Clinicopathological value and underlying molecular mechanism of annexin A2 in 992 cases of thyroid carcinoma

BackgroundThyroid carcinoma (THCA) is one of the most frequent endocrine cancers and has increasing morbidity. Annexin A2 (ANXA2) has been found to be highly expressed in various cancers; however, its expression level and potential mechanism in THCA remain unknown. This study investigated the clinicopathological value and primary molecular machinery of ANXA2 in THCA.Material and MethodsPublic RNA-sequencing and microarray data were obtained and analyzed with ANXA2 expression in THCA and corresponding non-cancerous thyroid tissue. A Pearson correlation coefficient calculation was used for the acquisition of ANXA2 coexpressed genes, while edgR, limma, and Robust Rank Aggregation were employed for differentially expressed gene (DEG) in THCA. The probable mechanism of ANXA2 in THCA was predicted by gene ontology and pathway enrichment. A dual-luciferase reporter assay was employed to confirm the targeting relationships between ANXA2 and its predicted microRNA (miRNA).ResultsExpression of ANXA2 was significantly upregulated in THCA tissues with a summarized standardized mean difference of 1.09 (P < 0.0001) based on 992 THCA cases and 589 cases of normal thyroid tissue. Expression of ANXA2 was related to pathologic stage. Subsequently, 1442 genes were obtained when overlapping 4542 ANXA2 coexpressed genes with 2248 DEGs in THCA; these genes were mostly enriched in pathways of extracellular matrix-receptor interaction, cell adhesion molecules, and complement and coagulation cascades. MiR-23b-3p was confirmed to target ANXA2 by dual-luciferase reporter assay.ConclusionsUpregulated expression of ANXA2 may promote the malignant biological behavior of THCA by affecting the involving pathways or being targeted by miR-23b-3p.     

LSD1: more than demethylation of histone lysine residues

Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a special role in the epigenetic regulation of gene expression, as it removes methyl groups from mono- and dimethylated lysine 4 and/or lysine 9 on histone H3 (H3K4me1/2 and H3K9me1/2), behaving as a repressor or activator of gene expression, respectively. Moreover, it has been recently found to demethylate monomethylated and dimethylated lysine 20 in histone H4 and to contribute to the balance of several other methylated lysine residues in histone H3 (i.e., H3K27, H3K36, and H3K79). Furthermore, in recent years, a plethora of nonhistone proteins have been detected as targets of LSD1 activity, suggesting that this demethylase is a fundamental player in the regulation of multiple pathways triggered in several cellular processes, including cancer progression. In this review, we analyze the molecular mechanism by which LSD1 displays its dual effect on gene expression (related to the specific lysine target), placing final emphasis on the use of pharmacological inhibitors of its activity in future clinical studies to fight cancer.Subject terms: Epigenetics, Histone post-translational modifications     

Investigating ego modules involved in TGFβ3-induced chondrogenesis in mesenchymal stem cells based on ego network

ObjectiveThis paper aimed to investigate ego modules for TGFβ3-induced chondrogenesis in mesenchymal stem cells (MSCs) using ego network algorithm.MethodsThe ego network algorithm comprised three parts, extracting differential expression network (DEN) based on gene expression data and protein-protein interaction (PPI) data; exploring ego genes by reweighting DEN; and searching ego modules by ego gene expansions. Subsequently, permutation test was carried out to evaluate the statistical significance of the ego modules. Finally, pathway enrichment analysis was conducted to investigate ego pathways enriched by the ego modules.ResultsA total of 15 ego genes were obtained from the DEN, such as PSMA4, HNRNPM and WDR77. Starting with each ego genes, 15 candidate modules were gained. When setting the thresholds of the area under the receiver operating characteristics curve (AUC) ≥0.9 and gene size ≥4, three ego modules (Module 3, Module 8 and Module 14) were identified, and all of them had statistical significances between normal and TGFβ3-induced chondrogenesis in MSCs. By mapping module genes to confirmed pathway database, their ego pathways were detected, Cdc20:Phospho-APC/C mediated degradation of Cyclin A for Module 3, Mitotic G1-G1/S phases for Module 8, and mRNA Splicing for Module 14.ConclusionsWe have successfully identified three ego modules, evaluated their statistical significances and investigated their functional enriched ego pathways. The findings might provide potential biomarkers and give great insights to reveal molecular mechanism underlying this process.     

In silico study of cancer stage-specific DNA methylation pattern in White breast cancer patients based on TCGA dataset

BackgroundBreast cancer is one of the most common types of cancer among women. As current breast cancer treatments are still ineffective, we assess the methylation pattern of White breast cancer patients across cancer stage based on The Cancer Genome Atlas (TCGA) dataset. Significant hypermethylation and hypomethylation can regulate the gene expression, thus becoming potential biomarkers in breast cancer tumorigenesis.MethodsDNA methylation data was downloaded using TCGA Assembler 2 based on race-specific metadata of TCGA - Breast Invasive Carcinoma (TCGA-BRCA) project from Genomic Data Commons (GDC) Data Portal. After the data was divided into each cancer stage, duplicated data of each patient was removed using OMICSBind, while differentially-expressed probes were identified using edgeR. The resulting probes were validated based on correlation and regression analysis with the gene expression, ANOVA between cancer stages, ROC curve per stage, as well as databases.ResultsBased on the White dataset, we found 66 significant hypermethylated genes with logFC > 1.8 between Stage I-III. From this number, three epigenetic-regulated, stage-specific genes are proposed to be the detection biomarkers of breast cancer due to significant aberrant gene expression and/or low mutation ratio among breast cancer patients: ABCC9 (Stage III), SHISA3 (Stage II), and POU4F1 (Stage I-II).ConclusionsOur study shows that ABCC9, SHISA3, and POU4F1 are potential stage-specific detection biomarkers of breast cancer for White individuals, whereas their roles in other races need to be studied further.     

Characterizing mutation–expression network relationships in multiple cancers

BackgroundData made available through large cancer consortia like The Cancer Genome Atlas make for a rich source of information to be studied across and between cancers. In recent years, network approaches have been applied to such data in uncovering the complex interrelationships between mutational and expression profiles, but lack direct testing for expression changes via mutation. In this pan-cancer study we analyze mutation and gene expression information in an integrative manner by considering the networks generated by testing for differences in expression in direct association with specific mutations. We relate our findings among the 19 cancers examined to identify commonalities and differences as well as their characteristics.ResultsUsing somatic mutation and gene expression information across 19 cancers, we generated mutation–expression networks per cancer. On evaluation we found that our generated networks were significantly enriched for known cancer-related genes, such as skin cutaneous melanoma (p < 0.01 using Network of Cancer Genes 4.0). Our framework identified that while different cancers contained commonly mutated genes, there was little concordance between associated gene expression changes among cancers. Comparison between cancers showed a greater overlap of network nodes for cancers with higher overall non-silent mutation load, compared to those with a lower overall non-silent mutation load.ConclusionsThis study offers a framework that explores network information through co-analysis of somatic mutations and gene expression profiles. Our pan-cancer application of this approach suggests that while mutations are frequently common among cancer types, the impact they have on the surrounding networks via gene expression changes varies. Despite this finding, there are some cancers for which mutation-associated network behaviour appears to be similar: suggesting a potential framework for uncovering related cancers for which similar therapeutic strategies may be applicable. Our framework for understanding relationships among cancers has been integrated into an interactive R Shiny application, PAn Cancer Mutation Expression Networks (PACMEN), containing dynamic and static network visualization of the mutation–expression networks. PACMEN also features tools for further examination of network topology characteristics among cancers.     

Anti-inflammatory and anticancer activities of erythrodiol-3-acetate and 2,4-di-tert-butylphenol isolated from Humboldtia unijuga

Abstract

Humboldtia unijuga Bedd., endemic to Agasthyamala in Western Ghats in India, is traditionally used by local Kani tribes for chicken pox, head ache and snake bite. This study reports the isolation of erythrodiol-3-acetate (HU-1) and 2,4-di-tert-butylphenol (HU-2) from H. unijuga roots and their anti-inflammatory and anticancer activities in macrophage, skin and breast cancer cell lines. Effects of HU-1 and HU-2 treatments (50, 100?µg/mL) on gene expression profiles of pro-inflammatory cytokines TNFα, IL-6 and IL-1β, and apoptosis genes p53 and caspase 7 were studied. HU-2 exerted a significantly superior anti-inflammatory effect compared to HU-1 in all three pro-inflammatory genes. HU-2 showed a superior dose dependent anticancer effect through activation of p53 gene over HU-1 in MCF-7 cells. HU-1 exhibited a dose dependent effect on caspase 7 gene in both cell lines while HU-2 was more effective in A431. HU-2 has potential for development as a novel anti-inflammatory and anticancer agent.     

Quantitative study of cellular heterogeneity in doxorubicin uptake and its pharmacological effect on cancer cells

Cellular heterogeneity in doxorubicin (DOX) uptake and its relationship with pharmacological effect on cancer cells were quantitatively investigated for the first time. An in vitro experimental model was established by treating human leukemia K562 and breast cancer MCF‐7 cells with different schedules of DOX with or without surface P‐glycoprotein (P‐gp) inhibitor verapamil (VER). The cellular heterogeneity in DOX uptake was quantitatively examined by single‐cell analysis using capillary electrophoresis coupled with laser‐induced fluorescence detection. The corresponding cytotoxic effect was tested by cellular morphology, 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐tetrazolium and flow cytometry assays. The expression of cellular membrane surface P‐gp was determined by flow cytometry. Results showed that the cellular heterogeneity exists in DOX uptake. The single‐high DOX schedule leads to lower uptake heterogeneity and higher mean drug uptake. The cellular heterogeneity in DOX uptake was found to be negatively correlated with drug cytotoxicity and surface P‐gp expression, with r = ?0.7680 to ~ ?0.9587. VER reduces the cellular variation in DOX uptake, suggesting that surface P‐gp may be one of the causes of the cellular heterogeneity in DOX uptake. This research demonstrates the importance of quantitative study of cellular heterogeneity in drug uptake and its potential application in drug schedule design, response prediction and therapy modulation. Copyright © 2014 John Wiley & Sons, Ltd.     

DERL3 functions as a tumor suppressor in gastric cancer

BackgroundGastric cancer is a common malignant tumor in the clinic with a high mortality rate, ranking the first among malignant tumors of the digestive system. Early gastric cancer exhibits no specific clinical symptoms and signs, and most of the patients were diagnosed as advanced gastric cancer. The prognosis is poor, and the 5-year overall survival rate is still lower than 30%, seriously threatening people’s life and health. However, the pathogenesis of gastric cancer is still unclear.MethodsThis study aimed to identify methylated differentially expressed genes in gastric cancer and to study the cellular functions and pathways that may be involved in its regulation, as well as the biological functions of key methylated differentially expressed genes. The gene expression data set and methylation data set of gastric cancer genes based on TCGA were analyzed to identify prognostic methylated genes.ResultsThis study showed that the methylation of the DERL3 promoter was correlated with the clinical analysis of tumors. Further studies were conducted on genes co-expressed with DERL3, whose functions and pathways to inhibit gastric cancer were adaptive immune response, T cell activation, immune response-regulating pathway, cell surface on molecules, and natural killer cell-mediated cytotoxicity. Finally, cell proliferation assay, cell scratch assay, and cell invasion assay confirmed that DERL3 as a tumor suppressor gene inhibited the malignant evolution of gastric cancer.ConclusionsThe analysis of key methylated differentially expressed genes helped elucidate the epigenetic regulation mechanism in the development of gastric cancer. DERL3, as a methylation biomarker, has a predictive and prognostic value in the accurate diagnosis and treatment of gastric cancer and provides potential targets for the precision treatment of gastric cancer.Trial RegistrationNot applicable.     

A Gibbs sampling method to determine biomarkers for asthma

PurposeTo identify potential biomarkers and to uncover the mechanisms underlying asthma based on Gibbs sampling.MethodsThe molecular functions (MFs) with genes greater than 5 were determined using AnnotationMFGO of BAGS package, and the obtained MFs were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Meanwhile, the average probabilities of MFs were computed via MC Monte Carlo (MCMC) algorithm, followed by identification of differentially expressed MFs based on the probabilities of MF more than 0.6. Moreover, the differentially expressed genes (DEGs) and their correlated genes were screened and merged, called as co-expressed genes. Pathways enrichment analysis was implemented for the co-expressed genes.ResultsBased on the gene set more than 5, overall 396 MFs were determined. After Gibbs sampling, 5 differentially expressed MF were acquired according to alfa.pi > 0.6. Moreover, the genes in these 5 differentially expressed MF were merged, and 110 DEGs were identified. Subsequently, 338 co-expressed genes were gained. Based on the P value < 0.01, the co-expressed genes were significantly enriched in 6 pathways. Among these, ubiquitin mediated proteolysis contained the maximum numbers of 35 co-expressed genes, and cell cycle were enriched by the second largest number of 11 co-expressed genes, respectively.ConclusionsThe identified pathways such as ubiquitin mediated proteolysis and cell cycle might play important roles in the development of asthma and may be useful for developing the credible therapeutic approaches for diagnosis and treatment of asthma in future.     

Evaluation of the Anticancer Potential of Crude,Irradiated Cerastes cerastes Snake Venom and Propolis Ethanolic Extract & Related Biological Alterations

We aimed to evaluate the anticancer potential of crude venom (CV), γ irradiated Certastes cerastes venom (IRRV), and propolis ethanolic extract (PEE). IRRV showed a higher toxicity than CV, while CV-PEE showed higher toxicity than IRRV and CV against lung [A549] and prostate [PC3] cancer cells. Toxicity to [A549] and [PC3] cells was concentration and cell type dependent. In comparison to controls, apoptotic genes showed a significant upregulation of P53 and Casp-3 and a downregulation of Bcl-2. Also, induced elevated DNA accumulation in the [S] phase post PC3 cell treatment with IRRV and CV, as well as a significant DNA accumulation at G2/M phase after IRRV treatment of A549 cells. In contrast, PC3 cells showed a negligible cellular DNA accumulation after PEE treatment. Glutathione reductase [GR] was reduced in case of PC3 and A549 cell treated with IRRV, CV, and PEE compared with its values in untreated cell control. The Malondialdehyde [MDA] values in both cells recorded a significant elevation post IRRV treatment compared to the rest of the treatment regimen and untreated cell control. Similarly, IRRV and CV-PEE mix showed obviously higher reactive oxygen species [ROS] values than PC3 and A549 cell treatments with CV and PEE.     

Insights regarding novel biomarkers and the pathogenesis of primary colorectal carcinoma based on bioinformatic analysis

BackgroundBiomarkers are important in the study of tumor processes for early detection and precise treatment. The biomarkers that have been previously detected are not useful for clinical application for primary colorectal carcinoma (PCRC). The aim of this study was to explore clinically valuable biomarkers of PCRC based on integrated bioinformatic analysis.Material and methodsGene expression data were acquired from the GSE41258 dataset, and the differentially expressed genes were determined between PCRC and normal colorectal samples. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were implemented via Gene Set Enrichment Analysis. A protein-protein interaction (PPI) network was constructed. The significant modules and hub genes were screened and identified in the PPI network.ResultsA total of 202 DEGs were identified, including 58 upregulated and 144 downregulated genes in PCRC samples compared to those in normal colorectal samples. Enrichment analysis demonstrated that the gene sets enriched in PCRC were significantly related to bicarbonate transport, regulation of sodium ion transport, potassium ion homeostasis, regulation of telomere maintenance, and other processes. A total of 10 hub genes was identified by cytoHubba: PYY, CXCL3, CXCL11, CXCL8, CXCL12, CCL20, MMP3, P2RY14, NPY1R, and CXCL1.ConclusionThe hub genes, such as NPY1R, P2RY14, and CXCL12, and the electrolyte disequilibrium resulting from the differential expression of genes, especially bicarbonate imbalance, may provide novel insights and evidence for the future diagnosis and targeted therapy of PCRC.     

Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma

BackgroundIt is estimated that there are 338,000 new renal-cell carcinoma releases every year in the world. Renal cell carcinoma (RCC) is a heterogeneous tumor, of which more than 70% is clear cell renal cell carcinoma (ccRCC). It is estimated that about 30% of new renal-cell carcinoma patients have metastases at the time of diagnosis. However, the pathogenesis of renal clear cell carcinoma has not been elucidated. Therefore, it is necessary to further study the pathogenesis of ccRCC.MethodsTwo expression profiling datasets (GSE68417, GSE71963) were downloaded from the GEO database. Differentially expressed genes (DEGs) between ccRCC and normal tissue samples were identified by GEO2R. Functional enrichment analysis was made by the DAVID tool. Protein-protein interaction (PPI) network was constructed. The hub genes were excavated. The clustering analysis of expression level of hub genes was performed by UCSC (University of California Santa Cruz) Xena database. The hub gene on overall survival rate (OS) in patients with ccRCC was performed by Kaplan-Meier Plotter. Finally, we used the ccRCC renal tissue samples to verify the hub genes.Results1182 common DEGs between the two datasets were identified. The results of GO and KEGG analysis revealed that variations in were predominantly enriched in intracellular signaling cascade, oxidation reduction, intrinsic to membrane, integral to membrane, nucleoside binding, purine nucleoside binding, pathways in cancer, focal adhesion, cell adhesion molecules. 10 hub genes ITGAX, CD86, LY86, TLR2, TYROBP, FCGR2A, FCGR2B, PTPRC, ITGB2, ITGAM were identified. FCGR2B and TYROBP were negatively correlated with the overall survival rate in patients with ccRCC (P < 0.05). RT-qPCR analysis showed that the relative expression levels of CD86, FCGR2A, FCGR2B, TYROBP, LY86, and TLR2 were significantly higher in ccRCC samples, compared with the adjacent renal tissue groups.ConclusionsIn summary, bioinformatics technology could be a useful tool to predict the progression of ccRCC. In addition, there are DEGs between ccRCC tumor tissue and normal renal tissue, and these DEGs might be considered as biomarkers for ccRCC.     

The temperature dependence of hydrogen and anion adsorption at a Pt( 100) electrode in aqueous H2SO4 solution

Research on the underpotential deposition of H (upd H) and anion adsorption on Pt( 100) in 0.5 M aqueous H₂SO₄ solution by cyclic voltammetry (CV) indicates that the overall adsorption/desorption charge density is affected strongly by variation of the temperature T, and that it decreases by about 1/3 when T is raised from 293 to 328 K. The sharp peak at 0.375 V vs. RHE assigned to the anion adsorption decreases its potential, current density and charge density. The CV feature assigned to the upd H, a wide shoulder overlapping the sharp peak, also decreases with T augmentation, but the decline of its charge density is less pronounced. The results indicate that the H_upd and anion surface coverages, θ_HAN and θ_AN respectively are strongly temperature-dependent. This behavior may be assigned to lateral repulsive interactions.     

Selection of Peptide Ligands Specific for Baculovirus DNA‐Binding Protein from the Flitrx™ Random Peptide Display Library

Abstract

Autographa californica nucleopolyhedrovirus (AcNPV) is a baculovirus that is widely employed as a vector for the expression of foreign genes and pest control. Although baculoviruses, including AcNPV, efficiently replicate in the nuclei of arthropod cells, the dynamics and mechanism of DNA replication within the infected cell are still poorly understood. It has been found that the DNA‐binding protein (DBP) is an early gene product and appears to be crucial for viral DNA replication.

Presented here is the selection of peptide ligands that specifically bind to DBP for AcNPV from the FliTrx? random peptide display library; this entails the amplification, cloning of the DNA‐binding protein (DBP) gene from AcNPV and the construction of the expression plasmid for DBP, and the expression and purification of the recombinant His.Tag AcNPV DBP that was used as a target molecule for the selection of the peptide ligands specific for AcNPV DBP. The affinity and efficiency of such peptide ligands were then measured by ELISA procedures.

The beneficial aspect of this research is the monospecificity quality of the peptide ligands specific for AcNPV DBP. They could be used for the study of the dynamics of the viral genome and its replication within the infected cell, for the development of a quantitative method for the determination of the presence of baculovirus in various samples, for the development of a peptide ligandbased assay for the determination of baculovirus titers; or they could be immobilized on a chromatographic support for an improved affinity purification of AcNPV DBP.