Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification

Clinically relevant biomarkers are useful to determine cancer patients' prognosis and treatments. To discover new putative biomarkers, we performed in silico analysis of a 325-gene panel previously associated with breast epithelial cell biology and clinical outcomes. Sixteen public datasets of microarray samples representing 8 cancer types and a total of 3,663 patients' samples were used for the analyses. Feature selection was used to identify the best subsets of the 325 genes for each classification, and linear discriminant analysis was used to quantify the accuracy of the classifications. A subset of 102 of the 325 genes were found to be housekeeping (HK) genes, and the classifications were repeated using only the 102 HK subset. The 325-gene panel and 102 HK subset were able to distinguish colon, gastric, lung, ovarian, pancreatic, and prostate tumors and leukemia from normal adjacent tissue, and classify disease subtypes of breast and lung cancers and leukemia with 70% or higher accuracy. HK genes have been overlooked as potential biomarkers due to their relative stability. This study describes a set of HK genes as putative biomarkers applicable to multiple cancer types worth following in subsequent validation studies.

Application progress of multilocus-sequence typing in the adaptive evolution of Helicobacter pylori / 国际外科学杂志

Helicobacter pylori (HP) is a kind of gram-negative bacillus parasitizing in human gastric mucosal tissue,which coevolved with human body.HP is one of the most genetically diverse bacterial species,which is mainly attributed to its high mutation and recombination rate.After tens of thousands of years of historical evolution,HP experienced numerous genetic polymorphisms and adaptive evolution in order to maintain a relatively stable colonization relationship with human hosts,making it became one of the species with the largest genome variation among prokaryotes.With such a long history with human beings,HP can be used as reference information for human migration in a sense.With the development of biological information technology,multilocus-sequence typing (MLST) technology plays a great role in the study of the evolution of bacterial strains.It has the characteristics of high repeatability and resolution,and the analysis results can be compared between different countries and laboratories.This paper mainly reviews the research and application progress of MLST technology in the genetic evolution of HP.

Validation of Housekeeping Genes for Gene Expression Analysis in Glioblastoma Using Quantitative Real-Time Polymerase Chain Reaction

BACKGROUND: Quantitative real-time polymerase chain reaction (qPCR) is the most reliable tool for gene expression studies. Selection of housekeeping genes (HKGs) that are having most stable expression is critical to carry out accurate gene expression profiling. There is no 'universal' HKG having stable expression in all kinds of tissues under all experimental conditions. METHODS: The present study aims to identify most appropriate HKGs for gene expression analysis in glioblastoma (GBM) samples. Based on literature survey, six most commonly used HKGs that are invariant in GBM were chosen. We performed qPCR using RNA from formalin fixed paraffin embedded GBM samples and normal brain samples to investigate the expression pattern of HPRT, GAPDH, TBP, B2M, B2M, RPL13A, and RN18S1 with different abundance. A simple Deltacycle threshold approach was employed to calculate the fold change. RESULTS: Our study shows that the expression of RPL13A and TBP were found to be most stable across all the samples and are thus suitable for gene expression analysis in human GBM. Except for TBP, none of the other conventionally used HKGs in GBM studies e.g., HPRT and GAPDH were found to be suitable as they showed variation in RNA expression. CONCLUSION: Validation of HKGs is therefore immensely specific for a particular experimental setup and is crucial in assessing any new setup.

Relationship between the density difference of microRNA binding and the evolution-ary conservation of 3′UTRs in housekeeping and non-housekeeping human genes / 军事医学

Objective To study the microRNA ( miRNA) regulation on the expression of housekeeping and non-house-keeping human genes from the systemic level , and to reveal the influence of conservation at 3′UTRs region for the density difference of miRNA regulatory between the two classes of genes .Methods We obtained miRNA regulation informations for the two classes of genes through the integration analysis of three sequence-based target gene prediction softwares and the conjoint analysis based on gene expression profile data .We also used phastCons-score based evolution analysis to study the conservation of 3′UTRs regions between the two classes of genes .Results Our results showed that housekeeping genes have a significantly higher density of miRNA binding sites and their 3′UTR are relatively conservative .Conclusion These findings highlight the importance of miRNA regulation in housekeeping genes , suggesting that investigating the roles of miR-NAs on the robustness of housekeeping genes expression is highly necessary .