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The use of dental restorative materials is a routine task in clinical dentistry. Upon exposure to the oral cavity, continuous adsorption of salivary proteins and other macromolecules to all surfaces occurs, representing the first step in dental biofilm formation. Different physico-chemical properties of substrate materials potentially influence the composition of the initial biofilm, termed pellicle. This study aimed at characterizing and comparing the individual proteomic composition of the 3-min pellicle formed on bovine enamel and six restorative materials.After chemical elution, pellicle proteins were identified by nano-LC-HR-MS/MS. Proteomic profiles were analyzed in terms of molecular weights, isoelectric points, molecular functions and compared to saliva to reveal substrate material-specific adsorption patterns.A total of 1348 different pellicle proteins were identified, with 187-686 proteins in individual 3-min pellicles. Unexpectedly, this yielded quite similar distribution patterns independent of the substrate materials. Furthermore, overall similar fold changes were obtained for the major part of commonly enriched or depleted proteins in the pellicles.The current results point to a minor role of the substrate material on the proteomic composition of the 3-min pellicle and represent core data for understanding the complex surface interactions in the oral cavity.

The growing smooth talk in the field of natural compounds is due to the ancient and current interest in herbal medicine and their potentially positive effects on health. Dozens of antidiabetic natural compounds were reported and tested in vivo, in silico, and in vitro. The role of these natural compounds, their actions on the insulin signaling pathway, and the stimulation of the glucose transporter-4 (GLUT4) insulin-responsive translocation to the plasma membrane (PM) are all crucial in the treatment of diabetes and insulin resistance. In this review, we collected and summarized a group of available in vivo and in vitro studies which targeted isolated phytochemicals with possible antidiabetic activity. Moreover, the in silico docking of natural compounds with some of the insulin signaling cascade key proteins is also summarized based on the current literature. In this review, hundreds of recent studies on pure natural compounds that alleviate type II diabetes mellitus (type II DM) were revised. We focused on natural compounds that could potentially regulate blood glucose and stimulate GLUT4 translocation through the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway. On attempt to point out potential new natural antidiabetic compounds, this review also focuses on natural ingredients that were shown to interact with proteins in the insulin signaling pathway in silico, regardless of their in vitro/in vivo antidiabetic activity. We invite interested researchers to test these compounds as potential novel type II DM drugs and explore their therapeutic mechanisms.

Non-alcoholic steatohepatitis (NASH) represents a risk factor for the development of hepatocellular carcinoma (HCC) and is characterized by quantitative and qualitative changes in hepatic lipids. Since elongation of fatty acids from C16 to C18 has recently been reported to promote both hepatic lipid accumulation and inflammation we aimed to investigate whether a frequently used mouse NASH model reflects this clinically relevant feature and whether C16 to C18 elongation can be observed in HCC development. Feeding mice a methionine and choline deficient diet to model NASH not only increased total hepatic fatty acids and cholesterol, but also distinctly elevated the C18/C16 ratio, which was not changed in a model of simple steatosis (ob/ob mice). Depletion of Kupffer cells abrogated both quantitative and qualitative methionine-and-choline deficient (MCD)-induced alterations in hepatic lipids. Interestingly, mimicking inflammatory events in early hepatocarcinogenesis by diethylnitrosamine-induced carcinogenesis (48 h) increased hepatic lipids and the C18/C16 ratio. Analyses of human liver samples from patients with NASH or NASH-related HCC showed an elevated expression of the elongase ELOVL6, which is responsible for the elongation of C16 fatty acids. Taken together, our findings suggest a detrimental role of an altered fatty acid pattern in the progression of NASH-related liver disease.

Recently, first insights into the regulation and the role of the RNA-binding protein IMP2 in macrophage activation have been published by Wang et al. This study addresses differences in the regulation of IMP2 between the human and murine system. While the expression of IMP2 in anti-inflammatory macrophages is synchronous in mice and men, IMP2 expression is regulated differently in inflammatory macrophages.

The long non-coding RNA (lncRNA) H19 represents a maternally expressed and epigenetically regulated imprinted gene product and is discussed to have either tumor-promoting or tumor-suppressive actions. Recently, H19 was shown to be regulated under inflammatory conditions. Therefore, aim of this study was to determine the function of H19 in hepatocellular carcinoma (HCC), an inflammation-associated type of tumor. In four different human HCC patient cohorts H19 was distinctly downregulated in tumor tissue compared to normal or non-tumorous adjacent tissue. We therefore determined the action of H19 in three different human hepatoma cell lines (HepG2, Plc/Prf5, and Huh7). Clonogenicity and proliferation assays showed that H19 overexpression could suppress tumor cell survival and proliferation after treatment with either sorafenib or doxorubicin, suggesting chemosensitizing actions of H19. Since HCC displays a highly chemoresistant tumor entity, cell lines resistant to doxorubicin or sorafenib were established. In all six chemoresistant cell lines H19 expression was significantly downregulated. The promoter methylation of the H19 gene was significantly different in chemoresistant cell lines compared to their sensitive counterparts. Chemoresistant cells were sensitized after H19 overexpression by either increasing the cytotoxic action of doxorubicin or decreasing cell proliferation upon sorafenib treatment. An H19 knockout mouse model (H19Δ3) showed increased tumor development and tumor cell proliferation after treatment with the carcinogen diethylnitrosamine (DEN) independent of the reciprocally imprinted insulin-like growth factor 2 (IGF2). In conclusion, H19 suppresses hepatocarcinogenesis, hepatoma cell growth, and HCC chemoresistance. Thus, mimicking H19 action might be a potential target to overcome chemoresistance in future HCC therapy.

Purpose Dental pellicle formation starts instantaneously after oral hygiene due to the adsorption of salivary proteins to all orally exposed surfaces. The pellicle acts as a physiological mediator, protects the tooth surface from mechanical damages and reduces acid-induced enamel demineralization. The aim of this pilot study is to identify and characterize individual proteomic profiles of the initial pellicle formed on dental enamel and to compare the profiles with the corresponding saliva to analyze specific adsorption patterns occurring during pellicle formation. Experimental design The 3-min pellicle of five subjects formed in situ on bovine enamel is eluted chemically and analyzed separately by nano-mass spectrometry. The analysis of the corresponding saliva is conducted in parallel. Results Up to 498 pellicle proteins and up to 1032 salivary proteins are identified on an individual level. Comparison of the salivary and pellicle protein profiles demonstrates the pellicle formation to be highly individual. Nineteen proteins are significantly enriched in the 3-min pellicle of all subjects and 22 proteins are significantly depleted indicating that pellicle formation relies on selective adsorption. Conclusions and clinical relevance The short-term enamel pellicle is composed of several hundreds of adsorbed salivary proteins and reveals a highly individual proteomic profile.

The insulin-like growth factor 2 (IGF2) mRNA binding protein IMP2 (IGF2BP2) is an oncogenic protein known to be overexpressed in different tumor types. Pancreatic cancer is a very lethal cancer that requires early diagnosis and new treatment options. The aim of our study was to investigate the role of IMP2 in the initiation and progression of pancreatic ductal adenocarcinoma (PDAC). IMP2 was significantly overexpressed in a human precursor (PanIN) lesions suggesting IMP2 as a marker for early stages of PDAC. In a PDAC cohort of matched normal and tumor samples IMP2 showed overexpression in tumor tissues compared with normal pancreatic tissue. Strict correlation analysis (threshold R2 &gt, 0.75) revealed 22 genes highly positively and 9 genes highly negatively correlating with IMP2. Besides genes involved in the inhibition of apoptosis (Bcl-XL), especially factors involved in ubiquitination were strongly correlated with IMP2 expression: SMURF1 and FBXO45. Moreover, protein kinase C (PKC) signaling pathway was distinctly affected: DXS1179E encoding PKC iota, PKC substrate PLEK2, and inositol triphosphate receptor IP3R3 were positively correlated with IMP2 expression. Besides tumor initiation, IMP2 also seemed to have an impact on tumor progression. TGF-&beta, treatment of Panc-1 pancreatic cancer cells to induce epithelial-mesenchymal transition (EMT) was accompanied by increased IMP2 expression. EMT is important for cancer cells to gain migratory and invasive potential, which is essential for metastasis. Concordantly, circulating tumor cells showed higher IMP2 levels as compared with normal tissue from tumor origin and with normal hematological cells. Accordingly, IMP2 protein levels correlated with poor survival. In conclusion, as IMP2 seems to promote tumor progression of PDAC, it might be an interesting diagnostic and prognostic marker as well as a novel target for the treatment of PDAC.

The long non-coding RNA (lncRNA) H19 represents a maternally expressed and epigenetically regulated imprinted gene product and is discussed to have either tumor-promoting or tumor-suppressive actions. Recently, H19 was shown to be regulated under inflammatory conditions. Therefore, aim of this study was to determine the function of H19 in hepatocellular carcinoma (HCC), an inflammation-associated type of tumor. In four different human HCC patient cohorts H19 was distinctly downregulated in tumor tissue compared to normal or non-tumorous adjacent tissue. We therefore determined the action of H19 in three different human hepatoma cell lines (HepG2, Plc/Prf5, and Huh7). Clonogenicity and proliferation assays showed that H19 overexpression could suppress tumor cell survival and proliferation after treatment with either sorafenib or doxorubicin, suggesting chemosensitizing actions of H19. Since HCC displays a highly chemoresistant tumor entity, cell lines resistant to doxorubicin or sorafenib were established. In all six chemoresistant cell lines H19 expression was significantly downregulated. The promoter methylation of the H19 gene was significantly different in chemoresistant cell lines compared to their sensitive counterparts. Chemoresistant cells were sensitized after H19 overexpression by either increasing the cytotoxic action of doxorubicin or decreasing cell proliferation upon sorafenib treatment. An H19 knockout mouse model (H19Δ3) showed increased tumor development and tumor cell proliferation after treatment with the carcinogen diethylnitrosamine (DEN) independent of the reciprocally imprinted insulin-like growth factor 2 (IGF2). In conclusion, H19 suppresses hepatocarcinogenesis, hepatoma cell growth, and HCC chemoresistance. Thus, mimicking H19 action might be a potential target to overcome chemoresistance in future HCC therapy.

Proteins are of key importance in virtually every cellular process but many proteins have still not been annotated with functions due to experimental difficulties involved with functional assays. To address this problem, many computational methods based on sequence homology, three-dimensional structure, genomic context, and gene expression were developed to predict functions of proteins. Here, we tested the performance of a novel approach that is motivated by the concept of bacterial operons. To predict the substrate specificities of membrane transporters we combined genomic context-based methods with Gene Ontology and gene expression data whereby using SVM for classifying genes. We found that in Escherichia coli, the substrate-specificities of membrane transporters can be predicted with ca. 90% accuracy from the biological functions of co-expressed neighboring genes. In Saccharomyces cerevisiae and Homo sapiens, the respective accuracies are lower at around 80%. When applying the same strategy to enzymes of four metabolic classes of Escherichia coli, we found lower accuracies of 77% (2-class prediction) and 68% (4-class prediction), respectively. This suggests that transfer of functional associations between co-expressed neighbor genes may be case-specific

Purpose To 1) elucidate individual proteomic profiles of the 3-min biofilm of caries-active and caries-free individuals and 2) compare these proteomic profiles against the background of caries. Experimental design The initial oral pellicle of 12 caries-active and 12 caries-free individuals is generated in situ on ceramics specimens. The individual, host-specific proteomic profiles of this basic pellicle layer are analyzed by a chemical elution protocol combined with an elaborate mass spectrometry and evaluated bioinformatically. Results A total of 1188 different proteins are identified. Additionally, 68 proteins are present in the profiles of all individuals, suggesting them as ubiquitously occurring base-proteins of the initial human pellicle. Thereof, the single profiles exhibit high inter-individual differences independent of their group affiliation, stating the initial pellicle to represent a rather "individual fingerprint". Quantitative analyses imply slight indication for 23 proteins potentially capable of counting for caries-specific biomarkers. Conclusions and clinical relevance The introduced protocol enables the individual analysis of minimal protein amounts and allows for highly precise characterizations and comparisons of individual proteomic profiles. The results contain a considerable higher extent of protein identifications and might serve as a base for future large scale analyzes to identify discrimination factors for the development of caries susceptibility tests.

Expression and methylation datasets are standard genomic techniques and an increasing number of computational methods are implemented to aid in analyzing the huge and complex amount of generated data. Such generated datasets often contain a sizeable fraction of outliers that cause misleading results in downstream analysis. Here, we present a comprehensive approach to detect sample and gene outliers in expression or methylation datasets. The core algorithms detected most outliers that were artificially introduced by us. Sample outliers detected by hierarchical clustering are validated by the Silhouette coefficient. At the gene level, the GESD, Boxplot, and MAD algorithms detected with f-measure of at least 83% the simulated outlier genes in non-intersected distributions. This combined approach detected many outliers in publicly available datasets from the TCGA and GEO portals. Frequently, some functionally similar genes marked as outliers turned out to have outlier observations in common samples. As such cases may be of special interest, they are labeled for further investigations. Expression and DNA methylation datasets should clearly be checked for outlier points before proceeding with any further analysis. We suggest that already 2 outlier observations are enough to label an outlier gene as they are enough to ruin a perfect co-expression. Besides, outliers might also carry useful information and thus functionally similar outliers should be labeled for further investigation. The presented software is freely available via github

// Ahmad Barghash 1, 2 , Nicole Golob-Schwarzl 3 , Volkhard Helms 1 , Johannes Haybaeck 3 , Sonja M. Kessler 4 1 Center for Bioinformatics, Saarland University, Saarbruecken, Germany 2 School of Computer Engineering and Information Technology, German Jordanian University, Amman, Jordan 3 Institute of Pathology, Medical University of Graz, Austria 4 Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany Correspondence to: Sonja M. Kessler, email: s.kessler@mx.uni-saarland.de Keywords: IGF2BP2/IMP2/p62, barret’s esophagus, esophageal squamous carcinoma, esophageal adenocarcinoma, metastasis Received: November 17, 2015 Accepted: June 26, 2016 Published: July 06, 2016 ABSTRACT Esophageal adenocarcinoma (EAC) represents the sixth leading cause of cancer-related deaths and develops in Barret’s esophagus affected tissues. The IGF2 mRNA binding protein IMP2/IGF2BP2/p62 was originally identified as an autoantigen in hepatocellular carcinoma. Aim of this study was to investigate the expression and prognostic role of IMP2 in EAC. Human EAC and Barret’s esophagus tissue showed overexpression of IMP2, particularly in tumors of increased size and in metastatic tissues. Molecular classification based on published gene signatures of esophageal cancer revealed a specific subtype, in which the expression of IMP2 is high. According to GO and KEGG pathway analyses, genes showing highly correlated expression with IMP2 are associated with growth, proliferation, metabolism, inflammation, and cancerous processes. Clustering of EAC samples according to published survival marker genes strongly suggests that IMP2 overexpressing samples show poor survival. Finally, IMP2 expression correlated with short survival in patients with EAC or esophageal squamous carcinoma. Our data indicate that IMP2 might be a useful prognostic marker for Barret’s esophagus and EAC.

The purpose of this study was to understand the autoimmune response and immunogenicity of a tumor-associated antigen IMP2/p62 in breast cancer. Autoantibody responses to IMP2/p62 were evaluated by enzyme-linked immunosorbent assay (ELISA), western blotting and indirect immunofluorescence assay in sera from patients with breast cancer, benign breast tumor and normal human individuals. Immunohistochemistry (IHC) study with breast cancer tissues was also performed to analyze protein expression of IMP2/p62. The results have demonstrated that IMP2/p62 can induce a relatively higher frequency of autoantibody response in breast cancer (14.3%, 7/49) compared to patients with benign breast tumor (5.6%, 2/36) and normal individuals (2.2%, 1/44). The frequency of IMP2/p62 expression in breast cancer tissues was significantly higher than that in normal tissues (P

Background Membrane transporters catalyze the transport of small solute molecules across biological barriers such as lipid bilayer membranes. Experimental identification of the transported substrates is very tedious. Once a particular transport mechanism has been identified in one organism, it is thus highly desirable to transfer this information to related transporter sequences in different organisms based on bioinformatics evidence. Results We present a thorough benchmark at which level of sequence identity membrane transporters from Escherichia coli, Saccharomyces cerevisiae, and Arabidopsis thaliana belong to the same families of the Transporter Classification (TC) system, and at what level these membrane transporters mediate the transport of the same substrate. We found that two membrane transporter sequences from different organisms that are aligned with normalized BLAST expectation value better than E-value 1e-8 are highly likely to belong to the same TC family (F-measure around 90%). Enriched sequence motifs identified by MEME at thresholds below 1e-12 support accurate classification into TC families for about two thirds of the sequences (F-measure 80% and higher). For the comparison of transported substrates, we focused on the four largest substrate classes of amino acids, sugars, metal ions, and phosphate. At similar identity thresholds, the nature of the transported substrates was more divergent (F-measure 40 - 75% at the same thresholds) than the TC family membership. Conclusions We suggest an acceptable threshold of 1e-8 for BLAST and HMMER where at least three quarters of the sequences are classified according to the TC system with a reasonably high accuracy. Researchers who wish to apply these thresholds in their studies should multiply these thresholds by the size of the database they search against. Our findings should be useful to those who wish to transfer transporter functional annotations across species.