A Nuclear Magnetic Resonance-Based Metabolomic Study to Identify Metabolite Differences between Iranian Isolates of Leishmania major and Leishmania tropica

Background

Cutaneous leishmaniasis caused by Leishmania species (L. spp) is one of the most important parasitic diseases in humans. To gain information on the metabolite variations and biochemical pathways between L. spp, we used the comparative metabolome of metacyclic promastigotes in the Iranian isolates of L. major and L. tropica by proton nuclear magnetic resonance (¹H-NMR).

Methods

L. tropica and L. major were collected from three areas of Iran, namely Gonbad, Mashhad, and Bam, between 2017 and 2018, and were cultured. The metacyclic promastigote of each species was separated, and cell metabolites were extracted. ¹H-NMR spectroscopy was applied, and the data were processed using ProMatab in MATLAB (version 7.8.0.347). Multivariate statistical analyses, including the principal component analysis and the orthogonal projections to latent structures discriminant analysis, were performed to identify the discriminative metabolites between the two L. spp. Metabolites with variable influences in projection values of more than one and a P value of less than 0.05 were marked as significant differences.

Results

A set of metabolites were detected, and 24 significantly differentially expressed metabolites were found between the metacyclic forms of L. major and L. tropica isolates. The top differential metabolites were methionine, aspartate, betaine, and acetylcarnitine, which were increased more in L. tropica than L. major (P<0.005), whereas asparagine, 3-hydroxybutyrate, L-proline, and kynurenine were increased significantly in L. major (P<0.01). The significantly altered metabolites were involved in eight metabolic pathways.

Conclusion

Metabolomics, as an invaluable technique, yielded significant metabolites, and their biochemical pathways related to the metacyclic promastigotes of L. major and L. tropica. The findings offer greater insights into parasite biology and how pathogens adapt to their hosts.

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.

Introducing Critical Pain-related Genes: A System Biology Approach

Introduction:

Pain is valuable in diagnosis and also warning of the patients. Many molecular reagents are introduced which are related to pain. In this research, the pain-related genes are screened to identify the critical ones.

Methods:

First, the pain-related genes were pulling out from the STRING database, and Cytoscape software was used to make the interactome unit. Then the central genes and their neighbors were analyzed. Finally, the genes were clustered, and the essential genes were introduced.

Results:

After analyzing 159 genes of the network, FOS, IL6, TNF, TAC1, IL8, and KNG1 were identified as the essential genes. Further analysis revealed that 88 genes are directly connected to the central genes. More resolution led to ignoring TNF and IL8 and considering SCN-alpha and PAICS as additional critical nodes.

Conclusion:

Six critical genes related to pain were identified. They can be potentially considered as new drug targets. Further investigation is required to introduce the central genes as a pain killer.

Evaluation of gene expression change in eosinophilic gastroenteritis

AIM

Screening differentially expressed genes (DEGs) related to Eosinophilic gastroenteritis (EG) to introduce possible biomarkers.

BACKGROUND

EG as a rare gastrointestinal disorder is characterized with gastrointestinal bleeding, crampy generalized abdominal pain, diarrhea, nausea, vomiting, and weight loss. In this study gene expression profile of patients is analysis via protein-protein interaction (PPI) analysis to reveal new prospective of disease.

METHODS

Top significant genes of gene expression profiles of 5 gastric antrum EG patients and 5gastric antrum control from GEO which were matched via boxplot analysis were screened via PPI network by using Cytoscape software and STRING database. Numbers of 20 top nodes of query DEGs based on degree value were introduced as central nodes which 7 critical central genes among them were identified. Gene ontology enrichment for the 20 central genes was done by using CluGO. Action map for the central genes was performed by applying CluePedia.

RESULTS

Among 20 central nodes, TXN, PRDX2, NR3C1, GRB2, PIK3C3, AP2B1 and REPS1 were recognized as critical central genes. Nine biological terms were determined that most of them were involved in the transport processes.

CONCLUSION

The introduced possible biomarkers can be used in the differential diagnosis of the disease and also in treatment of disorder.

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.

Prevalence of pterygium in Iran: a systematic review and meta-analysis study

Background and aim

Pterygium is one of the most prevalent pathologies involving the cornea, which can lead to various vision signs and even reduction in eyesight. No accurate estimate has been reported about the prevalence of pterygium in Iran. Hence, this study aimed to determine the pterygium prevalence in Iran by meta-analysis method.

Methods

Searching for data of the last eleven years (from 2004 to 2015) was conducted using the keywords of pterygium, eye, and Iran in International and domestic indexing services and databases including Iranmedex, Scientific Information Database (SID), Magiran, Irandoc, Medlib, IranPsych, Science Direct, Web of Science (Thomson Reuters), PubMed, and Scopus. The data were analyzed using the meta-analysis method (the random effects model). The disharmony of the studies was investigated using the I2 index. The data were analyzed by STATA Ver.11 software.

Results

In 5 studies conducted in Iran, with a sample size of 10,838 people between 2004 and 2015, the extent of the prevalence was estimated to be 11% (95% CI: 3 to 18%). Also, the prevalence of pterygium in women and men was 18% and 13%, respectively.

Conclusion

According to the published reports from Iran and its comparison with other points in the world, the prevalence of pterygium in Iran is high, especially among women.

Proteome evaluation of human cystic echinococcosis sera using two dimensional gel electrophoresis

AIM

Detection of protein expression changes in human cystic echinococcosis sera by 2D gel electrophoresis.

BACKGROUND

Diagnosis and successful treatment of cystic echinococcosis (CE) is a major challenge, up to now. Identification of related expressed proteins using proteomics tools and bioinformatics analysis of patients' sera have not been investigated, so far.

METHODS

Sera from eight confirmed CE patients and three healthy controls were collected, tested by 2-DE for total protein separation of serum and analyzed using proteomics and bioinformatics methods. The gels were stained by Coomassie blue followed by scan imaging of the gels. The protein spots in each gel were analyzed using progenesis same spots software. Proteins names were obtained from TagIdent server.

RESULTS

A total of 263 protein spots with different expression were detected in both normal and diseased samples. Comparison between diseased and normal gels showed the expression of 45 up-regulated protein spots with fold≥2 in diseased gel of which 10 were new proteins with statistical difference by normal gel (p-value<0.05). On the other hand, the expression of 50 down-regulated protein spots were observed of which 11 proteins have been suppressed. Clustering of all detected sera proteins (263) using correlation analysis, divided the proteins into 2 clusters based on up-regulated and down-regulated expression of proteins. Clustering results were approved by principal component analysis (PCA).

CONCLUSION

Significant protein expression changes in human CE sera which is demonstrable by application of proteomics and bioinformatics analysis makes it an impressing tool for diagnosis of CE patients.

Barrett's esophagus transits to a cancer condition via potential biomarkers

AIM

In this study, the transcriptome profile of Barrett's esophagus (BE) was examined for identification potential related biomarkers in view of interacting charactering.

BACKGROUND

Since BE is known as a precursor of esophageal cancer, the molecular studies of this condition could be essential.

METHODS

Gene expression data of BE in comparison with normal cases, GSE34619 was retrieved from Gene Expression Omnibus. Differentially expressed genes (DEGs) were determined applying GEO2R online software. The DEGs then were analyzed in terms of centrality properties via constructing an interaction network.

RESULTS

The data indicate that there are two sets of hub-bottlenecks panels with distinguishable values in BE. The first group shows that BE is very susceptible to develop cancer, and the second one implied on central characteristic of some DEGs as previously were also reported for BE pathogenicity. In addition, these genes are also implicated in cancer shift from certain conditions.

CONCLUSION

On the whole, taking together these findings explain and support the cancerous origin of BE and introduced a panel of nominated biomarkers that could be more specific for BE rather than other types of esophageal problems. However, a complementary study to support this claim is suggested.

Protein-Protein Interaction Analysis of Common Top Genes in Obsessive-Compulsive Disorder (OCD) and Schizophrenia: Towards New Drug Approach Obsessive-Compulsive disorder (OCD) and Schizophrenia Comorbidity Gene Analysis

Comorbidty is common among psychiatric disorders including obsessive-compulsive disorder and schizophrenia with a high rate. Many studies suggested that the disorders may have same etiological bases. In this regard, shared pathways of glutamate, dopaminergic, and serotonin are the known ones. Here, the common significant genes are examined to understand the possible molecular origin of the disorders in terms of sequence and functional features. Exploring the underling mechanisms of OCD and schizophrenia is important to achieve a better treatment options. Methods of Cytoscape software following R statistical software were applied for this purpose. Needleman-Wunsch global alignment algorithm was used to determine pair-wise similarities followed by clustering methods, AGNES and PAM in R statistical programming software. The results indicate that SLC1A1, DRD2, DRD4, BDNF, ESR1, CDH2, GRIN2B, TNFa, GABBR1, and OLIG2 are significantly common for the two disorders and PPI network analysis showed the important key genes in the interaction profile. ESR1 (estrogen receptor α) as a key hub-bottleneck gene regulates many underling mechanisms of the brain. Application of global alignments indicates some of the genes with sequence similarities also elucidate similar biological terms.

Impact of HIV infection in patients infected with chronic HCV (genotypes 1a and 3a): virological and clinical changes

BACKGROUND

Human immunodeficiency virus (HIV)/hepatitis C virus (HCV) coinfection has become a serious public health problem. The influence of HIV/HCV coinfection on plasma HCV RNA loads and clinical criteria which are usually regarded as a predictor of the progress of liver disease have not been reliably evaluated.

OBJECTIVES

This study investigated the impact of HIV infection on HCV RNA load and clinical indexes in Yazd and Tehran.

MATERIALS AND METHODS

HCV/HIV-coinfected patients and HCV-monoinfected controls were examined and compared for plasma HCV RNA and related risk factors such as HCV genotypes, liver enzymes, and transmission routes.

RESULTS

A total of 54 HCV/HIV-coinfected patients and 88 HCV-monoinfected controls were studied. The HCV RNA load mean was significantly higher in HCV/HIV-coinfected patients than in HCV-monoinfected patients (p < 0.001). HCV RNA load mean in patients infected with HCV without anti-HCV therapy was lower than HIV/HCV patients with and without highly active antiretroviral therapy that this difference was significant (p < 0.001). The HCV RNA levels were significantly higher in HIV/HCV genotype 3a coinfected patients than in genotype 3a monoinfected patients (p < 0.001). HIV RNA levels were lower in genotype 1a infected patients than in genotype 3a infected patients, but this difference was not significant statistically. The ALT mean levels were significantly higher in genotype 3a HIV/HCV-coinfected patients than in genotype 3a HCV-monoinfected patients (p < 0.001).

CONCLUSIONS

HIV/HCV coinfection leads to a significant increase in plasma HCV RNA. Further evaluations of the effects of ART and HIV infection on the course of HCV infection and the response to treatment against HCV infection in other and different genotypes are also needed. Moreover, HIV-infected patients should be screened regularly for HCV coinfection, particularly if they are in high-risk groups such as IDUs and recipients of blood transfusions.

Distribution of IL-28B genotypes in patients with hepatitis C and healthy individuals in Jahrom city

AIM

The purpose of this study was to compare the distribution of interleukin (IL)-28B genotypes between Iranian healthy individuals and patients with chronic hepatitis C based on the genotype.

BACKGROUND

Polymorphisms in the region of IL-28B gene have been identified as the strongest genetic pretreatment predictor of sustained virological response (SVR) in hepatitis C infection.

PATIENTS AND METHODS

In this study, 147 patients with chronic hepatitis C and 80 healthy individuals were included. The IL-28B rs12979860 and rs8099917 polymorphisms were genotyped by PCR-RFLP method and the frequency of IL-28B polymorphisms with respect to HCV genotypes was also determined.

RESULTS

The frequencies of rs12979860 TT, CC and CT genotypes in the chronic hepatitis C patients and healthy individuals were as follows: 10.8% vs. 11.3%, 38.7% vs. 46.2% and 50.3% vs. 42.5%. Also, the frequencies of rs8099917 TT, GG and GT genotypes in the chronic hepatitis C patients was 61.9%, 6.1% and 32% and in controls was 47.5%, 11.2% and 41.3%. The differences in the distribution of rs12979860 genotypes and alleles between HCV genotype 1 and HCV genotype 3a infected patients were statistically significant.

CONCLUSION

The rs12979860 C allele is the favorable allele for the spontaneous clearance of HCV. It seems that the impact of IL-28B polymorphism on the spontaneous clearance of HCV genotype 3 is more prominent than HCV genotype 1, which results in the observation of higher rs12979860 C allele frequency in chronic hepatitis C patients with HCV genotype 3 than HCV genotype 1.

Analytical assessment of interleukin - 23 and -27 cytokines in healthy people and patients with hepatitis C virus infection (genotypes 1 and 3a)

BACKGROUND

The immune system plays important roles in determining the outcomes of hepatitis C virus (HCV) infection. Interleukin-23 and -27 (IL-23 and IL-27) are two novel IL-12 cytokine family members known to enhance the T-lymphocyte response, but their precise involvement in HCV infection is not well known.

OBJECTIVES

We investigated the serum IL-27 and IL-23 levels in patients with HCV infection and in healthy individuals.

PATIENTS AND METHODS

In this case-control study, we assessed IL-23 and IL-27 levels in serum of 37 healthy individuals and 64 patients with chronic HCV using Enzyme-linked immunosorbent assay (ELISA). The relationship of cytokines level with liver enzymes (ALT, AST, and ALP), HCV genotype and viral load were analyzed. The differences of these cytokine levels in the groups of treatment and no treatment was compared. HCV genotypes were classified by HCV-specific primers methods. HCV RNA loads were determined by fluorescence quantitative PCR.

RESULTS

Serum level of IL-23 was higher in HCV infected patients compared to control group (P = 0.005). However, no significant difference was seen in IL-27 serum level between patients compared to the control group (P = 0.65). There was no significant difference in IL-23 and IL-27 level between genotype 1 HCV-infected- and 3a HCV-infected- patients. Positive moderate correlation between IL-23 and IL-27 with viral load was found in type 3a and 1 HCV-infected patient. Positive relative correlation was seen between ALT and IL-23 in 1a HCV-infected patients, which was higher than 3a HCV-infected patients; but there were no significant difference between serums liver enzymes with IL-23 and IL-27 in respect to genotype 3a and 1a HCV-infected patients.

CONCLUSIONS

These findings may reflect a vigorous pro-inflammatory reaction orchestrated by the host immune system against chronic HCV. Also, a better understanding of the involvement mechanism considering the correlation between other genotypes with inflammatory cytokines in various stages of disease can be obtained.

WITHDRAWN: An overview of the present status of hospital waste management in Kerman, Iran

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Molecular epidemiology of different hepatitis C genotypes in serum and peripheral blood mononuclear cells in jahrom city of iran

BACKGROUND

The Hepatitis C Virus (HCV) is considered essentially hepatotropic, yet the virus compartments have also been found in important extra hepatic sites. Detection of HCV RNA in extra hepatic reservoirs such as peripheral blood mononuclear cells (PBMCs) is important for determining disease progression and treatment effectiveness.

OBJECTIVES

The present study aimed to determine different HCV genotypes in patients' plasma and PBMC specimens, in Jahrom city of Iran.

PATIENTS AND METHODS

Blood samples of 137 patients with established HCV were collected at the Honari clinic. These patients were anti-HCV and plasma HCV RNA positive. After plasma RNA extraction and obtaining a pellet of approximately 3-5 × 10(6) PBMCs, Real-time PCR was performed, using specific-genotype primers. Finally, data analysis was done by the Statistical Package for Social Sciences (SPSS) software.

RESULTS

Subtype 3 was the most common genotype in plasma (57.7%) and PBMCs (51.1%). Subtype 1a was detected in 36.5% and 30.7% of plasma samples and PBMCs, respectively whereas subtype 4 was not detected in any of the cases. There was a genotype difference between plasma and PBMCs of 12.4% of patients. In four patients no genotype was detected in their plasma but genotype 3 was detected in the PBMCs.

CONCLUSIONS

It is suggested that determination of the target genotype by plasma subtyping for choosing the proper antiviral therapy is essential but may result in therapy failure. HCV genotyping in PBMC samples, along with plasma specimens, might be more beneficial. Therefore determining the HCV genotype in PBMCs, before beginning the therapy is useful due to the possibility of occult infection detection.

First survey of cutaneous leishmaniasis in Borujerd county, western Islamic Republic of Iran

Lorestan province in the Islamic Republic of Iran has not previously been known as a focus for cutaneous leishmaniasis (CL). Clinical and epidemiological studies were carried out on patients diagnosed with active CL at the central laboratory in Borujerd city during 1998-2010. A total of 137 patients with corroborated CL were studied (mean estimated annual incidence 4.36 per 100 000 inhabitants). The male:female ratio was > 11:1. Patients ranged in age from 8-63 years but > 70% were aged 21-40 years and only 1 was < or = 10 years. The rate of CL was highest in rural residents (56.9%) and among those working as labourers (38.0%) and drivers (32.8%). The rate of active lesions on the upper limbs (69.3%) was significantly higher than other locations, and more cases were dry sores (57.7%) than wet sores (42.3%). The majority of patients (61.3%) had a single active lesion (mean 1.8 ulcers per patient). This is the first report of CL in the area.

Using morphometry of the larval rostellar hooks to distinguish Iranian strains ofEchinococcus granulosus

Human cystic echinococcosis is widely distributed throughout Iran, where sheep, cattle, goats, camels and other animals act as intermediate hosts. It appears that morphometry of the rostellar hooks on the protoscoleces of the causative parasite, Echinococcus granulosus, can be used to separate the strains or variants of the parasite to be found in humans and livestock in Iran. Multivariate statistical procedures, including principal-component analysis and discriminant-function analysis (DFA), were used to explore the morphometric data obtained from the larval hooks of Iranian samples of E. granulosus. Although five physical variables were initially considered, the results of the PCA indicated that just two factors (based on the length of hooks and number of hooks) accounted for 91.6% of the variance observed in the hook measurements. The results of the DFA allowed the correct classification of all the samples. The presence in Iran of the sheep and camel strains of the parasite was confirmed. The sheep strain was the most common variant encountered, being recovered from sheep, cattle, goats, humans and occasionally camels. Most of the metacestode samples from camels and a few of those from cattle (five of 30), sheep (one of 27) and humans (two of 23) were found to be of the camel strain. These results indicate that larval-hook morphology is a valid method for identifying E. granulosus strains in Iran, and one that is potentially useful for epidemiological studies.

Human hydatidosis in Tehran, Iran: a retrospective epidemiological study of surgical cases between 1999 and 2009 at two university medical centers

This study was conducted to evaluate retrospectively 203 patients diagnosed with hydatid cyst disease and treated surgically at two university medical centers between 1999 and 2009 in Tehran, the capital of Iran. Cystic echinococcosis (CE) affected more females 117 (57.6%) than males 86 (42.4%). A remarkable gender difference skewed towards females was observed, and the male/female ratio among CE cases ≤20 and ≥61 years old was 1.18 and 0.52, respectively. The age of the patients ranged from 8 to 82 years, and the age group 21-40 years (42.8%) was the most affected. A significantly higher number of hydatid cysts were recorded in the liver than in other sites (P<0.001), and more females had higher hepatic cysts (48.8%) than males (35.0%). The ratio of hepatic hydatidosis to pulmonary hydatidosis was about 11. There was a relative direct relationship between the ratio of liver to lung cases and age, and this ratio was significantly (P<0.01) higher in individuals >40 years of age (liver/lung ratio ≥43) than in those <40 years of age (liver/lung ratio 2.8-7.6). Unusual cyst locations in kidneys, brain and pelvic area, followed by spleen and spine was also observed. Single organ involvement was found in 95% of the patients, and was more common in females (55.2%) than in males (39.9%). Housewives had the highest rate of infection (53.5%) followed by labourers with 14.8%, which showed a significant difference (P<0.001). Similarly, urban dwellers was also over-represented among the cases (87% urban vs. 13% rural; P<0.001). In 69.5% of cases there was only one cyst, 16.3% had two cysts, 4.7% with three cysts, and 9.5% had four cysts or more. The results showed that further studies are needed to determine the prevalence, economic impact and risk factors of the disease in the area.

Hydatidosis in camels (Camelus dromedarius) and their potential role in the epidemiology of Echinococcus granulosus in Iran

Hydatid cysts were recovered from 35.2% (233/661) of camels (Camelus dromedarius) slaughtered in five different regions of Iran. The degree of prevalence between males (34.4%) and females (36.6%) was not statistically significant. The highest rate of infection (59.3%) was found in the Isfahan region (in the central part of Iran) while the lowest (25.7%) was found in Kerman province. The organ distribution of cysts was 49.4% in lungs alone, 30.0% in both liver and lungs, 14.6% in liver only and 6.0% in other organs. Therefore, the lungs were the predominant sites of the hydatid cyst. The range in the number of cysts was 1–48 in infected animals. The majority of the camels had 1–5 cysts, with 21.9%, 11.6% and 5.6% of infected camels having 6–10, 11–20 and 21 or more cysts respectively. There was a direct relationship between the rate and intensity of infection and host age. The fertility rate of lung cysts (69.7%) was higher than that of liver cysts (58.7%) and other organs (50.0%) whilst the viability rate of protoscoleces of liver fertile cysts (80.3%) was significantly higher than that of lung cysts (55.8%) and other organs (57.1%). The role of camels in the epidemiology of Echinococcus granulosus in Iran is discussed.