction and pathways still could not clear the appearance and development of oral squamous cell carcinoma (OSCC), completely. The aim of this study is to investigate the key genes and microRNAs interaction in OSCC. Materials and Methods: The microarray datasets GSE13601 and GSE98463, including mRNA and miRNA profiles, were extracted from the GEO database and were analyzed using GEO2R. Functional and pathway enrichment analyses were performed by using the DAVID database. The protein-protein interaction (PPI) network was constructed and analyzed using STRING database and Cytoscape software, respectively. Finally, miRDB was applied to predict the targets of the differentially expressed miRNAs (DEMs). Results: Totally, 97 differentially expressed genes (DEGs) were found in OSCC, including 66 up-regulated and 31 down-regulated genes. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that up-regulated genes were significantly enriched in movement of cell or subcellular component, cell adhesion, biological adhesion, cellular localization, apoptotic signaling pathway, while the downregulated genes were enriched in muscle system process and oxidation-reduction process. From the PPI network, the top 10 nodes with the highest degree were detected as hub genes. In addition, 18 DEMs were screened, which included 7 up-regulated and 11 down-regulated miRNAs. STAT1 was potentially targeted by three miRNAs, including has-miR- 6825-5P, has-miR-4495, and has-miR-5580-3P. Conclusion: The roles of DEMs such as hsa-mir-5580-3p in OSCC through interactions with DEGs CD44, ACLY, ACTR3, STAT1, LAMC2 and YWHAZ may offer a suitable candidate biomarker pattern for diagnosis, prognosis and treatment processes in OSCC.

The impact of continuous positive airway pressure therapy on circulating levels of malondialdehyde: a systematic review and meta-analysis

BACKGROUND

Obstructive sleep apnea (OSA) is a highly prevalent sleep disorder which associated with increased oxidative stress and cardiovascular diseases. Malondialdehyde (MDA) is a reliable marker of lipid peroxidation and is elevated in patients with OSA. Studies reported inconsistent findings on the effect of continuous positive airway pressure (CPAP) therapy on MDA levels. As the study power maybe a reason for the inconsistent findings, we aimed to use meta-analysis to assess effect of CPAP therapy on MDA in patients with OSA.

METHOD

Electronic search was performed to find out studies on the effect of CAPA on MDA levels in OSA patients. Search carried out in databases of PubMed, EMBASE, Scopus, Cochrane library and web of science.

RESULTS

Search resulted in 161 records of which 83 remained after removing duplicated records. Further, 51 articles were removed by title and abstract and 22 records evaluated by full text. Finally 13 articles were included in the intended meta-analysis. Pooled analysis demonstrated that CPAP therapy reduced MDA levels significantly [SMD (-1.51) (95% CI, -2.06 to -0.97) p < 0.05]. Subgroup analyses showed that CPAP therapy was effective in categories of age (≤50 and > 50 years), BMI (≤30 and > 30 kg/m²) and therapy duration (≤12 week and >12 week).

CONCLUSION

the results of the present study demonstrated considerable effect of CPAP therapy on MDA as independent risk factor for cardiovascular diseases and robust marker of lipid peroxidation.

Effect of garlic intake on inflammatory mediators: a systematic review and meta-analysis of randomised controlled trials

BACKGROUND

Garlic is a species in the onion genus, Allium. Data have shown that garlic has anti-inflammatory activity; however, the findings are inconclusive and inconsistent. We aimed to evaluate the impact of garlic intake on inflammatory mediators through systematic review and meta-analysis of existing data.

METHODS

Electronic databases were completely investigated using databases of ISI Web of Science, Medline, Scopus, Cochrane Library and EMBASE until October 2019. A random effects model and the generic reverse variance procedure were used for quantitative data production. Sensitivity analyses and prespecified subgroup were done to evaluate potential heterogeneity. Random effect meta-regression was conducted to investigate the effects of possible confounders on the assessed effect size.

RESULTS

Ten trials with one observational study, including 530 participants, met the eligibility criteria. The findings showed reduction in the tumour necrosis factor alpha (TNF-α) (-0.31 pg/mL, 95% CI -1.07 to 0.46) and C reactive protein (CRP) levels (-0.20 mg/L, 95% CI -1.4 to 1.05) following supplementation with garlic, although it had no marked impact on the interleukin 6 (IL-6) level (0.37 pg/mL, 95% CI -0.58 to 1.33). In the subgroup analysis, we found that garlic supplementation significantly decreased TNF-α, highly sensitive CRP and IL-6 levels in subgroups of >8, >6 and ≥4 weeks of intervention duration, respectively, and dose of garlic consumption between 2 and 2.4 g/day.

CONCLUSION

These findings suggested that current evidence may support garlic as an adjunct to pharmacological management of metabolic diseases.

PROSPERO REGISTRATION NUMBER

CRD42018108816.

The effect of resveratrol supplementation on C-reactive protein (CRP) in type 2 diabetic patients: Results from a systematic review and meta-analysis of randomized controlled trials

OBJECTIVE

C-reactive protein (CRP) is considered to be an inflammatory marker in type 2 diabetes (T2D) and it is produced by liver cells. The evidence has suggested that resveratrol has anti-inflammatory effect. This study aimed to evaluate the effect of resveratrol supplementation on CRP level in patients with T2D using a systematic review and meta-analysis of randomized controlled trials.

METHODS

Electronic databases were completely searched using Medline, ISI Web of Science, EMBASE and Cochrane Library and Scopus until October 2019. Meta-analysis was performed using random-effects model and inverse variance method. Heterogeneity and publication bias were evaluated in selected studies. Sensitivity analyses and prespecified subgroup were conducted to evaluate potential heterogeneity. Meta-regression was performed to assess the effect of potential confounders on the estimated effect sizes.

RESULTS

Six trials comprising a total of 491 subjects were included in this meta-analysis. The results showed significant reduction in the level of CRP [SMD (-0.34 mg/l) (95 % CI, -0.52, to -0.16) p < 0.05] in participants with T2D following supplementation with resveratrol. No significant publication bias was observed in the meta-analysis. Subgroup and sensitivity analyses indicated that the pooled effects of resveratrol supplementation on CRP level in T2D patients were affected by resveratrol dose and duration of resveratrol. Random-effects meta-regression did not indicate any significant association of CRP level with potential confounders including resveratrol dose, duration of treatment, age and gender of type 2 diabetic patients.

CONCLUSION

We found a significant reduction in CRP level in patients with type 2 diabetes, who received resveratrol supplementation.

Gastrointestinal symptoms in patients with mild and severe COVID-19: a scoping review and meta-analysis

AIM

The current research aimed to analyze and summarize observational studies that compared the incidence of gastrointestinal symptoms in mild and severe COVID-19 infection.

BACKGROUND

Coronavirus disease 2019 (COVID-19) has been identified as a public health threat worldwide. Previous studies, however, have reported contradictory results of COVID-19-related gastrointestinal symptoms in severe and mild forms.

METHODS

A search of Medline, ISI Web of Science, EMBASE, and Cochrane Library databases was conducted for articles published up to May 2020. Data from each study was combined using the random-effects model to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs). Sensitivity was examined by sequentially excluding one study in each turn. Publication bias was evaluated using the Egger's and Begg's tests.

RESULTS

Twenty studies (4,265 patients) were reviewed. It was found that the prevalence of diarrhea [OR (0.40), (95% CI 0.91, -2.16), p = 0.03, I2 = 88.1%, PHeterogenity = 0.00)] and nausea and vomiting [OR (0.27), (95% CI 0.07, 1.01), p = 0.05, I2 = 89.3%, PHeterogenity = 0.00)] increased significantly in the severe form compared to the mild form of COVID-19, while abdominal pain and anorexia had no significant increased prevalence in admitted and hospitalized COVID-19 patients. Moreover, COVID-19-related gastrointestinal symptoms were seen in higher rates in males [OR (1.42), (95% CI 1.23, 1.65), p < 0.05, I2= 18.4%, PHeterogenity = 0.23] than in females. No significant publication bias was observed in the meta-analysis. Sensitivity analyses showed a similar effect size while reducing the heterogeneity.

CONCLUSION

The data provides valuable information for the discovery of prognosis biomarkers to diagnosis more severe disease in the early stages of COVID-19.

Increased inflammatory markers correlate with liver damage and predict severe COVID-19: a systematic review and meta-analysis

AIM

This study aimed to determine whether patients with elevated CRP, TNFα, and IL-6 levels may be at increased risk for severe infection and liver damage of COVID-19.

BACKGROUND

The COVID-19 outbreak is a serious health problem to human beings. The evidence suggests that inflammatory markers related to liver damage increase in severe forms of COVID-19 compared to mild cases.

METHODS

The electronic databases ISI Web of Science, EMBASE, and Cochrane Library were comprehensively searched for articles published up to May, 2020. Data from each identified study was combined using the random effects model to estimate standardized mean difference (SMD) and 95% confidence intervals (95% CIs). Sensitivity and publication bias were also calculated.

RESULTS

Totally, 23 studies were included in this meta-analysis comprising 4313 patients with COVID-19. The random effects results demonstrated that patients with severe COVID-19 had significantly higher levels of CRP [SMD = 3.26 mg/L; (95% CI 2.5, 3.9); p<0.05; I2 = 98.02%; PHeterogeneity = 0.00], TNFα [SMD = 1.78 ng/mL; (95% CI 0.39, 3.1); p=0.012; I2 = 98.2%; PHeterogeneity = 0.00], and IL-6 [ SMD = 3.67 ng/mL; (95% CI 2.4, 4.8); p<0.05; I2 = 97.8%; PHeterogeneity = 0.00] compared with those with the mild form of the disease. Significant heterogeneity was present. No significant publication bias was observed in the meta-analysis. Sensitivity analyses showed a similar effect size while reducing the heterogeneity.

CONCLUSION

The data suggests that enhanced inflammation may be associated with COVID-19-related liver damage, possibly involving inflammatory marker-related mechanisms.

Resveratrol Reduces Lipid Accumulation through Upregulating the Expression of MicroRNAs Regulating Fatty Acid Bet Oxidation in Liver Cells: Evidence from In-vivo and In-vitro Studies

MicroRNAs have been shown to regulate lipogenesis in liver. The aim of the present study was to investigate whether the effects of resveratrol (RSV) on lipogenesis are associated with the changes in the expression of two miRNAs (miR-107 and miR-10b) that regulate lipogenic pathways. 30 wild type C57BL/6j male mice were randomly fed three diets: a standard chow diet (ND), a high fat diet (HFD, 60% fat) and the high fat diet supplemented with 0.4% RSV (HFD-RSV) for 16 weeks. HepG2 cells were treated with high glucose (33 mM) and RSV (20 µM) for 24 h. The expression of the genes and miRNAs were measured by real-time PCR. Triglyceride level was increased in the liver of mice and HepG2 cells. In both animal and In-vitro experiments, triglyceride level was significantly decreased in groups treated with RSV. The expression of the miR-107 and miR-10b was significantly upregulated in the liver of HFD mice, whereas HFD-RSV group demonstrated a significant lower expression of both miRNAs compared to HFD group. In addition, RSV treatment significantly upregulated the expression of CPT-1a and PPARα genes in the liver of HFD mice. Moreover, treatment with RSV could reduce the expression of miR-107 and miR-10b and increase the expression of CPT-1a and PPARα in HG-treated HepG2 cells. These evidence, as a whole, suggest that RSV could exert its anti-lipogenic effect partially through alterations in the expression of miR-107 and miR-10b in liver cells.

Comparison of gene expression of pyruvate kinase and tryparedoxin peroxidase in metacyclic promastigote forms of Leishmania (L.) tropica and L. major by real-time PCR

Two predominant forms of cutaneous leishmaniosis are anthroponotic CL (ACL) and zoonotic CL (ZCL) caused by Leishmania (L.) tropica and L. major in Iran and many countries, respectively. Since differential gene expression play an important role in outcome of the infection, we compared relative gene expression value of pyruvate kinase (PyrK) and tryparedoxin peroxidase (TryP) in metacyclic forms of Iranian isolates of L. major and L. tropica. Clinical isolates of CL patients were sampled in endemic foci of Iran and identified by PCR-RFLP. Then, we employed real-time PCR to evaluation of the expression level of PyrK and Tryp genes in L. major and L. tropica. By this comparison, up-regulation of PyrK and Tryp genes was observed in metacyclic stage. Moreover, the average mRNA expression of PyrK and Tryp genes in L. major was 1.69 and 3.72 folds of its expression in L. tropica isolates. The results of this study could open the new window for further investigations of the correspondence between parasite gene expression level and disease pathology. Species-specific parasite factors contributing to virulence and pathogenicity in the host may be mostly due to the some of the differential regulation of conserved genes between species.

Inhibiting miR-27a and miR-142-5p attenuate nonalcoholic fatty liver disease by regulating Nrf2 signaling pathway

The gene Nrf2 (nuclear factor-erythroid 2-related factor 2) is the most important regulator of the cellular antioxidant system and its dysregulation has a role in the etiology of nonalcoholic fatty liver disease (NAFLD). The aim of this study was to investigate the association between Nrf2 targeted miRNAs (miR-27a, miR-142-5p, miR-153, and miR-128) with lipid accumulation in vitro and in vivo models of NAFLD. We used two in vivo and in vitro models of NAFLD. The expression of the genes and miRNAs was assessed by real-time PCR and the protein level was evaluated using western blot. To investigate the potential role of miRNAs in NAFLD, the inhibitors or mimics of the miR-27a and miR-142-5p were transfected into HepG2 cells. The mRNA and protein levels of Nrf2 were significantly decreased in the liver of high fat diet-fed mice as well as in HepG2 cells treated with high glucose (HG). Reduced expression of Nrf2 was associated with increased expression levels of miR-27a and miR-142-5p in both models of NAFLD. HG-induced triglyceride accumulation was attenuated by inhibition of miR-27a or miR-142-5p in HepG2 cells. Overexpression of miR-27a or miR-142-5p suppressed the expression of Nrf2 and its downstream antioxidant genes and increased production of reactive oxygen species, whereas inhibition of miR-27a or miR-142-5p reversed these effects. In conclusion, the data of this study may suggest that miR-27a and miR-142-5p are increased in NAFLD, where they suppress Nrf2 expression and contribute to the accumulation of lipids in the hepatocytes.

Resveratrol alleviates non-alcoholic fatty liver disease through epigenetic modification of the Nrf2 signaling pathway

Recent findings have demonstrated the aberrant DNA methylation of the Nrf2-Keap1 genes in human cancers; however, the epigenetic control of this pathway in non-alcoholic fatty liver disease (NAFLD) is unknown. Resveratrol can modify epigenetic mechanisms. Our objectives in this study were to explore the correlation between promoter methylation of the Nrf2-Keap1 genes and NAFLD, and that investigate the effect of resveratrol on the epigenetic regulation Nrf2-Keap1 in vitro and in vivo models of NAFLD. Resveratrol attenuated high fat-diet (HFD)-induced methylation of the Nrf2 promoter in the liver of mice, and this effect was correlated with reduction in triglyceride level and decrease in the expression of lipogenesis-related genes such as FAS and SREBP-1c. In addition, treatment of HepG2 cells with high glucose (HG) enhanced methylation level of the Nrf2 promoter, whereas resveratrol reversed this effect. Treatment of the cells with resveratrol or 5-aza, a demethylating agent, could prevent HG-induced reactive oxygen species production and expression of Nrf2-controlled antioxidant genes. Moreover, resveratrol or 5-aza could significantly attenuate HG-induced triglyceride accumulation in HepG2 cells. These findings indicate that resveratrol attenuates NAFLD through the epigenetic modification the Nrf2 signaling.

Therapeutic effect of resveratrol supplementation on oxidative stress: a systematic review and meta-analysis of randomised controlled trials

Background

Resveratrol is a naturally occurring polyphenol compound mainly found in grapes and red wine. The evidence has suggested that resveratrol has an antioxidant effect. However, the results are inconsistent and inconclusive. Thus, we conducted a systematic review and meta-analysis to evaluate the effect of resveratrol supplementation on markers of oxidative stress.

Methods

We searched PubMed, ISI Web of Science, EMBASE, Scopus and the Cochrane library up to December 2018 to identify randomised controlled trials (RCTs) assessing resveratrol supplementation effects on oxidative markers. Heterogeneity, publication bias, risk of bias and subgroup analysis were analysed. This meta-analysis was conducted in accordance with the guidelines of the Preferred ReportingItems for Systematic Reviews and Meta-Analysis (PRISMA).

Results

Meta-analysis of data from 12 RCTs did not support significant effect of resveratrol supplementation on circulating levels of superoxide dismutase (SOD) (standardized mean difference (SMD) (1.12), (95% CI −0.91 to 3.1), p=0.28), catalase (CAT) (SMD (−0.07), (95% CI −1.4 to 1.3), p=0.92) and glutathione peroxidase (GPx) (SMD (−0.76), (95% CI −2.56 to 1.04), p=0.40). Although, resveratrol supplementation increased significantly circulating total antioxidant capacity (TAC) concentrations (SMD (0.52), (95% CI −0.02 to 1.07), p=0.05). Severe heterogeneity was observed between studies, and no obvious publication bias was observed in included RCTs.

Conclusion

Collectively, our findings of available RCTs did no show any benefit of resveratrol supplementation on SOD, CAT and GPx except for TAC. Well-designed RCTs are necessary to confirm these results.

Therapeutic effects of hydro-alcoholic extract of Achillea wilhelmsii C. Koch on indomethacin-induced gastric ulcer in rats: a proteomic and metabolomic approach

Background

Gastric ulcer is one of the most prevalent diseases worldwide. In Iranian folk medicine, Achillea wilhelmsii (AW) is used as a treatment for gastric ulcer. Previous reports also mentioned Antiulcerogenic properties for this herbal plant. This study investigated the therapeutic effects of Achillea wilhelmsii C. Koch extract on indomethacin-induced gastric lesion in rats, from both proteomic and metabolomic perspectives.

Methods

The rats were divided into 4 groups. Gastric ulceration was induced by a single dose of indomethacin (45 mg/kg) by oral gavage. An amount of 800 mg/kg of AW extract was administered orally. Serum and tissue samples were collected for further investigations. The metabolomic study was performed by ¹H-NMR CPMG spectrometry. Proteomic analysis was also executed by using two dimensional gel electrophoresis (2DE) followed by liquid chromatography coupled to tandem mass spectrometry (LC-ESI/MS/MS). Real time PCR was used to confirm some of the genes.

Results

The macroscopic and microscopic investigations confirmed the effectiveness of the AW extract. There was a panel of metabolites which showed alteration during gastric lesion development. The levels of some of these metabolite reversed nearly to their control values after the administration of AW extract. There were also changes in the levels of some proteins including Alb, Fabp5, Hspb1, Tagln, Lgals7, Csta and Myl9 which were reversed after AW administration.

Conclusions

Our findings suggested that Achillea wilhelmsii C. Koch extract could be a potential therapy to be used for indomethacin-induced gastric lesion treatment in the future. However, further investigations are needed to confirm the results.

Electronic supplementary material

The online version of this article (10.1186/s12906-019-2623-4) contains supplementary material, which is available to authorized users.

A Metabolomic Study to Identify Potential Tissue Biomarkers for Indomethacin-Induced Gastric Ulcer in Rats

BACKGROUND

Gastric Ulcer (GU) is the most prevalent gastrointestinal disorder induced by various factors and Non-Steroid Anti-Inflammatory Drugs (NSAIDs) as one of the most common reasons. Due to the absence of appropriate molecular markers for GU, the aim of this study was to utilize a metabolomics approach in order to find potential metabolite markers for the disease.

METHODS

Stomach tissue samples from indomethacin-treated rats and normal controls were used to perform a 1H-NMR metabolomics study. The altered metabolites were identified using random forest multivariate analysis.

RESULTS

ROC curves showed that the random forest model had a good predictive performance with AUC of 1 for the test and 0.708 for the training sets. Seventeen differentially expressed metabolites were found between GU and normal tissue sample. These metabolites included trimethylamine, betaine, carnitine, methionine, acetylcho line, choline, N,N-Dimethylglycine, cis-aconitate, tryptophan, spermidine, acetylcarnitine, creatinine, pantothenate, taurine, isoleucine, glucose and kynurenine.

CONCLUSION

The results of the study demonstrated that metabolomics approach could serve as a viable method to find potential markers for GU. Surely, further studies are needed for the validation of the results.

Resveratrol: A miraculous natural compound for diseases treatment

Resveratrol (3, 5, 4'-trihydroxystilbene) is a nonflavonoid polyphenol that naturally occurs as phytoalexin. It is produced by plant sources such as grapes, apples, blueberries, plums, and peanut. This compound has critical roles in human health and is well known for its diverse biological activities such as antioxidant and anti-inflammatory properties. Nowadays, due to rising incidence of different diseases such as cancer and diabetes, efforts to find novel and effective disease-protective agents have led to the identification of plant-derived compounds such as resveratrol. Furthermore, several in vitro and in vivo studies have revealed the effectiveness of resveratrol in various diseases such as diabetes mellitus, cardiovascular disease, metabolic syndrome, obesity, inflammatory, neurodegenerative, and age-related diseases. This review presents an overview of currently available studies on preventive properties and essential molecular mechanisms involved in various diseases.

Assessment of Correlation Between miR-210 Expression and Pre-Eclampsia Risk: A Meta-Analysis

BACKGROUND

Pre-eclampsia (PE) is a pregnancy disorder characterized by hypertension and proteinuria. The evidence has suggested that microRNAs (miRs) are associated with pre-eclampsia pathogenesis; however, these results are inconsistent. The aim of this study was to assess the association between miR-210 expression and PE risk.

METHODS

Previous studies were selected using PubMed, Scopus, MEDLINE, EMBASE, Science Direct, Google Scholar, Directory of Open Access Journals (DOAJ), and Scientific Information Database (SID). This metaanalysis includes 12 studies associated with miR-210 and pre-eclampsia and necessary information was extracted.

RESULTS

The standardized mean differences [(SMD (0.32) 95% CI (014-0.49), p=0.97] and heterogeneity were determined with the chi-square test (Q=3.63 df =11 p= 0.97), which found no heterogeneity between these studies. Additionally, publication bias was evaluated by Egger's and Begg´s tests. Visual inspection of the funnel plot graphically, and statistically with Egger's weighted regression [(p= 0.35) (95% CI -0.90 - 2.29)] and Begg's rank correlation (p= 0.21), found no important publication bias between studies within the meta-analysis.

CONCLUSION

Our findings suggest that miR-210 contributes to the pathogenesis of PE; therefore, miR-210 could serve as a novel biomarker to predict PE pathophysiology. Further studies are required in this field to characterize the mechanism involved in this process.

Effect of Resveratrol Supplementation on Inflammatory Markers: A Systematic Review and Meta-analysis of Randomized Controlled Trials

PURPOSE

The evidence has suggested that resveratrol has anti-inflammatory effect; however, the results are inconsistent and inconclusive. The aim of this study was to assess the effect of resveratrol supplementation on the levels of inflammatory markers through a systematic review and meta-analysis of available randomized controlled trials (RCTs).

METHODS

A search strategy was completed using Medline, ISI Web of Science, Directory of Open Access Journal, SID, ProQuest, Cochrane Library, Scopus, and EMBASE up to May 2017, to identify placebo-controlled RCTs that assessed resveratrol effects on circulating (serum and plasma) inflammatory markers (interleukin [IL]-6, tumor necrosis factor-α [TNF-α], and high-sensitivity C-reactive protein [hs-CRP]) among adult participants aged 17 years and older in 17 RCTs with a total of 736 subjects. The evaluation of study quality was performed using the Jadad scale. Weighted mean difference (WMD) was calculated for evaluating the changes in the inflammatory markers using fixed-effects or random-effects models. We performed subgroup and sensitivity analyses to evaluate the heterogeneity of the studies.

FINDINGS

Seventeen RCTs, including 736 subjects, fulfilled the eligibility criteria and were selected for analyses. The results of meta-analysis found significant reductions in the level of TNF-α (WMD, -0.44; 95% CI, -0.71 to -0.164; P = 0.002; Q statistic = 21.60; I² = 49.1%; P = 0.02) and hs-CRP (WMD, -0.27; 95% CI, -0.5 to -0.02; P = 0.033; Q statistic = 26.95; I² = 51.8%; P = 0.013) after supplementation with resveratrol. Resveratrol supplementation had no significant effect on the level of IL-6 (WMD, -0.16; 95% CI, -0.53 to 0.20; P = 0.38; Q statistic = 36.0; I² = 72.3%; P = 0.001). Statistically significant heterogeneity was observed for the type of sample in IL-6 and study duration in inflammatory markers IL-6, TNF-α, and hs-CRP.

IMPLICATIONS

Available evidence from RCTs suggests that resveratrol supplementation significantly reduced TNF-α and hs-CRP levels. Significant improvement in inflammatory markers support resveratrol as an adjunct to pharmacologic management of metabolic diseases.

Protein-Protein Interaction Network Analysis of Salivary Proteomic Data in Oral Cancer Cases

Background:

Oral cancer is a frequently encountered neoplasm of the head and neck region, being the eight most common type of human malignancy worldwide. Despite improvement in its control, morbidity and mortality rates have improved little in the past decades. Therefore, prevention and/or early detection are a high priority. Proteomics with network analysis have emerged as a powerful tool to identify important proteins associated with cancer development and progression that can be potential targets for early diagnosis. In the present study, network- based protein- protein interactions (PPI) for oral cancer were identified and then analyzed for use as key proteins/potential biomarkers.

Material and Methods:

Gene expression data in articles which focused on saliva proteomics of oral cancer were collected and 74 candidate genes or proteins were extracted. Related protein networks of differentially expressed proteins were explored and visualized using cytoscape software. Further PPI analysis was performed by Molecular Complex Detection (MCODE) and BiNGO methods.

Results:

Network analysis of genes/proteins related to oral cancer identified kininogen-1, angiotensinogen, annexin A1, IL-8, IgG heavy variable and constant chains, CRP, collagen alpha-1 and fibronectin as 9 hub-bottleneck proteins. In addition, based on clustering with the MCODE tool, vitronectin, collagen alpha-2, IL-8 and integrin alpha-v were established as 5 distinct seed proteins.

Conclusion:

A hub-bottleneck protein panel may offer a potential /candidate biomarker pattern for diagnosis and treatment of oral cancer disease. Further investigation and validation of these proteins are warranted.

Prediction of Leishmania major Key Proteins Via Topological Analysis of Protein-Protein Interaction Network

Background:

Although leishmaniasis is regarded as a public health problem, no effective vaccine or decisive treatment has been introduced for this disease. Therefore, representing novel therapeutic proteins is essential. Protein-protein Interaction network analysis is a suitable tool to discover novel drug targets for leishmania major. To this aim, gene and protein expression data is used for instructing protein network and the key proteins are highlighted.

Materials and Methods:

In this computational and bioinformatics study, the protein/gene expression data related to leishmania major were studied, and 252 candidate proteins were extracted. Then, the protein networks of these proteins were explored and visualized by using String database and Cytoscape software. Finally, clustering and gene ontology were performed by MCODE and PANTHER databases, respectively.

Results:

Based on gene ontology analysis, most of the leishmania major proteins were located in cell compartments and membrane. Catalytic activity and binding were regarded as the relevant molecular functions and metabolic and cellular processes were the significant biological process. In this network analysis, UB-EP52, EF-2, chaperonin, Hsp70.4, Hsp60, tubulin alpha and beta chain, and ENOL and LACK were introduced as hub-bottleneck proteins. Based on clustering analysis, Lmjf.32.3270, ENOL and Lmjf.13.0290 were determined as seed proteins in each cluster.

Conclusion:

The results indicated that hub proteins play a significant role in pathogenesis and life cycle of leishmania major. Further studies of hubs will provide a better understanding of leishmaniasis mechanisms. Finally, these key hub proteins could be a suitable and helpful potential for drug targets and treating leishmaniasis by considering their validation.

Proteomics Applications in Health: Biomarker and Drug Discovery and Food Industry

Advancing in genome sequencing has greatly propelled the understanding of the living world; however, it is insufficient for full description of a biological system. Focusing on proteomics has emerged as another large-scale platform for improving the understanding of biology. Proteomic experiments can be used for different aspects of clinical and health sciences such as food technology, biomarker discovery and drug target identification. Since proteins are main constituents of foods, proteomic technology can monitor and characterize protein content of foods and their change during production process. The proteomic biomarker discovery is advanced in various diseases such as cancer, cardiovascular diseases, AIDS, and renal diseases which provide non-invasive methods by the use of body fluids such as urine and serum. Proteomics is also used in drug target identification using different approaches such as chemical proteomics and protein interaction networks. The development and application of proteomics has increased tremendously over the last decade. Advances in proteomics methods offer many promising new directions of studying in clinical fields. In this regard, we want to discuss proteomics technology application in food investigations, drug, and biomarker discovery.

Type 2 diabetes mellitus and non-alcoholic fatty liver disease: a systematic review and meta-analysis

AIM

The aim of this study was the evaluation of the prevalence of NAFLD in patients with type 2 diabetes mellitus.

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is an emerging disease with high prevalence in patients with type 2 diabetes mellitus (T2DM). Many studies have reported the prevalence of NAFLD in type 2 diabetes mellitus patients. However, these results are inconsistent.

METHODS

A Literature search was conducted in PubMed, Scopus, web of science and Science Direct from 2005 to August 2017. The necessary information was extracted. Heterogeneity was evaluated using I² statistic. Meta-regression analyses were performed to the estimation of the relationship between the year of study and sample size with the prevalence of NAFLD. Publication bias was assessed by both Begg rank correlation and Egger tests. Subgroup analysis was performed for identification of sources heterogeneity.

RESULTS

Seventeen studies involving 10897 type 2 diabetes mellitus patients with NAFLD were included in this meta-analysis. The overall prevalence of NAFLD in type 2 diabetes mellitus patients by random effects models was 54% (95% CI, 45%- 64%). There is a significant heterogeneity across studies with (I²= 99%, p> 0.01). The funnel plot as graphically and Begg and Egger as statistically showed no publication bias among studies. Subgroup analysis indicated that the prevalence of NAFLD in type 2 diabetes mellitus patients differed in predictive factors such as lipid profile, BMI, HbA1c, AST, and ALT. This finding in spite of heterogeneity of documents is corresponding to the positive correlation between NAFLD and type 2 diabetes mellitus.

CONCLUSION

The findings indicated that the overall prevalence of NAFLD among type 2 diabetes mellitus patients is significantly higher. It can be concluded that type 2 diabetes mellitus patients should be managed to prevent NAFLD.