Genomic expression profiling and bioinformatics analysis of pancreatic cancer

Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer

The incorporation of histone variants has structural ramifications on nucleosome dynamics and stability. Due to their unique sequences, histone variants can alter histone-histone or histone-DNA interactions, impacting the folding of DNA around the histone octamer and the overall higher-order structure of chromatin fibers. These structural modifications alter chromatin compaction and accessibility of DNA by transcription factors and other regulatory proteins to influence gene regulatory processes such as DNA damage and repair, as well as transcriptional activation or repression. Histone variants can also generate a unique interactome composed of histone chaperones and chromatin remodeling complexes. Any of these perturbations can contribute to cellular plasticity and the progression of human diseases. Here, we focus on a frequently overlooked group of histone variants lying within the four human histone gene clusters and their contribution to breast cancer.

An Integrated Data Analysis of mRNA, miRNA and Signaling Pathways in Pancreatic Cancer

Although many genes and miRNAs have been reported for various cancers, pancreatic cancer's specific genes or miRNAs have not been studied precisely yet. Therefore, we have analyzed the gene and miRNA expression profile of pancreatic cancer data in the gene expression omnibus (GEO) database. The microarray-derived miRNAs and mRNAs were annotated by gene ontology (GO) and signaling pathway analysis. We also recognized mRNAs that were targeted by miRNA through the mirDIP database. An integrated analysis of the microarray revealed that only 6 out of 43 common miRNAs had significant differences in their expression profiles between the tumor and normal groups (P value < 0.05 and |log Fold Changes (logFC)|> 1). The hsa-miR-210 had upregulation, whereas hsa-miR-375, hsa-miR-216a, hsa-miR-217, hsa-miR-216b and hsa-miR-634 had downregulation in pancreatic cancer (PC). The analysis results also revealed 109 common mRNAs by microarray and mirDIP 4.1 databases. Pathway analysis showed that amoebiasis, axon guidance, PI3K-Akt signaling pathway, absorption and focal adhesion, adherens junction, platelet activation, protein digestion, human papillomavirus infection, extracellular matrix (ECM) receptor interaction, and riboflavin metabolism played important roles in pancreatic cancer. GO analysis revealed the significant enrichment in the three terms of biological process, cellular component, and molecular function, which were identified as the most important processes associated strongly with pancreatic cancer. In conclusion, DTL, CDH11, COL5A1, ITGA2, KIF14, SMC4, VCAN, hsa-mir-210, hsa-mir-217, hsa-mir-216a, hsa-mir-216b, hsa-mir-375 and hsa-mir-634 can be reported as the novel diagnostic or even therapeutic markers for the future studies. Also, the hsa-mir-107 and hsa-mir-125a-5p with COL5A1, CDH11 and TGFBR1 genes can be introduced as major miRNA and genes on the miRNA-drug-mRNA network. The new regulatory network created in our study could give a deeper knowledge of the pancreatic cancer.

Decreased Risk in the Pancreatic Cancer With History of Hay Fever: A Meta-Analysis

Background: An increasing incidence of pancreatic cancer has been observed worldwide over the last few decades. Previous reports suggested that hay fever, a common allergic disease, may function in pancreatic cancer. Data on hay fever as a risk or protective factor for pancreatic cancer was controversial in several case–control reports. So, we here did a meta-analysis on published studies to evaluate the association of hay fever and the risk of pancreatic cancer.

Methods: A comprehensive literature search was performed through public databases. The association between hay fever and pancreatic cancer was evaluated by odds ratios (ORs) and 95% confidence intervals (CIs). The Cochran's Q test and I² index were used to evaluate heterogeneity.

Results: We included 8 population-based case–control studies involving 10,454 participants from 1986 to 2014. A history of hay fever was associated with a decreased risk of pancreatic cancer (OR, 0.57; 95% CI, 0.50–0.64, P < 0.00001) through fixed effect model.

Conclusion: The result of our study suggested that hay fever may significantly decrease the risk of pancreatic cancer.

Identification of Key Genes and Pathways in Pancreatic Cancer Gene Expression Profile by Integrative Analysis

Background: Pancreatic cancer is one of the malignant tumors that threaten human health. Methods: The gene expression profiles of GSE15471, GSE19650, GSE32676 and GSE71989 were downloaded from the gene expression omnibus database including pancreatic cancer and normal samples. The differentially expressed genes between the two types of samples were identified with the Limma package using R language. The gene ontology functional and pathway enrichment analyses of differentially-expressed genes were performed by the DAVID software followed by the construction of a protein–protein interaction network. Hub gene identification was performed by the plug-in cytoHubba in cytoscape software, and the reliability and survival analysis of hub genes was carried out in The Cancer Genome Atlas gene expression data. Results: The 138 differentially expressed genes were significantly enriched in biological processes including cell migration, cell adhesion and several pathways, mainly associated with extracellular matrix-receptor interaction and focal adhesion pathway in pancreatic cancer. The top hub genes, namely thrombospondin 1, DNA topoisomerase II alpha, syndecan 1, maternal embryonic leucine zipper kinase and proto-oncogene receptor tyrosine kinase Met were identified from the protein–protein interaction network. The expression levels of hub genes were consistent with data obtained in The Cancer Genome Atlas. DNA topoisomerase II alpha, syndecan 1, maternal embryonic leucine zipper kinase and proto-oncogene receptor tyrosine kinase Met were significantly linked with poor survival in pancreatic adenocarcinoma. Conclusions: These hub genes may be used as potential targets for pancreatic cancer diagnosis and treatment.

Environmental cadmium exposure and pancreatic cancer: Evidence from case control, animal and in vitro studies

Although profoundly studied, etiology of pancreatic cancer (PC) is still rather scarce. Some of established risk factors of PC are connected to an increased cadmium (Cd) body burden. Hence, the aim of this study was to investigate the role of this environmental pollutant in PC development by conducting human observational, experimental and in vitro studies. The case-control study included 31 patients with a histologically based diagnosis of exocrine PC subjected to radical surgical intervention as cases and 29 accidental fatalities or subjects who died of a nonmalignant illness as controls. Animal study included two treated groups of Wistar rats (15 and 30 mg Cd/kg b.w) and untreated control group, sacrificed 24 h after single oral exposure. In in vitro study pancreas hTERT-HPNE and AsPC-1 cells were exposed to different Cd concentrations corresponding to levels measured in human cancerous pancreatic tissue. Cd content in cancer tissue significantly differed from the content in healthy controls. Odds ratio levels for PC development were 2.79 (95% CI 0.91-8.50) and 3.44 (95% CI 1.19-9.95) in the third and fourth quartiles of Cd distribution, respectively. Animal study confirmed Cd deposition in pancreatic tissue. In vitro studies revealed that Cd produces disturbances in intrinsic pathway of apoptotic activity and the elevation in oxidative stress in pancreatic cells. This study presents three different lines of evidence pointing towards Cd as an agent responsible for the development of PC.

Identification of genes and pathways in esophageal adenocarcinoma using bioinformatics analysis

Esophageal adenocarcinoma (EAC) is one of the most common subtypes of esophageal cancer, and is associated with a low 5-year survival rate. The present study aimed to identify key genes and pathways associated with EAC using bioinformatics analysis. The gene expression profiles of GSE92396, which includes 12 EAC samples and 9 normal esophageal samples, were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between the EAC and normal samples were identified using the limma package in R language. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the identified DEGs were conducted using the online analysis tool, the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of the DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software. Finally, module analysis was conducted for the PPI network using the MCODE plug-in in Cytoscape. Of the 386 DEGs identified, the 150 upregulated genes were mainly enriched in the KEGG pathways of complement and coagulation cascades, maturity onset diabetes of the young and protein digestion and absorption; and the 236 downregulated genes were mainly enriched in amoebiasis, retinol metabolism and drug metabolism-cytochrome P450. Based on information from the STRING database, a PPI network comprising of 369 nodes and 534 edges was constructed in Cytoscape. The top 10 hub nodes with the highest degrees were determined as interleukin-8, involucrin, tissue inhibitor of metalloproteinase 1, fibronectin 1, serpin family E member 1, serpin family A member 1, cystic fibrosis transmembrane conductance regulator, secreted phosphoprotein 1, collagen type I alpha 1 chain and angiotensinogen. A total of 6 modules were detected from the PPI network that satisfied the criteria of MCODE score >4 and number of nodes >4. KEGG pathways enriched for the module DEGs were mainly within arachidonic acid metabolism, complement and coagulation cascades and rheumatoid arthritis. In conclusion, identification of these key genes and pathways may improve understanding of the mechanisms underlying the development of EAC, and may be used as diagnostic and therapeutic targets in EAC.