Protein-protein interaction analysis of Alzheimer`s disease and NAFLD based on systems biology methods unhide common ancestor pathways

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

TGF-beta1 polymorphisms -509 C>T and +915 G>C and risk of pancreatic cancer

Aim: Our aim was to determine the association between TGF-beta1 polymorphisms at position -509 C>T [rs1800469] and +915 G>C [rs1800471] and pancreatic cancer susceptibility in Iranian population

Background: Ninety percent of pancreatic cancer patients have less than 5-year overall survival and approximately 50% of cases were diagnosed with metastasis in the time of admission. Previous evidences have demonstrated the strong association between TGF-beta1 variations and cancer susceptibility so far

Methods: A total of 78 patients with pancreatic cancer and 94 healthy controls were enrolled in this case control study from 2007-2012. Genomic DNA was isolated from peripheral blood samples according to phenol chloroform extraction. The genotypes of TGF-beta1 rs rs1800469 and rs1800471 were determined using the polymerase chain reaction-restriction fragment length polymorphism method

Results: The mean age of cases and the control group were 64.50 +/- 13.718 and 40.12 +/- 16.001, respectively. For polymorphism-509 C>T, the frequency of TT genotype were 31 [33.0], CT, 47[50] and CC, 16 [17] in control and 19 [24.4], 45 [57.7] and 14 [17.9] in cases respectively. In position +915 G>C, the frequency of GG genotype was 84 [89.4] and GC, 10 [10.6] in control and 71 [91.0] and 7 [9] in cases, respectively. We did not observe any significant differences in the genotype and allele frequencies of the TGF-beta1-509 C>T [rs1800469] and codon +915 G>C [rs1800471] between the two study groups [P>0.05]

Conclusion: we found that TGF-beta1 gene polymorphisms rs1800469 and rs1800471 might not play a role in pancreatic cancer susceptibility in Iranian population

Person centered prediction of survival in population based screening program by an intelligent clinical decision support system

Aim: To survey person centered survival rate in population based screening program by an intelligent clinical decision support system

Background: Colorectal cancer is the most common malignancy and major cause of morbidity and mortality throughout the world. Colorectal cancer is the sixth leading cause of cancer death in Iran. In this survey, we used cosine similarity as data mining technique and intelligent system for estimating survival of at risk groups in the screening plan

Methods: In the first step, we determined minimum data set [MDS]. MDS was approved by experts and reviewing literatures. In the second step, MDS were coded by python language and matched with cosine similarity formula. Finally, survival rate by percent was illustrated in the user interface of national intelligent system. The national intelligent system was designed in PyCharm environment

Results: Main data elements of intelligent system consist demographic information, age, referral type, risk group, recommendation and survival rate. Minimum data set related to survival comprise of clinical status, past medical history and socio-demographic information. Information of the covered population as a comprehensive database was connected to intelligent system and survival rate estimated for each patient. Mean range of survival of HNPCC patients and FAP patients were respectively 77.7% and 75.1%. Also, the mean range of the survival rate and other calculations have changed with the entry of new patients in the CRC registry by real-time

Conclusion: National intelligent system monitors the entire of risk group and reports survival rates by electronic guidelines and data mining technique and also operates according to the clinical process. This web base software has a critical role in the estimation survival rate in order to health care planning

Economic burden made celiac disease an expensive and challenging condition for Iranian patients

Aim: The aim of this study was to estimate the economic burden of celiac disease [CD] in Iran

Background: The assessment of burden of CD has become an important primary or secondary outcome measure in clinical and epidemiologic studies

Methods: Information regarding medical costs and gluten free diet [GFD] costs were gathered using questionnaire and checklists offered to the selected patients with CD. The data included the direct medical cost [including Doctor Visit, hospitalization, clinical test examinations, endoscopies, etc.], GFD cost and loss productivity cost [as the indirect cost] for CD patient were estimated. The factors used for cost estimation included frequency of health resource utilization and gluten free diet basket. Purchasing Power Parity Dollar [PPP dollars] was used in order to make inter-country comparisons

Results: Total of 213 celiac patients entered to this study. The mean [standard deviation] of total cost per patient per year was 3377 [1853] PPP dollars. This total cost including direct medical cost, GFD costs and loss productivity cost per patients per year. Also the mean and standard deviation of medical cost and GFD cost were 195 [128] PPP dollars and 932 [734] PPP dollars respectively. The total costs of CD were significantly higher for male. Also GFD cost and total cost were higher for unmarried patients

Conclusion: In conclusion, our estimation of CD economic burden is indicating that CD patients face substantial expense that might not be affordable for a good number of these patients. The estimated economic burden may put these patients at high risk for dietary neglect resulting in increasing the risk of long term complications

Network analysis of common genes related to esophageal, gastric, and colon cancers

Aim: The aim of this study was to provide a biomarker panel for esophageal, gastric and colorectal cancers. It can help introducing some diagnostic biomarkers for these diseases

Background: Gastrointestinal cancers [GICs] including esophageal, gastric and colorectal cancers are the most common cancers in the world which are usually diagnosed in the final stages and due to heterogeneity of these diseases, the treatments usually are not successful. For this reason, many studies have been conducted to discover predictive biomarkers

Methods: In the present study, 507 genes related to esophageal, gastric and colon cancers were extracted. The network was constructed by Cytoscape software [version 3.4.0]. Then a main component of the network was analyzed considering centrality parameters including degree, betweenness, closeness and stress. Three clusters of the protein network accompanied with their seed nodes were determined by MCODE application in Cytoscape software. Furthermore, Gene Ontology [GO] analysis of the key genes in combination to the seed nodes was performed

Results: The network of 17 common differential expressed genes in three esophageal, gastric and colon adenocarcinomas including 1730 nodes and 9188 edges were constructed. Eight crucial genes were determined. Three Clusters of the network were analyzed by GO analysis

Conclusion: The analyses of common genes of the three cancers showed that there are some common crucial genes including TP53, EGFR, MYC, AKT1, CDKN2A, CCND1 and HSP90AA1 which are tightly related to gastrointestinal cancers and can be predictive biomarkers for these cancers

systems biology analysis protein-protein interaction of NASH and IBD based on comprehensive gene information

Aim: Analysis reconstruction networks from two diseases, IBD and NASH and their relationship, based on systems biology methods

Background: IBD and NASH are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on co-existence of these two diseases. In addition, they have some similar risk factors such as age, obesity, and insulin resistance. 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. Based on degree and Betweenness, hubs and bottleneck nodes were defined

Results: Common genes between IBD and NASH construct a network with 99 nodes. Common genes between IBD and NASH were extracted and imported to STRING database to construct PPI network. The resulting network contained 99 nodes and 333 edges. Five genes were selected as hubs: JAK2, TLR2, TP53, TLR4 and STAT3 and five genes were selected as bottleneck including: JAK2, TP53, AGT, CYP3A4 and TLR4. These genes were hubs in analysis network that was constructed from hubs of NASH and IBD networks

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

Coexistence of KRAS and BRAF mutations in colorectal cancer: a case report supporting the concept of tumoral heterogeneity

The detection of KRAS and BRAF mutations is a crucial step for the correct therapeutic approach and predicting the epidermal growth factor receptor [EGFR]-targeted therapy resistance of colorectal carcinomas. The concomitant KRAS and BRAF mutations occur rarely in the colorectal cancers [CRCs] with the prevalence of less than 0.001% of the cases. In patients with KRAS-mutant tumors, BRAF mutations should not regularly be tested unless the patient is participating in a clinical trial enriching for the presence of KRAS or BRAF-mutated tumor. The current report demonstrates a case with advanced adenocarcinoma of the colon showing the coexistence of KRAS and BRAF mutations and may have profound clinical implications for disease progression and therapeutic responses

Syphacia obvelata: A New Hope to Induction of Intestinal Immunological Tolerance in C57BL/6 Mice

The ability of nematodes to manipulate the immune system of their host towards a Th2 and T regulatory responses has been proposed to suppress the inflammatory response. Clinical trials have proposed a useful effect of helminth infections on improvement of inflammatory disorders. In this study, we investigated the immunomodulatory effect of Syphacia obvelata infection to induce intestinal tolerance in C57BL/6 mice. Mice were infected through the cagemates with self-infected BALB/c mice. Four weeks post-infection, expression levels of IFN-γ, TNF-α, IL-17, and IL-10 were assessed in the supernatant of mesenteric lymph node (MLN) culture. Foxp3⁺Treg were measured in MLN cells by flow cytometry. In the S. obvelata-infected group, the percentage of Tregs (5.2±0.4) was significantly higher than the control (3.6±0.5) (P<0.05). The levels of IL-10 (55.3±2.2 vs 35.2±3.2), IL-17 (52.9±3.8 vs 41±1.8), IFN-γ (44.8±4.8 vs 22.3±2.3) and TNF-α (71.1±5.8 vs 60.1±3.3) were significantly increased in infected mice compared to the control group (P<0.05). The above results showed the potential effects of S. obvelata to induce intestinal tolerance. Therefore, it seems that S. obvelata may increase the immunological suppressive function in the intestinal tract.

experimental model of colitis induced by dextran sulfate sodium from acute progresses to chronicity in C57BL/6: correlation between conditions of mice and the environment

Aim: To induce acute colitis progresses to chronicity in C57BL/6 mice by dextran sulfate sodium

Background: Murine models are essential tools to understand IBD pathogenesis. Among different types of chemically induced colitis models, the dextran sulfate sodium [DSS]-induced colitis model is the most common model of IBD, due to its simplicity

Patients and methods: Male C57BL/6 mice 6-8 weeks old, were collected and matched by age with controls. C57BL/6 mice treated with 2 cycles of 3.5% DSS for 4 days and 4 days of pure water between each cycle. After that, mice were sacrificed and the entire colon was removed. Small sections of the colon were fixed in formaldehyde, embedded in paraffin and sectioned with a microtome. Sections were stained with hematoxylin eosin to analyses the degree of inflammation

Results: After the first cycle oral administration of DSS, mice with severe and visible rectal bleeding and diarrhea entered into the acute phase. After day 4-5, bleeding and diarrhea were improved and mice entered into the chronic phase with peak levels of weight loss. Macroscopically, the inflammation was predominantly located in the distal colon. Microscopically, examination of the distal colon sections showed a decrease number of goblet cells, loss of crypts, signs of surface epithelial regeneration and moderate to severe infiltration of inflammatory cells in the mucosa

Conclusion: In order to achieve an experimental colitis model, our protocol is recommended for future therapies in IBD experimental modeling

[Methanobrevibacter smithii isolation from human stool using specific rpoB gene]

Background: Archaea are Extrtermophile microorganisms and for several decades it has been believed that they are only found in harsh environments, such as volcanoes, deep oceans and salt lakes. However, at present time, their existence in human and mammal's intestine has been proved. The most important Archaea in human intestine is Methanobrevibacter smithii, which has a major role is some gastrointestinal disorders, as well as obesity. Therefore, Methanogens isolation and detection has such a crucial clinical importance. In this study, we isolated this microorganism for the first time using local technique

Materials and methods: In this study, Archaea DNA was extracted from healthy subject's stool samples, considering the specific criteria for choosing the healthy group. PCR reaction was performed to amplify the rpoB. Enzyme digestion was operated using restriction enzyme to confirm the rpoB gene. The PCR product was then cloned in E.coli [DH5alpha] host and sequencing process was performed

Results: Of 20 stool samples, the rpoB gene was confirmed in 18 samples [90%] and also the AVAII enzyme digestion results proved the gene identity. Sequencing results in NCBI site proved that isolated microorganisms were Methanobrevibacter smithii

Conclusion: This study revealed that by considering the microorganisms' variety in intestine, the precise gene detection methods for selecting the specific microbiota, in order to prevent existing similarities between homolog microbiota is vital in microbiota isolation

Comparison of three methods for mitochondria isolation from the human liver cell line [HepG2]

Aim: The aim of this study was to evaluate and compare three available methods for mitochondrial isolation from a human cell line to predict the best method for each probable application

Background: Organelle isolation is gaining importance in experimental laboratory settings. Mitochondrial dysfunction may affect tumorgenesis process. There are some evidences that transplantation of healthy, intact and active mitochondria into cells containing defective mitochondria may reduce the proliferation. Therefore, isolated mitochondria could be considered as an effective tool for assessment and management of mitochondrial related disorders

Patients and methods: Mitochondrial isolation from the human liver cell line [HepG2] was performed using two commercially available kits, including Qproteome [Qiagen] and MITOISO2 [Sigma-Aldrich], as well as a manual method. Integrity of inner membrane of mitochondria was assessed by JC-1 staining. Activity of isolated mitochondria was evaluated by DCFH-DA staining, and total yield of isolated mitochondria determined by micro-Lowry method. Finally, relative quantification using Real-time PCR was conducted to compare the mtDNA copy number of mitochondria isolated by three different methods

Results: Compared to other methods, manual kit resulted in higher yields of total amount of mitochondrial protein and mtDNA copy numbers. Isolated mitochondria by Qproteome kit, showed a higher activity. Finally, the integrity of inner-membrane of isolated mitochondria was significantly higher in Qproteome when compared with the other two methods

Conclusion: Due to differences in quality, quantity and activity of isolated mitochondria using three techniques discussed here, the method in which best-suited to each research project should be selected according to the distinct features of isolated mitochondria

Effect of vitamin D[3] supplementation on TNF-alpha serum level and disease activity index in Iranian IBD patients

The aim of the study was to assess the effectiveness of vitamin D[3] [1, 25[OH][2]D[3]] treatment in IBD with regard to tumor necrosis factor-alpha [TNF-alpha] serum level and clinical disease activity index [CDAI]. Vitamin D has immune-regulatory functions in experimental inflammatory bowel disease [IBD] and vitamin D deficiency is common in IBD patients. This was a randomized clinical trial on 108 IBD patients with serum 25-OHD levels less than 30ng/ml, which divided into vitamin D and control groups. Vitamin D group received 50000 IU vitamin D[3] for 12 weeks. Before and after the study, TNF-alpha and 25-OHD serum levels were measured by ELISA method. Data were analyzed using paired t-test, chi-square test and Spearman correlation coefficient. P-values less than 0.05 were considered statistically significant. Before the intervention no significant difference was found between baseline characteristics and TNF-alpha serum level of two groups. After intervention TNF-alpha serum level reduced but this reduction was not statistically significant [p=0.07, 95% CI: -0.45 to 8.14]. The mean serum 25-OHD level of vitamin D increased from 15.54 to 67.89, which was statistically significant [p= 0.00, 95% CI: -61.40 to -43.30]. TNF-alpha level was also associated significantly with CDAI before [Spearman's rho: 0.3, p<0.0001] and after [Spearman's rho: 0.27, P=0.01] intervention. Oral supplementation vitamin D[3] significantly increased serum vitamin D levels and insignificantly reduced serum TNF-alpha level. More studies with larger samples would be beneficial to assess vitamin D[3] supplementation efficient effect in IBD

Time trend analysis and demographic features of inflammatory bowel disease in Tehran

This retrospective study is aimed to review demographic and clinical characteristics of IBD to elucidate the probable factors associating with IBD development in Taleghani Hospital in Iran since 2001 during a 12-year-period. Ulcerative colitis [UC] and Crohn's disease [CD] are two major idiopathic entities of inflammatory bowel disease [IBD]. Previous studies have reported an increased incidence of IBD in Middle East countries. In the present study 1914 patients with UC, 318 patients with CD and 25 with indeterminate colitis [IC] were included. Demographic information, clinical features, extraintestinal manifestations, complications and extension of disease were collected and interpreted for all participants. According to the time of registration, patients were divided into seven groups. Statistical analysis was performed using the chi-square test. In seven groups of IBD patients, disease registry was estimated for UC, CD, and total IBD during a 12-year-period. From 2001 to 2005, a relative increased registry was observed among UC patients. However, in the years 2006 and 2007 a significant reduction in the number of patients was reported. Then an increasing trend was observed in UC patients. UC presented mostly with diarrhea, hematochezia and bloody diarrhea, while most of CD patients complained of abdominal pain. Evaluation of data related to registered IBD patients in Iran shows that probable incidence and prevalence of IBD [UC and CD] is increasing compared to previous decades

Polymorphism of SMAD 7 gene [rs2337104] and risk of colorectal cancer in an Iranian population: a case-control study

The purpose of this study was to evaluate the influence of intronic polymorphism of the SMAD7 [Mothers Against Decantaplegic Homolog 7] gene [rs2337104] on the risk of colorectal cancer [CRC] and clinicopathological features in an Iranian population. SMAD7 has been identified as an antagonist of transforming growth factor beta [TGF-b]-mediating fibrosis, carcinogenesis, and inflammation. Regarding to the recent genome-wide scan, a risk locus for colorectal cancer at 18q21 has been found, which maps to the SMAD7 gene. This case-control study was performed on 109 CRC patients and 109 healthy controls recruited in Taleghani Hospital. The genotyping of all samples were done by TaqMan assay via an ABI 7500 Real Time PCR System [Applied Biosystems] with DNA from peripheral blood. The association of this polymorphism with the risk of CRC and clinico pathological features was investigated. Our results indicated that there were no significant association between genotypic and allelic frequencies of SMAD7 polymorphism [rs2337104] and CRC risk in our population. Although the T allele is the most frequent one in this population and its frequency was 86.7% in patients compared with 91.7% in controls [OR=1.705, 95% CI= 0.916-3.172]. Also, the SMAD7 genotypes were not associated with any clinicopathological characteristics in CRC patients [P>0.05]. For the first time, this study results revealed that this SMAD7 polymorphism couldn't be a potential risk factor for CRC or a prognostic biomarker for prediction of clinicopathological features in an Iranian population. A large-scale case-control study is needed to validate our results

Potential treatment of inflammatory bowel disease: a review of helminths therapy

An inflammatory bowel disease [IBD] is most common in highly industrialized Western countries but uncommon in less developed areas of the world where helminths are frequent. The hygiene hypothesis proposes that the recent increase in allergic and autoimmune diseases is due to modern highly hygienic life styles and medical conditions. Loss of routine exposure to parasitic helminths, as a result of increasing lifestyle-associated factors, may be one factor leading to the increased disease prevalence. In animal models and clinical trials of IBD, gastrointestinal nematodes colonization suppresses intestinal inflammation through multiple mechanisms including induction of innate and adaptive regulatory circuits. Studies using helminths like Trichuris suis or Necator americanus showed that these helminths are safe and may be effective therapeutic approaches for the control of IBD and other immune diseases. The aim of present review was to exploring the therapeutic use of helminths for the control of IBD

Programmed death-1 gene polymorphism [PD-1.5 C/T] is associated with gastric cancer

This study aimed to determine the association between PD-1.5C/T [rs2227981, +7785] and the risk of gastric cancer [GC] in an Iranian population. Gastric cancer is the fourth most common cancer in the world. The programmed death 1 [PD-1] is a member of the CD28 super family. PD-1 is a negative regulator of T-cell effector mechanisms which decrease immune responses against cancer. we conducted case- control study to investigate the association of PD-1.5 C/T polymorphism in 122 GC patients and 166 control individuals. DNA was extracted from blood specimens. Genotypes were analyzed using polymerase chain reaction-restriction fragment length polymorphism [PCR-RFLP] assay. The frequency of CC, CT and TT genotypes was 53.6%, 42.2% and 4.2% in control group and 41%, 54.1% and 4.9% in gastric cancer patients respectively. CC genotype was more frequent in control individuals than in patients but we found no statically significant association. The frequencies of PD-1.5CT genotypes were significantly higher in GC patient compared with control individuals [OR= 1.77, 95% CI= 1.077-2.931; P=0.026]. Allele distribution was similar in patients and healthy individuals [p=0.061].Frequency of C and T alleles was 74.7%, 25.3% in control individuals and 68.03% and 31.97% in gastric cancer patients respectively. These results suggest that PD-1.5 C/T polymorphism may affect the GC risk and prognosis in an Iranian population

Clinical implications of BRAF mutation test in colorectal cancer

Knowledge about the clinical significance of V-Raf Murine Sarcoma Viral Oncogene Homolog B1 [BRAF] mutations in colorectal cancer [CRC] is growing. BRAF encodes a protein kinase involved with intracellular signaling and cell division. The gene product is a downstream effector of Kirsten Ras [KRAS] within the RAS/RAF/MAPK cellular signaling pathway. Evidence suggests that BRAF mutations, like KRAS mutations, result in uncontrolled, non-growth factor-dependent cellular proliferation. Similar to the rationale that KRAS mutation precludes effective treatment with anti-EGFR drugs. Recently, BRAF mutation testing has been introduced into routine clinical laboratories because its significance has become clearer in terms of effect on pathogenesis of CRC, utility in differentiating sporadic CRC from Lynch syndrome [LS], prognosis, and potential for predicting patient outcome in response to targeted drug therapy. In this review we describe the impact of BRAF mutations for these aspects

CpG island methylator phenotype [CIMP] in colorectal cancer

It is clear that colorectal cancer [CRC] develops through multiple genetic and epigenetic pathways. These pathways may be determined on the basis of three molecular features: [i] mutations in DNA mismatch repair genes, leading to a DNA microsatellite instability [MSI] phenotype, [ii] mutations in APC and other genes that activate Wnt pathway, characterized by chromosomal instability [CIN] phenotype, and [iii] global genome hypermethylation, resulting in switch off of tumor suppressor genes, indicated as CpG island methylator phenotype [CIMP]. Each of these pathways is characterized by specific pathological features, mechanisms of carcinogenesis and process of tumor development. The molecular aspects of these pathways have been used clinically in the diagnosis, screening and management of patients with colorectal cancer. In this review we especially describe various aspects of CIMP, one of the important and rather recently discovered pathways that lead to colorectal cancer

Polymorphism in two short tandem repeat loci [R-R and S -Q] linked to tRNA genes in entamoeba dispar isolates

In this study, genetic polymorphism of two tRNA-liked short tandem repeat [STR]-containing loci, R-R and S-Q, was analyzed in order to clarify further the genotypic differences among E. dispar isolates. Entamoeba dispar is closely related to the human pathogen E. histolytica, the agent of amebic dysentery and amebic liver abscesses. E. dispar is, to some extent, capable of producing variable focal intestinal lesions in animals and of destroying epithelial cell monolayers in vitro, and some have reported it to be capable of producing amoebic liver abscess in hamsters. However no evidence exists at present to link E. dispar with human disease. A total of 28 E. dispar samples from gastrointestinal disorder patients were characterized using PCR and sequencing. The sequences obtained were edited manually and aligned. Sequence analysis showed 9 and 6 different patterns of units in the repeat-containing region of R-R and S-Q, respectively. The repeat-containing regions of R-R and S -Q loci were found to be extensively polymorphic, varying in size, number and order of repeat units. The results demonstrate extensive genetic variability among Iranian E. dispar clinical isolates. The genetic diversity of tRNA gene-linked STR loci shows them to be suitable for epidemiological studies such as the characterization of the routes of transmission of these parasites in Iran