Genomic data mining for functional annotation of human long noncoding RNAs

Life may have begun in an RNA world, which is supported by increasing evidence of the vital role that RNAs perform in biological systems. In the human genome, most genes actually do not encode proteins; they are noncoding RNA genes. The largest class of noncoding genes is known as long noncoding RNAs (lncRNAs), which are transcripts greater in length than 200 nucleotides, but with no protein-coding capacity. While some lncRNAs have been demonstrated to be key regulators of gene expression and 3D genome organization, most lncRNAs are still uncharacterized. We thus propose several data mining and machine learning approaches for the functional annotation of human lncRNAs by leveraging the vast amount of data from genetic and genomic studies. Recent results from our studies and those of other groups indicate that genomic data mining can give insights into lncRNA functions and provide valuable information for experimental studies of candidate lncRNAs associated with human disease.

[Epidemiologic features of hand-foot-mouth disease in Haikou city from 2008 to 2015]

Objective: To analyze the epidemiologic features of hand-foot-mouth disease (HFMD) in Haikou city from 2008 to 2015. Methods: Descriptive methods on epidemiology and detection on pathogens were conducted in Haikou city from 2008 to 2015. Results: A total of 71 611 patients were diagnosed as HFMD in Haikou city from 2008 to 2015, including 728 severe cases, accounting for 1.02% among all the cases. The average annual incidence was 458.89/100 000. A total of 11 deaths were caused by the disease, with the average annual mortality rate as 0.07/100 000. Two peaks of incidence were seen, from April to July and from September to November. Age of the patients mainly fell in children aged 5 and below, taking up 95.78% of the total cases. Among all the patients, 1-year-olds presented the highest incidence as 12 881.24/100 000. The reported incidence for males was higher than that in females. There were 4 districts in Haikou city that reported the disease. Residential areas of the patients were scattered around, with a percentage of 79.89%. Spectrums of pathogens that causing the prevalence of HFMD were EV71 type, Cox A16 type and other enteroviruses, which prevailing in turns, since 2011. Conclusions: Haikou city had been an area with high incidence of HFMD. The incidence started to show a rising trend recently. It is suggested that programs as surveillance, case management, health education and comprehensive prevention and control of disease on HFMD targeting on key population should be intensively implemented to reduce the mortality of the disease.

The regulation of microRNA expression by DNA methylation in hepatocellular carcinoma

Emerging evidence indicates that microRNAs (miRNAs) are often dysregulated and play a fundamental role in hepatocellular carcinoma (HCC). However, the mechanism underlying miRNA dysregulation is still elusive. In the present study, we adopted an integrated analysis strategy combining data from genome-wide methylated DNA immunoprecipitation chip and miRNA expression microarray to study the regulation of DNA methylation on miRNA expression in HCC. We first characterized 864 differentially methylated regions (DMRs) located in 236 miRNA regions between cancerous and normal hepatocytes in HCC. We observed that the occurrence of miRNA DNA hypomethylation was more common than its hypermethylation while miRNA DNA hypermethylation was usually found in CpG islands. Then through correlation analysis between miRNA methylation and expression data, we identified 10 dysregulated miRNAs under the potential regulation of DNA methylation in HCC. Five of them (miR-148a, miR-375, miR-195, miR-497 and miR-378) were in hypermethylation and down-regulation status, while another five (miR-106b, miR-25, miR-93, miR-23a and miR-27a) were in hypomethylation and up-regulation status in HCC. Bioinformatics analysis showed that miR-148a may form a negative feedback loop with its targets DNMT1 and DNMT3B and the expression of the miR-195/497 cluster may be affected not only by their hypermethylated promoter region but also by their hypermethylated transcription factors NEUROG2 and DDIT3.

CONCLUSION

our preliminary data and bioinformatics analysis suggest that DNA methylation plays an important and complex role in the regulation of miRNA expression in HCC, which may provide insights into the pathogenesis of HCC and thus may be used for diagnosis and intervention.

Hypoxia influences the vascular expansion and differentiation of embryonic stem cell cultures through the temporal expression of vascular endothelial growth factor receptors in an ARNT-dependent manner

Adaptive responses to low oxygen (O(2)) tension (hypoxia) are mediated by the heterodimeric transcription factor hypoxia inducible factor (HIF). When stabilized by hypoxia, bHLH-PAS alpha- and beta- (HIF-1beta or ARNT) HIF complex regulate the expression of multiple genes, including vascular endothelial growth factor (VEGF). To investigate the mechanism(s) through which hypoxia contributes to blood vessel development, we used embryonic stem cell (ESC) differentiation cultures that develop into embryoid bodies (EBs) mimicking early embryonic development. Significantly, low O(2) levels promote vascular development and maturation in wild-type (WT) ESC cultures measured by an increase in the numbers of CD31(+) endothelial cells (ECs) and sprouting angiogenic EBs, but refractory in Arnt(-/-) and Vegf(-/-) ESC cultures. Thus, we propose that hypoxia promotes the production of ECs and contributes to the development and maturation of vessels. Our findings further demonstrate that hypoxia alters the temporal expression of VEGF receptors Flk-1 (VEGFR-2) and the membrane and soluble forms of the antagonistic receptor Flt-1 (VEGFR-1). Moreover, these receptors are distinctly expressed in differentiating Arnt(-/-) and Vegf(-/-) EBs. These results support existing models in which VEGF signaling is tightly regulated during specific biologic events, but also provide important novel evidence that, in response to physiologic hypoxia, HIF mediates a distinct stoichiometric pattern of VEGF receptors throughout EB differentiation analogous to the formation of vascular networks during embryogenesis.