Identification of human age-associated gene co-expressions in functional modules using liquid association

Excessive supply of glucose elicits an NF-κB2-dependent glycolysis in lactating goat mammary glands

During lactation, an improper glucose supply often threatens mammary gland (MG) health. However, information is limited on the metabolic trajectories and molecules that regulate lactating MGs with an excessive glucose supply. Based on the network analysis of transcriptome and microRNAs, we found that the oversupply of glucose-induced severe glucose metabolic disorders in MGs of lactating goats, shifting lactose synthesis to acute fermentative glycolysis which caused increased flux of glucose metabolism into lactate. Moreover, NF-κB2 played a key role in regulating glycolysis, exhibiting a metabolic shift when MGs had an excessive supply of glucose. In primary mammary epithelial cells, fermentative glycolysis, and intracellular concentration of reactive oxygen species (ROS) were reduced by ganoderic acid A through blocking NF-κB2, while activation of NF-κB2 with phorbol myristate acetate (PMA) upregulated fermentative glycolysis and increased cellular ROS accumulation under excessive glucose. Thus, we established an NF-κB2-targeting method to reform the metabolic shift toward glycolysis caused by glucose oversupply by integrating NF-κB2 blockade and intracellular ROS scavenging.

LAceModule: Identification of Competing Endogenous RNA Modules by Integrating Dynamic Correlation

Competing endogenous RNAs (ceRNAs) regulate each other by competitively binding microRNAs they share. This is a vital post-transcriptional regulation mechanism and plays critical roles in physiological and pathological processes. Current computational methods for the identification of ceRNA pairs are mainly based on the correlation of the expression of ceRNA candidates and the number of shared microRNAs, without considering the sensitivity of the correlation to the expression levels of the shared microRNAs. To overcome this limitation, we introduced liquid association (LA), a dynamic correlation measure, which can evaluate the sensitivity of the correlation of ceRNAs to microRNAs, as an additional factor for the detection of ceRNAs. To this end, we firstly analyzed the effect of LA on detecting ceRNA pairs. Subsequently, we proposed an LA-based framework, termed LAceModule, to identify ceRNA modules by integrating the conventional Pearson correlation coefficient and dynamic correlation LA with multi-view non-negative matrix factorization. Using breast and liver cancer datasets, the experimental results demonstrated that LA is a useful measure in the detection of ceRNA pairs and modules. We found that the identified ceRNA modules play roles in cell adhesion, cell migration, and cell-cell communication. Furthermore, our results show that ceRNAs may represent potential drug targets and markers for the treatment and prognosis of cancer.

Male reproductive tract antimicrobial expression in the extremes of ages of rats

Alterations in the global gene expression profile are considered to contribute to the various physiological and pathological changes during the course of ageing. Genes that code for the molecular components of the innate system are alter markedly as ageing occurs; and this may define the susceptibility of very young and very old individuals to reproductive tract infections. The expression pattern of genes that code for beta-defensins (effectors of innate immune response) in male reproductive tract tissues of different stages of ageing is not yet reported. Further, the induction of beta-defensins during endotoxin challenge and whether epigenetic modulators can influence the expression of these genes in different stages of ageing are not reported. We analyzed the basal mRNA levels of beta-defensins and defensin-like proteins (Sperm Associated Antigen 11 (SPAG11) family members), their induction during endotoxin challenge and modulation by epigenetic modifiers (Trichostatin A and Azacytidine) in the caput, cauda, testis, prostate and seminal vesicle of rats that represent early stage to late stages of life (20 day to 730 day old). We observed differential basal gene expression pattern in the male reproductive tract tissues and the induction by LPS was not consistent neither among the age groups not the tissues analyzed. Trichostatin A and Azacytidine also influenced antimicrobial gene expression and the pattern was not consistent in different tissues obtained from different age groups. Results of this study demonstrate that antimicrobial gene expression varies to a great extent during ageing and is strongly influenced by endotoxins and epigenetic modulators.