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Aim: The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction network interpretation in comparison to esophageal adenocarcinoma
Background: Oral squamous cell cancer [OSCC] is a common disease worldwide, with poor prognosis and limited treatment. Thus, introducing molecular markers through network analysis can be helpful
Methods: STRING database [DB] was applied for network construction through Cytoscape 3.4.0. Clue GO handled the gene annotation for the retrieved clusters. Eight proteins were indicated to be differential in the network constitution
Results: The centrality and clustering analysis indicate that TP53 plays an over-significant role in network integrity among eight most central proteins including TP53, AKT1, EGFR, MYC, JUN, CDH1, CCND1, and CTNNB1. The suggested biomarker set is very similar to the related biomarker panel of esophageal adenocarcinoma
Conclusion: The ontology analysis implies that the prominent proteins are involved in regulation of smooth muscle cell proliferation, regulation of fibroblast proliferation, and response to UV-A processes. In conclusion, these proteins and their associated biological processes may be more critical compared to other reported biomarkers for OSCC. Nevertheless, validation studies are required for confirming the pivotal role of potential candidates. Similar biomarker panel of this disease and esophagus adenocarcinoma is corresponded to the origin of the two malignancies
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Aim: The main goal of this analysis was prioritization of co-expressed genes and miRNAs that are thought to have important influences in the pathogenesis of colon and lung cancers
Background: MicroRNAs [miRNAs] as small and endogenous noncoding RNAs which regulate gene expression by repressing mRNA translation or decreasing stability of mRNAs; they have proven pivotal roles in different types of cancers. Accumulating evidence indicates the role of miRNAs in a wide range of biological processes from oncogenesis and tumor suppressors to contribution to tumor progression. Colon and lung cancers are frequently encountered challenging types of cancers; therefore, exploring trade-off among underlying biological units such as miRNA with mRNAs will probably lead to identification of promising biomarkers involved in these malignancies
Methods: Colon cancer and lung cancer expression data were downloaded from Firehose and TCGA databases and varied genes extracted by DCGL software were subjected to build two gene regulatory networks by parmigene R package. Afterwards, a networkdriven integrative analysis was performed to explore prognosticates genes, miRNAs and underlying pathways
Results: A total of 192 differentially expressed miRNAs and their target genes within gene regulatory networks were derived by ARACNE algorithm. BTF3, TP53, MYC, CALR, NEM2, miR-29b-3p and miR-145 were identified as bottleneck nodes and enriched via biological gene ontology [GO] terms and pathways chiefly in biosynthesis and signaling pathways by further screening
Conclusion: Our study uncovered correlated alterations in gene expression that may relate with colon and lung cancers and highlighted the potent common biomarker candidates for the two diseases
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Aim: Evaluation of biological characteristics of 13 identified proteins of patients with cirrhotic liver disease is the main aim of this research
Background: In clinical usage, liver biopsy remains the gold standard for diagnosis of hepatic fibrosis. Evaluation and confirmation of liver fibrosis stages and severity of chronic diseases require a precise and noninvasive biomarkers. Since the early detection of cirrhosis is a clinical problem, achieving a sensitive, specific and predictive novel method based on biomarkers is an important task
Methods: Essential analysis, such as gene ontology [GO] enrichment and protein-protein interactions [PPI] was undergone EXPASy, STRING Database and DAVID Bioinformatics Resources query
Results: Based on GO analysis, most of proteins are located in the endoplasmic reticulum lumen, intracellular organelle lumen, membrane-enclosed lumen, and extracellular region. The relevant molecular functions are actin binding, metal ion binding, cation binding and ion binding. Cell adhesion, biological adhesion, cellular amino acid derivative, metabolic process and homeostatic process are the related processes. Protein-protein interaction network analysis introduced five proteins [fibroblast growth factor receptor 4, tropomyosin 4, tropomyosin 2 [beta], lectin, Lectin galactoside-binding soluble 3 binding protein and apolipoprotein A-I] as hub and bottleneck proteins
Conclusion: Our result indicates that regulation of lipid metabolism and cell survival are important biological processes involved in cirrhosis disease. More investigation of above mentioned proteins will provide a better understanding of cirrhosis disease
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Metabolome analysis is used to evaluate the characteristics and interactions of low molecular weight metabolites under a specific set of conditions. In cirrhosis, hepatocellular carcinoma, non-alcoholic fatty liver disease [NAFLD] and non-alcoholic steatotic hepatitis [NASH] the liver does not function thoroughly due to long-term damage. Unfortunately the early detection of cirrhosis, HCC, NAFLD and NASH is a clinical problem and determining a sensitive, specific and predictive novel method based on biomarker discovery is an important task. On the other hand, metabolomics has been reported as a new and powerful technology in biomarker discovery and dynamic field that cause global comprehension of system biology. In this review, it has been collected a heterogeneous set of metabolomics published studies to discovery of biomarkers in researches to introduce diagnostic biomarkers for early detection and the choice of patient-specific therapies
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Aim: The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease
Background: Celiac disease [CD] is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye andbarley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug targetdiscovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiacdisease
Material and Methods: In the present study, we collected the articles that focused on the proteomic data in celiac disease.According to the gene expression investigations of these articles, 31 candidate proteins were selected for this study. Thenetworks of related differentially expressed protein were explored using Cytoscape 3.3 and the PPI analysis methods suchas MCODE and ClueGO
Results: According to the network analysis Ubiquitin C, Heat shock protein 90kDa alpha [cytosolic and Grp94]; class A, Band 1 member, Heat shock 70kDa protein, and protein 5 [glucose-regulated protein, 78kDa], T-complex, Chaperon incontaining TCP1; subunit 7 [beta] and subunit 4 [delta] and subunit 2 [beta], have been introduced as hub-bottlnecksproteins. HSP90AA1, MKKS, EZR, HSPA14, APOB and CAD have been determined as seed proteins
Conclusion: Chaperons have a bold presentation in curtail area in network therefore these key proteins beside the other hubbottlneckproteins may be a suitable candidates biomarker panel for diagnosis, prognosis and treatment processes in celiac disease
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This study is aimed to elicit the possible correlation between breast and colon cancer from molecular prospective by analyzing and comparing pathway-based biomarkers. Breast and colon cancer are known to be frequent causes of morbidity and mortality in men and women around the world. There is some evidence that while the incident of breast cancer in young women is high, it is reported lower in the aged women. In fact, aged women are more prone to colorectal cancer than older men. . In addition, many studies showed that several biomarkers are common among these malignancies. The genes were retrieved and compared from KEGG database and WikiPathway, and subsequently, protein-protein interaction [PPI] network was constructed and analyzed using Cytoscape v:3.2.1 software and related algorithms. More than forty common genes were identified among these malignancies; however, by pathways comparison, twenty genes are related to both breast and colon cancer. Centrality and cluster screening identified hub genes, including SMAD2, SMAD3, [SMAD4, MYC], JUN, BAD, TP53. These seven genes are enriched in regulation of transforming growth factor beta receptor signaling pathway, positive regulation of Rac protein signal transduction, positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway, and positive regulation of mitotic metaphase/anaphase transition respectively. As there are numerous genes frequent between colorectal cancer and breast cancer, there may be a common molecular origin for these malignancies occurrences. It seems that breast cancer in females interferes with the rate of colorectal cancer incidence
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Cancer research is an attractive field in molecular biology and medicine. By applying large-scale tools such as advanced genomics and proteomics, cancer diagnosis and treatment have been improved greatly. Cancers of esophagus, gastric, and colon accounted for major health problem globally. Biomarker panel could bring out the accuracy for cancer evaluation tests as it can suggest a group of candidate molecules specified to particular malignancy in a way that distinguishing malignant tumors from benign, differentiating from other diseases, and identifying each stages with high specificity and sensitivity. In this review, a systematic search of unique protein markers reported by several proteomic literatures are classified in their specific cancer type group as novel panels for feasible accurate malignancy diagnosis and treatment. About thousands of introduced proteins were studied; however, a small number of them belonged to a specific kind of malignancy. In conclusion, despite the fact that combinatorial biomarkers appear to be hopeful, more evaluation of them is crucial to achieve the suitable biomarker panel for clinical application. This effort needs more investigations and researches for finding a specific and sensitive panel
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Different treatment strategies of Alzheimers disease [AD] are being studied for treating or slowing the progression of AD. Many pharmaceutically important regulation systems operate through proteins as drug targets. Here, we investigate the drug target proteins in beta-amyloid [A beta] injected rat hippocampus treated with Lavandula angustifolia [LA] by proteomics techniques. The reported study showed that lavender extract [LE] improves the spatial performance in AD animal model by diminishing A beta production in histopathology of hippocampus, so in this study neuroprotective proteins expressed in A beta injected rats treated with LE were scrutinized. Rats were divided into three groups including normal, A beta injected, and A beta injected that was treated with LE. Protein expression profiles of hippocampus tissue were determined by two-dimensional electrophoresis [2DE] method and dysregulated proteins such as Snca, NF-L, Hspa5, Prdx2, Apoa1, and Atp5a1were identified by MALDI-TOF/TOF. KEGG pathway and gene ontology [GO] categories were used by searching DAVID Bioinformatics Resources. All detected protein spots were used to determine predicted interactions with other proteins in STRING online database. Different isoforms of important protein, Snca that exhibited neuroprotective effects by anti-apoptotic properties were expressed. NF-L involved in the maintenance of neuronal caliber. Hspa5 likewise Prdx2 displays as anti-apoptotic protein that Prdx2 also involved in the neurotrophic effects. Apoa1 has anti-inflammatory activity and Atp5a1, produces ATP from ADP. To sum up, these proteins as potential drug targets were expressed in hippocampus in response to effective components in LA may have therapeutic properties for the treatment of AD and other neurodegenerative diseases
Subject(s)
Animals, Laboratory , Alzheimer Disease/drug therapy , Drug Delivery Systems , Protein Transport , Models, Animal , RatsABSTRACT
Glioblastoma Multiforme [GBM] or grade IV astrocytoma is the most common and lethal adult malignant brain tumor. Several of the molecular alterations detected in gliomas may have diagnostic and/or prognostic implications. Proteomics has been widely applied in various areas of science, ranging from the deciphering of molecular pathogen nests of discuses. In this study proteins were extracted from the tumor and normal brain tissues and then the protein purity was evaluated by Bradford test and spectrophotometry. In this study, proteins were separated by 2-Dimensional Gel [2DG] electrophoresis method and the spots were then analyzed and compared using statistical data and specific software. Protein clustering analysis was performed on the list of proteins deemed significantly altered in glioblastoma tumors [t-test and one-way ANOVA; P< 0.05]. The 2D gel showed totally 876 spots. We reported, 172 spots were exhibited differently in expression level [fold > 2] for glioblastoma. On each analytical 2D gel, an average of 876 spots was observed. In this study, 188 spots exhibited up regulation of expression level, whereas the remaining 232 spots were decreased in glioblastoma tumor relative to normal tissue. Results demonstrate that functional clustering [up and down regulated] and Principal Component Analysis [PCA] has considerable merits in aiding the interpretation of proteomic data. 2D gel electrophoresis is the core of proteomics which permitted the separation of thousands of proteins. High resolution 2DE can resolve up to 5,000 proteins simultaneously. Using cluster analysis, we can also form groups of related variables, similar to what is practiced in factor analysis
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Artificial neural networks are used in many smart apparatus and different fields such as signal processing pattern diagnoses, military systems, medicine, financial systems, and artificial intelligence. In this article using quality of neural networks in optimizing energy cost in moving limb and its effectiveness in organization a cognitive function founded by presenting an algorithm for use in human smart robotics and worldwide research will be described and discussed. Neural system contributes to minimal cost energy in decision-making and command exportation to skeletal muscle and suggested optimal energy cost in skeletal muscle that could be presented in software conformation
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Bacteriorhodopsin [BR] is the light harvesting and photoactive proton pump found in the membrane of a salt marsh bacteria. This protein has significant potential to use in optical computing and memory devices due to unique intrinsic physical properties of photo and bioelectric. All these features make BR one of the most promising protein candidates in protein memories. Protein memory is a kind of optical memory with a large storage capacity and high speed processing features. BR protein was used with the polymer film in order to create better stability. In order to investigate immobilization of electrostatic self-assembly of BR on glass and polycarbonate as protein memories was used. Polycarbonate is a layer of compact disc [CD] structure which considered dye immobilized on its surface and have reading and writing abilities of information via 0,1 bites. In this study, surfaces of polycarbonate modified by the mixture of 5% sulfuric acid and 20% acetic acid; furthermore, by using of PEI as cationic resin the surface of polycarbonate was charged and BR immobilized on it electrostatically. The modified surfaces were characterized by AFM technique. Also, light activity for reading data is retained. This is an appropriate method for optimal stability and activity assay of the protein and also is suitable for preparation of protein memories
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The overall goal of this review is to discuss the potential efficacy of herbal treatments. Plants are considered among the main sources of biologically active chemicals. Plant based drugs usage in our past decay became very renowned due to their fewer side effects and being less expensive than chemical ones. Recently, more abrupt tendency in this field has been increased. Furthermore, advances in molecular and cellular determinations revealed effective properties of these herbal components. Some plants extracts have shown multi-functional properties such as anti-oxidant, anti-amyloid, antimicrobial, and anti-inflammatory; further studies, besides, are required for detailed chemical characterization and more extensive biological evaluation of the most active ingredients. In summary, herbals can be considered as novel therapeutic approach against wide range of diseases. This review article draws the attention to some species of plants possessing biological activities on human health
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Albumin has a fundamental role in human body. Its main tasks in blood are to regulate osmotic blood pressure, maintaining the pH, and transporting metabolites and drugs throughout the vascular system. Pharmacological studies of the interaction of drugs on HSA are important due to structural and functional changes of this vital protein; thus, here in this research the effect of valproate as a common drug for epilepsy disorders is evaluated in the presence of hexadecyl pyridinium bromide [HPB] as a positive surfactant in normal and fever condition. Electrochemical method was used to investigate the binding number of HPB molecules to HSA in the absence and presence of valproate by evaluating the concentration of free HPB in 37 C and 42 C temperatures. HSA affinity for valproate binding studied via ligand binding process for normal and fever temperatures. The findings indicate that, there is a significant difference in valproate binding to albumin at physiological and pathological temperatures. The consequences are the same in the presence of HPB; in other words, HSA binding tendency to HPB in the presence of valproate was totally altered because of HSA major conformational changes in fever condition. In conclusion, corrected dosage of valproate is needed for fever condition relative to normal temperature and the patients under prescription of different medications in fever condition should have different orders due to the interferences of drugs
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Breast cancer [BC] accounts for one of the major health problems around the world. Since the diagnosis process can have great effect on therapy outcomes, we studied the biomarkers specific to breast tumors stage I based on examining different Iranian patients. Cases from different stages were examined to discover their highly expressed proteins. In addition, pathologic evaluations were performed as the diagnosis procedure. Considering positive percentage of over-expressed protein in different stages in the population, it is guessed that over-expression of ErBb2 and PR are positively correlated, while P53 is in negative correlation with them. Therefore, these molecules can probably account for stage I biological marker. This study suggests that alterations in over-expression of specific biomarkers in different stages may be associated to the stage classification, and can help achieve more effective therapies of this malignancy
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HSA plays an important role in transporting metabolites and drugs throughout the vascular system. In as much as its performance is very vital in the presents of different kinds of ligands at the specific body temperatures, its examination is crucial. This molecule can undergo increased glycation in diabetes. Therefore, glucose as the one of the most fundamental ligands dealing with albumin in human body is examined in this study at 100 mg/dl concentration in correspond to normal condition on human body, 175 mg/dl as a kidney glucose tolerance point and also 400 mg/dl as the critical point at the two most important temperatures in diabetic patients. Thermal conformational changes of [HSA] are important. These conformational alterations are accompanied by a mild alteration of secondary structures. For this reason, possible secondarystructural changes of HSA in presence of glucose has beeninvestigated by circular dichroism [CD] using Hepes bufferat the normal temperature 37 degree C and 42 degree C as a high fever condition.UV spectroscopystudies confirmed CD findings and indicate that critical concentration of glucoselead to generation of new structural feature of albumin similar to 42 degree C. However, as the temperature increases from 37 degree C to 42degreeC this process is no more capable of responding to glucose concentration changes. These results indicate that the native form of HSA is changed in the severe diabetic condition; likewise, same consequences can be achieved as the temperature arises from 37 degree C to 42 degree C
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There are several types of cancer, which cause millions of deaths worldwide every year. Many studies have confirmed that plants are adequate natural sources to be examined as anti-cancer drugs with fewer side effects than chemotherapy and radiotherapy. In this study the anti-cancer properties of Lavender aqueous extract on lymphocytes derived from patients with Hodgkin's lymphoma has been studied. In order to determine the cytotoxic effects of the extract on lymphocytes of patients in stages III and IV of Hodgkin's lymphoma and two different cell lines in the presence of different concentrations of aqueous extract of Lavender, MTT colorimetric assay and flow cytometry analysis were used. Findings indicated that Lavender inhibited cell proliferation in both lymphocytes and cell lines with different effects. The effective concentration of Lavender that decreased viability of Hodgkin's lymphoma cells below Lethal Concentration 50 [LC50] value was 100 micro g/ml and this was half of the therapeutic dose. In addition, apoptosis was the main mechanism the Hodgkin's lymphoma cell encountered when exposed to the aqueous extract of Lavender. Conclusion: This experiment proposes that aqueous Lavender extract can be regarded as a potential anti-cancer agent in future studies
Subject(s)
Humans , Plant Extracts , Hodgkin Disease , Lymphocytes , Cell Proliferation , Cell Line , CytotoxinsABSTRACT
In this study, we report the effect of the essential oil of Rosa Damascena on human colon cancer cell line [SW742] and human fibroblast cells. Colon cancer is the second most common fatal malignancy. Owing to the existence of many side effects and problems related to common treatments such as surgery, chemotherapy and radiotherapy, alternative treatments are being investigated. Some herbal medicines have shown promising results against different types of cancers. Herbal medicines used have included the use naturally occurring essential oils. The essential oil of Rosa Damascena was obtained by distillation and its effect on SW742 cell-line and fibroblast cells were investigated with cell culture. The cells were cultured and different volumes of essential oil were induced to the cells. After 48h incubation, cell survival was measured and using statistical analysis, the findings were evaluated and reported. This study showed that soluble part of Rosa Damascena oil increases cell proliferation in high volumes and the non-soluble component decreases cell proliferation. The effects of essential oils, such as Rosa Damascena, on cell proliferation require more thorough investigation
Subject(s)
Humans , Oils, Volatile , Colonic Neoplasms , Cell Line , FibroblastsABSTRACT
In this paper effect of combinational usage of calprotectin and etoposide on AGS cell line is studied. Application of combined toxic agents such as etoposide and cicplatin are commonly used for chemotherapy purposes. As a matter of fact, calprotectin and etoposide were both applied on human gastric adenocarcinoma cell line [AGS] as antitumor agents. Both calprotectin and etoposide are topo II inhibitor. Etoposide is a lipophilic agent that can easily transport from membrane while calprotectin active intracellular pathway, probably by membrane surface receptor. Calprotectin was purified from human neutrophil by chromatography methods. The human gastric adenocarcinoma cell line was exposed to different concentrations and combinations of calprotectin and etoposide. MTT assay was applied for evaluation of cytotoxicity assay. Viability of AGS cell line was reduced in high dosages of calprotectin and etposide. In fact, overnight incubation of these two agents together has been shown less effective than individual usage. The result indicates that, the combination of both calprotectin and etoposide is considerably less cytotoxic on gastric cancer cells [AGS] than applying individually
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In this study the anticancer activity of Lavender aqueous extract against MKN45 cell line was evaluated. Plant-based drugs are regarded as promising therapies. Lavender is a plant that has been cultivated from ancient times. An aqueous extract of Lavender has shown therapeutic effects on the nervous system in the high doses based on in-vivo studies. Gastric cancer is one of the frequent cancers in Iranian population. We therefore assessed the effect of Lavender upon a gastric cancer cell line. The MKN45 cancer cell line was selected for treatment with aqueous extract of Lavender Survival of MKN45 cell line was studied in the presence of various concentrations of Lavender extract by MTT assay method. Morphological studies were performed via microscopic analyses. Flow cytometry and proteomics techniques were applied to determining pharmaceutical mechanism of lavender cytotoxic effects. The survival and morphological studies revealed anticancer characteristics of extract. Flow cytometry findings indicate that Lavender extract had a cytotoxic effect upon the cell line. Proteomics analysis identified a significant spots showed changes in protein expression levels by informatics analysis. Of the proteins, expression of three cancer biomarkers, Annexin1, Anolase1 and HSP70 were suppressed by extract. This study suggest that Lavender extract is cytotoxic and alter protein expression in a gastric cancer cell line
Subject(s)
Stomach Neoplasms/therapy , Cell Line, Tumor/drug effects , Plant Extracts/pharmacology , Biomarkers , Plants, MedicinalABSTRACT
Chronic myeloid leukemia [CML] is a myeloproliferative disease of the hematopoietic stem cells, characterized by the presence of the Philadelphia [Ph] chromosome. Although imatinib inhibits the BCR-ABL kinase activity, clinical experiences confirm that imatinib may not target CML stem cells in vivo. The identification of signaling pathways responsible for the self-renewal properties of leukemic stem cells in CML will help in the discovery of novel therapeutic targets. Here we review signaling pathways including Wnt/beta-catenin, Hedgehog, Alox5, and Foxo which play crucial roles in the maintenance of stem cell functions in CML. It is thought that inhibition of key genes that are part of self-renewal associated signaling pathways may provide an effective way to reduce aberrant stem cell renewal in CML