Protein-protein interaction network analysis for a biomarker panel related to human esophageal adenocarcinoma

Background: Esophageal adenocarcinoma (EAC) is one of the mostlethal cancers in the world with a very poor prognosis. Identification of molecular diagnostic methods is an important goal. Since protein-protein interaction (PPI) network analysis is a suitable method for molecular assessment, in the present research a PPI network related to EAC was targeted. Material and Method: Cytoscape software and its applications including STRING DB, Cluster ONE and ClueGO were applied to analyze the PPI network. Result: Among 182 EAC-related proteins which were identified, 129 were included in a main connected component. Proteins based on centrality analysis of characteristics such as degree, betweenness, closeness and stress were screened and key nodes were introduced. Two clusters were determined of which only one was significant statistically. Gene ontology revealed 50 terms in three groups associated with EAC. Conclusion: The findings indicate nine crucial proteins could form a candidate biomarker panel for EAC. Furthermore, an important cluster with 27 proteins related to the disease was identified. Gene ontology analysis of this cluster showed main related terms to closely correspond with those for colorectal cancer

Protein-protein interaction network analysis for a biomarker panel related to human esophageal adenocarcinoma

Background: Esophageal adenocarcinoma (EAC) is one of the mostlethal cancers in the world with a very poor prognosis. Identification of molecular diagnostic methods is an important goal. Since protein-protein interaction (PPI) network analysis is a suitable method for molecular assessment, in the present research a PPI network related to EAC was targeted. Material and Method: Cytoscape software and its applications including STRING DB, Cluster ONE and ClueGO were applied to analyze the PPI network. Result: Among 182 EAC-related proteins which were identified, 129 were included in a main connected component. Proteins based on centrality analysis of characteristics such as degree, betweenness, closeness and stress were screened and key nodes were introduced. Two clusters were determined of which only one was significant statistically. Gene ontology revealed 50 terms in three groups associated with EAC. Conclusion: The findings indicate nine crucial proteins could form a candidate biomarker panel for EAC. Furthermore, an important cluster with 27 proteins related to the disease was identified. Gene ontology analysis of this cluster showed main related terms to closely correspond with those for colorectal cancer

Protein interaction mapping related to to becker muscular dystrophy

Objective Becker Muscular Dystrophy (BMD) is a neuromuscular disorder which is incurable. In this research protein interaction network of most associated proteins with BMD to provide better clarification of disorder underlying mechanism was investigated. Materials & Methods The related genes to BMD were retrieved via string database and conducted by Cytoscape and the related algorithms. The network centrality analysis was performed based on degree, betweenness, closeness, and stress parameters. Gene ontology and clustering were performed via ClueGO analysis. Results DMD as the super-hub as well as other central proteins including UTRN, TTN, DNM2, and RYR1 are important in BMD in terms of interactive features. The impairment of muscular contraction may be vital in BMD disease pathogenesis as it is the highlighted biological process term obtained by ClueGO analysis. Conclusion DMD targeting may be the main concern for dystrophy clinical approaches. However, the other suggested proteins should be evaluated. Targeting these key proteins are required for treatment goals following extensive validation studies. © 2019, Iranian Child Neurology Society. All rights reserved

Interpretation of tongue squamous cell carcinoma via protein-protein interaction network construction and analysis

Background: Tongue squamous cell carcinoma is one of the prominent cancers in the oral cavity. Molecular investigations based on interaction analysis can be promising towards providing a better resolution of malignant neoplasms. Here, the protein-protein interaction network of tongue cancer is studied. Methods: The protein-protein interaction network was constructed by the application of Cytoscape 3.5.1 and the related algorithms. Centrality analysis via the degree, betweenness, and closeness centralities was conducted. Results: The result indicated that there are seven chief proteins in the network foundation. Moreover, enrichment evaluation suggested two associated biological processes including Response to UV-A, Response to interlukin-7, cellular response to alcohol, and catenin import into nucleus process using CluePedia. Conclusions: It can be concluded that the identified central panel proteins and their related biological processes can shed light on the neoplasm mechanisms and are worth pursuing for clinical approaches. © 2018, Cancer Research Center (CRC), Shahid Beheshti University of Medical Sciences

Interpretation of tongue squamous cell carcinoma via protein-protein interaction network construction and analysis

Background: Tongue squamous cell carcinoma is one of the prominent cancers in the oral cavity. Molecular investigations based on interaction analysis can be promising towards providing a better resolution of malignant neoplasms. Here, the protein-protein interaction network of tongue cancer is studied. Methods: The protein-protein interaction network was constructed by the application of Cytoscape 3.5.1 and the related algorithms. Centrality analysis via the degree, betweenness, and closeness centralities was conducted. Results: The result indicated that there are seven chief proteins in the network foundation. Moreover, enrichment evaluation suggested two associated biological processes including Response to UV-A, Response to interlukin-7, cellular response to alcohol, and catenin import into nucleus process using CluePedia. Conclusions: It can be concluded that the identified central panel proteins and their related biological processes can shed light on the neoplasm mechanisms and are worth pursuing for clinical approaches. © 2018, Cancer Research Center (CRC), Shahid Beheshti University of Medical Sciences

Protein-protein interaction network analysis of human fibroblast cells treated with ethanol

Introduction: Studies show that ethanol can induce changes in proteomic profile of human fibroblast cells. Some of these proteins are important in promoting cancer. Thus, analyzing function and interaction networks of these proteins are essential for better understanding the carcinogenesis mechanism of ethanol. Materials and Methods: In this study the protein-protein interaction network (PPI) of six significant down-regulated proteins in human fibroblast cells (HFFF2) treated with ethanol were analyzed by using Cytoscape software and its algorithms. Results: PPI network analysis showed that the constructed network consisted of 756 nodes and 1166 edges. Results indicated that Heterogeneous nuclear ribonucleoprotein A1 with degree = 528 and Betweenness Centrality = 0.74 is a hub protein that ethanol can alter its expression. In addition, module evaluation showed that the hub protein has a key role in different overlapped complexes. On the other hand, annotation studies by using DAVID program indicated that this protein is involved in different important biological processes in the cell. Conclusion: The six down-regulated proteins treated with ethanol may become carcinogenic and can impose vast alterations in other vital biological processes of the cell. Among them, Heterogeneous nuclear ribonucleoprotein A1 is the most important one. © 2016, Semnan University of Medical Sciences. All rights reserved

Apoptosis/necrosis induction by ultraviolet, in ER positive and ER negative breast cancer cell lines

Background: Ultraviolet (UV) light exposure has been one of the major inducers of apoptosis. UV exposure has caused pyrimidine dimers and DNA fragmentation which might lead to cell cycle arrest and apoptosis signals activation. UV induced apoptosis has investigated in MDA-MB 468 as an ER negative breast adenocarcinoma and MCF-7 as an ER positive breast cancer cell line. Apoptosis induction rate by UV might be different in these two types of cells due to different biological characteristics of the cell. Objectives: In this paper we have evaluated serial dose of UV-B exposure on ER positive and ER negative breast cancer cell lines and its effect on apoptosis or necrosis induction in these cells. Materials and Methods: MDA-MB468 and MCF-7 cell lines have cultured for 24 hours and UV exposure has carried out at 290 nm at dose of 154 J/m2 to 18 KJ/m2 using UV lamp. UV exposed cells have incubated in cell culture condition for 24 or 48 hours following UV exposure and the cells have stained and analyzed by flow cytometry for apoptosis evaluation by Annexin V/PI method. Results: Apoptosis rate (PI and Annexin V double positive cells) after 24 hours incubation was higher in 24 hours in comparison with 48 hours incubation in both cell lines. The frequency of PI positive MDA-MB 468 cells was higher than PI and Annexin V double positive cells after 48 hours. PI positive MDA-MB 468 cells were significantly higher than MCF-7 cells in 24 hours incubation time. Conclusions: The results have shown that MDA-MB 468 cells were more sensitive to UV exposure and DNA fragmentation and necrosis pathway was dominant in these cells. © 2015, Iranian Journal of Cancer Prevention

Zn/Cu Levels in the Field of Autism Disorders: A Systematic Review and Meta-analysis

How to Cite This Article: Sayehmiri F, Babaknejad N, Bahrami S, Sayehmiri K, Darabi M, Rezaei-Tavirani M. Zn/Cu Levels in the Field of Autism Disorders: A Systematic Review and Meta-analysis. Iran J Child Neurol. Autumn 2015;9(4):1-9.AbstractObjectiveThere is probably a relationship between zinc/cupper concentration in individualswith autism. The present review was written to estimate this probability by using meta-analysis method.Martials & MethodsIn this meta-analysis of Fixed Effect Model, by searching PubMed, Scopusand Google scholar databases, 11 articles were selected and verified publishedin 1978 to 2012. I² statistics were calculated to examine heterogeneity. Theinformation was analyzed by R and STATA Ver. 11.2.ResultsDue to non-uniform measurement methods of Zn/Cu concentrations, theconcentration of these elements was measured in various subgroups (plasma,hair and general) in both study cases and controls. There was a significantstatistical difference between plasma OR=0.252 (95% CI: -0.001-0.504) andhair OR=0.27(95% CI: 0.059-0.481, P=0.01) concentrations of Zn/Cu statusesbetween controls and autistic patients. Using a Fixed Effects Model, the overall integration of data from the two groups was significant as risk factorOR=0.31(95% CI:0.16-0.46, P=0.001).ConclusionSignificant correlation existed between Zn/Cu levels and the development ofautistic disorders in general analysis. Therefore, Zn/Cu levels could be mentioned as a pathogenesis reason of autism spectrum disorders

Acellular Fish Skin for Deep Dermal Traumatic Wounds Management; Introducing a Novel Dressing

The optimal therapy for deep wounds is based on the early debridement of necrotic tissue followed by wound coverage to avoid a systemic inflammatory response and optimize scar-free healing. The outcomes are affected by available resources and underlying patient factors, which cause challenges in wound care and suboptimal outcomes. Here we report a patient with deep dermal injury wounds, who was treated with platelet-rich fibrin (PRF) gel, plasma rich in growth factor (PRGF) gel, and acellular fish skin. Patient’s outcomes regarding healing and scar quality were collected objectively and subjectively for one year after the injury. Wounds treated with acellular fish skin demonstrated accelerated wound healing, a significantly higher water-storage capacity, and better pain relief. Furthermore, improved functional and cosmetic outcomes, such as elasticity, skin thickness, and pigmentation, were demonstrated. It seems that, the PRGF gel and PRF in combination with acellular fish skin grafts resulted in the faster healing of wounds and better functional and aesthetic outcomes than split-thickness skin grafts treatment

The Main Targets of Okadaic Acid Toxin in Human Intestinal Caco-2 Cells: An Investigation of Biological Systems

Background: Okadaic acid (OA) is a toxin of polluted shellfish. Consuming the contaminated shellfish is accompanied by diarrhea and paralytic and amnesic disorders. There is a correlation between diarrhea and the consumed OA. Determining the critical targeted genes by OA was the aim of this study. Methods: The transcriptomic data about the effect of OA on human intestinal caco-2 cells were extracted from gene expression omnibus (GEO) and evaluated via the GEO2R program. The significant differentially expressed genes (DEGs) were included in a protein-protein interaction (PPI) network and the central nodes were enriched via gene ontology to find the crucial affected biological terms. Results: Among the 178 significant DEGs plus 50 added first neighbors, four hub-bottleneck genes (ALB, FOS, JUN, and MYC) were determined. Twenty-eight critical biological terms were identified as the dysregulated individuals in response to the presence of OA. “ERK1/2-activator protein-1 (AP-1) complex binds KDM6B promoter” was highlighted as the major class of biological terms. Conclusion: It can be concluded that down-regulation of ALB as a potent central gene leads to impairment of blood homeostasis in the presence of OA. Up-regulation of the other three central genes (JUN, FOS, and MYC) grossly affects the vital pathways in the human body