Gastroenterology and Hepatology from Bed to Bench

Gastrointestinal (GI) microbiota are known to play paramount role in inflammatory bowel disease (IBD). Innovative sequencing methods have radically expanded our ability to analyze the intestinal microbiome. However, alterations of the GI microbiome in IBD have not yet been fully evaluated. Irregular colonization of the gut has been implicated in chronic intestinal inflammation. Faecal microbiota transplantation (FMT) is a procedure which aims to restore microbial disturbances to the individual’s gut microbiome. The success of FMT in Clostridium difficile infection (CDI) has inspired studies to explore transplantation in other conditions such as IBD. Ulcerative colitis (UC) and Crohn’s disease (CD), the two principal manifestations of IBD, are emerging as a worldwide epidemic and are multifactorial in aetiology. There have been various case series in the past looking at the use of FMT in IBD, with a large number of them focusing on UC; however, two new randomized controlled trials shed up-to-date light on the complex interactions between the GI microbiome and patients. Regardless of these new studies, much more remains unknown about the efficacy and safety profile of FMT in IBD, ultimately casting a shadow over its use as a therapeutic intervention in conditions other than CDI. Further researches are necessary to fully evaluate the role of FMT as a management option in IBD. In this review, we discuss and summarize the functions of FMT in IBD, and the relationship between IBD and the GI microbial variations present.
Keywords: Inflammatory bowel disease, Ulcerative colitis, Crohn’s disease, Faecal microbiota transplantation.
(Please cite as: Patel K, Patel A, Hawes D, Shah J, Shah K. Faecal microbiota transplantation: looking beyond clostridium difficile infection at inflammatory bowel disease. Gastroenterol Hepatol Bed Bench 2018;11(1):1-8).

Aim: This study was intended to explore the effect of various drugs used to treat fatty liver on intimal-media thickness in patients with NAFLD.
Background: Nonalcoholic fatty liver disease (NAFLD) is an indicator of a broad spectrum of pathologic disorders, which is characterized with macro vesicular steatosis in the absent of alcohol use. It has a wide range of laboratory, clinical and pathological presentations such as simple steatosis to the diseases like non-alcoholic steatohepatitis, fibrosis, and cirrhosis and hepatocellular cancer.
Methods: In this cross - sectional study, as a part of a 10-year cohort study (from 2007-2017) at Tabriz University of Medical Sciences, a group of 100 patients with NAFLD were studied. They were examined by color doppler sonography of the carotid arteries to detect any carotid intima- media thickness, before and one year after treatment with various drugs. The effect of treatment on right and left carotid intima- media thickness (IMT) was examined by using SPSS. V21.
Results: Over all, 36 (36%) patients were male and 64 (64%) were female. The mean age of the patients was a 43.5±10.3 year, ranging from 16 to 64. The decrease in patients' intima- media thickness in both right and left carotids was statistically significant (P<0.0001).
Conclusion: Treatment of patients with nonalcoholic fatty liver has a significant role in reduction of their carotid intima -media thickness and consequently in reducing cerebrovascular events such as stroke.
Keywords: Carotid, Intima Media thickness; Color Doppler Sonography, Fatty Liver.
(Please cite as: Ghaffarifar S, Khoshbaten M, Dordaei F, Zareh Nahandi M, Javad-Rashid R, Shahnazi T. Is treatment of fatty liver effective on reducing carotid intima media thickness; a cohort study. Gastroenterol Hepatol Bed Bench 2018;11(1):9-14).

Aim: The aim of this study was to compare the Helicobacter pylori (HP) eradication regimens in patients with end stage renal disease.
Background: In patients undergoing hemodialysis, the pathologic changes seen in the stomach may be the result of high serum levels of gastrin, delayed gastric emptying or HP infection.
Methods: Our study was a randomized clinical trial in which 120 patients with ESRD (Patients who undergo hemodialysis) confirmed HP infection, were divided to four groups having 2-week eradication regimens; Group I: LCA (lansoprazole 30 mg-BD,clarithromycin 250 mg-BD, amoxicillin 500 mg-BD), Group II: LCM (lansoprazole 30 mg-BD,clarithromycin 250 mg-BD, metronidazole 500 mg-BD), Group III: LCAM (lansoprazole 30 mg-BD,clarithromycin 250 mg-BD,amoxicillin 500 mg-BD, metronidazole 500 mg-BD) and Group IV: Sequential (lansoprazole 30 mg-BDfor two weeks; first week: amoxicillin 500 mg-BD and second week: clarithromycin 250 mg-BD, metronidazole 500 mg-BD).6 weeks after treatment, Urea Breath Test (UBT) was performed for all patients.
Results: The mean age of patients was 43.1±11.2 years. 55.8% of patients were male. The success rates of HP eradication in 4 groups were76.7%, 70%, 90% and 90%, respectively. HP eradication rates were not statistically different among the regimens (p=0.11). There were not significant differences among the groups regarding demographic and anthropometric variables.
Conclusion: The results showed there was no significant difference between the success rates of HP eradication regimens for ESRD patients. According to approved regimen for 90% eradication rate, with a lower number of medications and given the less risk of side effects and drug interactions, the sequential regimen is the best.
Keywords: End Stage Renal Disease, Eradication therapy, Helicobacter pylori.
(Please cite as: Seyyed Majidi MR, Sanjari Pirayvatlou P, Rajabikashani M, Firoozabadi M, Seyed Majidi SA, Vafaeimanesh J. Comparison of Helicobacter pylori eradication regimens in patients with end stage renal disease. Gastroenterol Hepatol Bed Bench 2018;11(1):15-19).

Aim: This study was aimed to evaluating the efficacy of levofloxacin based sequential therapy vs clarithromycin based sequential therapy in h.pylori (HP) eradication.
Background: Several therapeutic regimen were investigated to treat HP infection. Sequential therapy is an alternative to classic triple therapy.
Methods: In this randomized clinical trial, 200 HP infected patients randomly divided into two therapeutic groups .1-Levofloxacin based sequential regimen (group A); omeprazole and amoxicillin for 7days followed by omeprazole, amoxicillin and levofloxacin for 7days. 2-clarithromycin based sequential regimen (group B): omeprazole and amoxicillin for 7days followed by omeprazole, amoxicillin and clarithromycin for 7days. HP eradication was evaluated with urea breath test with carbon 13 (UBT) 6 weeks after the end of treatment.
Results: Per protocol eradication rates of group A and B were 87.6% and 76% respectively. By intention to treat analysis, eradication rate of group A and B groups were 85.1% and 73% respectively. Levofloxacin based sequential regimen was more effective than clarithromycin based sequential regimen (Pv=0.028).
Adverse events were seen in 19.6% and 15.6% in group A and B respectively. Drug compliance was 97% in group A and 96% in group B. There was no significant difference between two groups in term of adverse events (p=0.470) and compliance (p=0.651).
Conclusion: Levofluxacin based sequential therapy was more effective than Clarithromycin based sequential therapy in HP eradication. The suggested Levofluxacin based sequential therapy could be an alternative therapy in area with high clarithromycin resistance. Further studies are needed to confirm these findings.
Keywords: sequential therapy, Levofluxacin, Clarithromycin, Helicobacter pylori eradication.
(Please cite as: Moradniani M, Mirbeik-Sabzevari Z, Jaferian S, Shafiezadeh SH, Ehsani Ardakani MJ, Mirzaee Roozbahany M, et al. Levofloxacin based vs clarithromycin based sequential therapy in helicobacter pylori eradication; a randomized clinical trial. Gastroenterol Hepatol Bed Bench 2018;11(1):20-26).

Aim: Analysis reconstruction networks from two diseases, NAFLD and Alzheimer`s diseases and their relationship based on systems biology methods.
Background: NAFLD and Alzheimer`s diseases are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on relation and same spreading pathways of these two diseases. In addition, they have some similar risk factors, exclusively lifestyle such as feeding, exercises and so on. Therefore, systems biology approach can help to discover their relationship.
Methods: DisGeNET and STRING databases were sources of disease genes and constructing networks. Three plugins of Cytoscape software, including ClusterONE, ClueGO and CluePedia, were used to analyze and cluster networks and enrichment of pathways. An R package used to define best centrality method. Finally, based on degree and Betweenness, hubs and bottleneck nodes were defined.
Results: Common genes between NAFLD and Alzheimer`s disease were 190 genes that used construct a network with STRING database. The resulting network contained 182 nodes and 2591 edges and comprises from four clusters. Enrichment of these clusters separately lead to carbohydrate metabolism, long chain fatty acid and regulation of JAK-STAT and IL-17 signaling pathways, respectively. Also seven genes selected as hub-bottleneck include: IL6, AKT1, TP53, TNF, JUN, VEGFA and PPARG. Enrichment of these proteins and their first neighbors in network by OMIM database lead to diabetes and obesity as ancestors of NAFLD and AD.
Conclusion: Systems biology methods, specifically PPI networks, can be useful for analyzing complicated related diseases. Finding Hub and bottleneck proteins should be the goal of drug designing and introducing disease markers.
Keywords: Alzheimer`s disease (AD), Non-alcoholic fatty liver disease (NAFLD), Protein-protein interaction (PPI) network analysis, Hub-bottlenecks, Protein clusters.
(Please cite as: Karbalaei R, Allahyari M, Rezaei-Tavirani M, Asadzadeh-Aghdaei H, Zali MR. Protein-protein interaction analysis of Alzheimer`s disease and NAFLD based on systems biology methods unhide common ancestor pathways. Gastroenterol Hepatol Bed Bench 2018;11(1):27-33).

Aim: In this study we attempt to indicate anti-carcinogenic influence of ether extracted metabolites of Streptomyces Levis sp. on gene expression in colon cancer.
Background: Colon cancer is one of the most prevalent cancers worldwide. In recent decades, researchers have been seeking the treatment for cancer. Natural products are valuable compounds with fewer side effects in comparison to chemotherapy drugs.
Methods: Secondary metabolites were extracted with the inoculation of bacterial sample in Mueller Hinton Broth. MTT assay was done to evaluate the cytotoxicity effect of metabolites on SW480 cells. qRT-PCR was performed to observe effects of metabolites on Bcl-2, P53, SOX2, KLF4, ?-Catenin, SMAD4, K-ras, BRAF genes expression in colon cancer.
Results: The metabolites exhibited cytotoxic effects on colon cancer in a dose/time dependent manner (P < 0.001). After 48 h treatment, fold expression of Bcl-2, SOX2, ?-catenin, K-ras, BRAF genes fold of expression were decreased, whereas P53, KLF4, SMAD4 genes were increased in treated cells (P < 0.001).
Conclusion: These findings indicate that ether extracted metabolites of Streptomyces Levis ABRIINW111 have anti-carcinogenic effects on colon cancer.
Keywords: Colon cancer, Metabolites, oncogenes, Streptomyces Levis ABRIINW111.
(Please cite as: Fatourachi P, Faramarziyan Azimi Maragheh B, Mohammadi SM, Valipour B, Dehnad A, Nozad Charoudeh H. Extracted metabolite from Streptomyces Levis ABRIINW111 altered the gene expression in colon cancer. Gastroenterol Hepatol Bed Bench 2018;11(1):34-41).

Aim: Our goal was to identify the putative association of rs4072111 variant in IL-16 gene and HCV susceptibility in an Iranian population.
Background: Interleukin 16 (IL-16), a multifunctional cytokine, plays a vital role in modulation of immune system.
Methods: In present case control and cross sectional study, IL-16 gene variant in 300 patients with hepatitis C (HCV) infection and 300 healthy individuals were analyzed. To evaluate this possible association, genomic DNA from venous blood was extracted and genotypes of IL-16 rs4072111 variant were determined by polymerase chain reaction- Fragments Length Polymorphism Technique (PCR-RFLP). Then, rs4072111 C/T genotypes frequency and allelic distribution were evaluated in each group.
Results: The results of genotyping showed 82% CC, 17.3% CT, 0.7% TT in the control group and 78% CC, 20% CT and 2% TT in the case group. The distribution of rs4072111 C allele was 90.7% in controls and 88% in case group respectively.
However, no correlation between IL-16 rs4072111 C/T variants and susceptibility to chronic HCV infection was found in the present study.
Conclusion: We concluded the rs4072111 C/T cannot be considered as a proper biomarker to identify susceptibility to chronic hepatitis C virus infection.
Keywords: profile.
(Please cite as: Karkhane M, Mohebbi SR, Azimzadeh P, Avarandeh H, Kazemian SH, Sharifian A, et al. Genetic association between a single nucleotide polymorphism in Interleukin-16 (rs4072111) and susceptibility to chronic HCV infection in an Iranian population. Gastroenterol Hepatol Bed Bench 2018;11(1):42-47).

Aim: In present study we have elucidated the role of 2758 A>G (rs696), in the recognition site of miR449a in the 3? UTR of NFKB inhibitor alpha (NFKBIA) gene, in development of sporadic colorectal cancer.
Background: Colorectal cancer (CRC) is rated as second cause of cancer death. Genetic determinants are considered as driving forces in development of sporadic CRC. Single nucleotide polymorphisms (SNPs), are attributed as the main genetic factor in cancers susceptibility. MicroRNAs, are key players in post-translational gene regulation by binding to their specific recognition sequences located at 3' untranslated region (UTR) of mRNAs.
Methods: A case–control study using 143 CRC patients and 137 noncancerous counterparts were undertaken in order to determine rs696 genotypes using polymerase chain reaction– restriction fragment length polymorphism (PCR–RFLP) method.
Results: There was a significant difference for the genotype frequencies of rs696 between patients and controls. The frequencies of GG, AG, AA genotypes in the control group were 38.7, 45.3, and 16.1 %, respectively, and the genotype frequencies in case group were 19.6, 40.6, and 39.9 %, respectively.
Conclusion: Our results suggest significant correlation between rs696 polymorphism and colorectal cancer risk.
Keywords: NFKBIA gene, microRNA, single-nucleotide polymorphism, colorectal Cancer.
(Please cite as: Simonian M, Mosallayi M, Miraghajani M, Feizi A, Khosravi SH, Salehi AR. Single nucleotide polymorphism rs696 in miR449a binding site of NFKBIA gene is correlated with risk of colorectal cancer.
Gastroenterol Hepatol Bed Bench 2018;11(1):48-53).

Aim: The aims of this study were to investigate antibiotic resistance pattern and molecular characterization of Salmonella Infantis strains, isolated from human sources in Tehran hospitals from 2008 to 2010.
Background: Infection caused by Salmonella is one of the major public health problems. Despite the clinical importance of Salmonella enteric subsp. enteric serovar Infantis in humans, there is no information available about the common clones of Salmonella Infantis in clinical isolates in Iran.
Methods: S. Infantis strains were identified by conventional microbiological and serological testing. The antimicrobial susceptibility of the S.Infantis isolates was determined using the disk diffusion method. The genetic relatedness and the dominant clones of S. Infantis strains were detected by the Multi Locus Sequence Typing (MLST) and pulsed-field gel electrophoresis (PFGE) techniques.
Results: More than 80% of the S. Infantis isolates represented multidrug-resistant patterns. PFGE revealed high genetic similarity among S. Infantis strains. While, MLST indicated high-clonal similarity among strains, where all S. Infantis strains were assigned to the ST32 sequence type.
Conclusion: This is the first study in Iran conducted to determine the sequence types of S. Infantis in clinical isolates using MLST. The genetically closed MDR S. Infantis clones were responsible for the apparent endemic occurrence of salmonellosis, caused by this Salmonella serovar, in Tehran.
Keywords: Salmonella Infantis, Multi Locus Sequence Typing, Iran.
(Please cite as: Ranjbar R, Rahmati H, Shokoohizadeh L. Detection of common clones of Salmonella enterica serotype Infantis from human sources in Tehran hospitals. Gastroenterol Hepatol Bed Bench 2018;11(1):54-59).

Aim: The present study was conducted to detect the occurrence, serogroups, virulence genes and phylogenetic relationship of shiga toxin-producing Escherichia coli (STEC) in human, clave and goat in Kerman (southeast of Iran).
Background: STEC have emerged as the important foodborne zoonotic pathogens causing human gastrointestinal disease and confirming the risk to public health.
Methods: A total of 671 fecal samples were collected from diarrheic patients (n=395) and healthy calves (n=156) and goats (n=120) and screened for the presence of stx gene. Furthermore, the prevalence of stx1 and stx2 variants, serotypes (O157, O145, O103, O26, O111, O91, O128, and O45), phylogenetic groups and the presence of ehxA, eae, hylA, iha and saa virulence genes were studied.
Results: Prevalence of STEC in human diarrheic isolates was 1.3% (5 isolates), in claves was 26.3% (41 isolates) and in goats was 27.5% (33 isolates). stx1 gene was the most prevalent variant and detected in 75 isolates. Furthermore, stx1c was the most predominant stx subtype, found in 56 isolates. The ehxA identified in 36 (45.6%) isolates, followed by iha 5 (6.3%), eaeA 4 (5.1%), hlyA 2 (2.5%) and saa 2 (2.5%). Most of the isolates belonged to phylogroup B1. Only two O26 and one O91 isolates were detected in our study.
Conclusion: Our results show that STEC strains were widespread among healthy domestic animals in the southeast of Iran
Keywords: Shiga toxin-producing E. coli, serogroup, virulence factors.
(Please cite as: Taghadosi R, Shakibaie MR, Alizade H, Hosseini-Nave H, Askari A, Ghanbarpour R. Serogroups, subtypes and virulence factors of shiga toxin-producing Escherichia coli isolated from human, calves and goats in Kerman, Iran. Gastroenterol Hepatol Bed Bench 2018;11(1):60-67).

Aim: This study is aimed to diagnose and analyze strongyloidiasis in a population of an endemic area of Iran using nested-PCR, coupled with parasitological methods.
Background: Screening of strongyloidiasis infected people using reliable diagnostic techniques are essential to decrease the mortality and morbidity associated with this infection. Molecular methods have been proved to be highly sensitive and specific for detection of Strongyloides stercoralis in stool samples.
Methods: A total of 155 fresh single stool samples were randomly collected from residents of north and northwest of Khouzestan Province, Iran. All samples were examined by parasitological methods including formalin-ether concentration and nutrient agar plate culture, and molecular method of nested-PCR. Infections with S. stercoralis were analyzed according to demographic criteria.
Results: Based on the results of nested-PCR method 15 cases (9.7%) were strongyloidiasis positive. Nested-PCR was more sensitive than parasitological techniques on single stool sampling. Elderly was the most important population index for higher infectivity with S. stercoralis.
Conclusion: In endemic areas of S. stercoralis, old age should be considered as one of the most important risk factors of infection, especially among the immunosuppressed individuals.
Keywords: elderly, molecular diagnosis, nested-PCR, Strongyloides stercoralis.
(Please cite as: Sharifdini M, Keyhani A, Eshraghian MR, Kia EB. Molecular diagnosis of strongyloidiasis in a population of an endemic area through nested-PCR. Gastroenterol Hepatol Bed Bench 2018;11(1):68-74).

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.
Keywords: Proteomics, cystic echinococcosis, Cluster, Hydatid cyst, 2-D electrophoresis (2?DE).
(Please cite as: Sadjjadi FS, Rezaie-Tavirani M, Ahmadi NA, Sadjjadi SM, Zali H. Proteome evaluation of human cystic echinococcosis sera using two dimensional gel electrophoresis. Gastroenterol Hepatol Bed Bench 2018;11(1):75-82).

A 13-year-old boy, known case renal stone disease came with the complaints of abdominal pain along with low grade fever. On examination, hepatosplenomegaly was noted while his lab reports showed a low hemoglobulin with a raised ESR. His blood and urine cultures showed no growth. Viral markers, autoimmune profile, C and p ANCA were all negative apart from a raised serum IgG level. Ultrasound abdomen showed a hyperechoic liver with an enlarged spleen along with splenic varices and minimum ascites. Ultrasound hepatic doppler was normal. Serum AFP levels were normal while workup for Wilson’s disease was negative. Fibroscan showed F4 fibosis. CT scan abdomen showed an enlarged left lobe of the liver along with an enlarged spleen. His EGD revealed varices. So liver biopsy was done that was suggestive of chronic granulomatous disease with ZN stain testing negative for TB.PPD, urine for AFB were both negative. Serum ACE levels were raised. He started ATT therapy but his condition did not improve. So, on the suspicion of hepatic sarcoidosis, he started on steroids and had a drastic improvement in his condition.
Keywords: Hepatic sarcoidosis; chronic granulomatous disease; steroids; Serum ACE levels.
(Please cite as: Achakzai IK, Majid Z, Khalid MA, Khan SA, Laeeq SM, Luck NH. Hepatic Sarcodosis presenting as portal hypertension in a young boy. Gastroenterol Hepatol Bed Bench 2018;11(1):220-228).

Melanosis of the stomach and duodenum is a rare entity and a striking finding diagnosed by upper gastrointestinal endoscopy. Here, we describe the case of an 83-year-old female, with a complicated medical history, who was referred to gastroenterologist to assess bleeding risk. From the endoscopy, it was determined that she had both melanosis gastri and duodeni. Although both are rare, gastric melanosis appears to be even more unusual than duodenal melanosis, with only a few reported cases documented in the literature thus far.
Keywords: Pseudomelanosis, Melanosis gastri, Melanosis duodeni, Hyperpigmentation
(Please cite as: Sunkara T, Caughey ME, Gaduputi V. Rare finding of concomitant pseudomelanosis of stomach and duodenum; case report and literature review. Gastroenterol Hepatol Bed Bench 2018;11(1):86-89).