RNA-Sequencing Data Reveal a Prognostic Four-lncRNA-Based Risk Score for Bladder Urothelial Carcinoma: An in Silico Update

BACKGROUND/AIMS

Current practical advances in high-throughput data technologies including RNA-sequencing have led to the identification of long non-coding RNAs (lncRNAs) for potential clinical application against bladder urothelial cancer (BLCA). However, most previous studies focused on the clinical value of individual lncRNAs, which has limited the potential for future clinical application.

METHODS

In this study, RNA-sequencing data of lncRNAs was downloaded from The Cancer Genome Atlas database. Risk score was constructed based on survival-associated lncRNAs identified using differential expression analysis as well as univariate and multivariate Cox proportional hazards regression analysis. Receiver operating characteristic and Kaplan-Meier curve analyses were employed to evaluate the clinical and prognostic value of risk scores. Bioinformatics analyses were used to investigate the potential mechanisms of newly identified lncRNAs.

RESULTS

Among 2,127 differentially expressed lncRNAs (DELs), four new lncRNAs (AC145124.1, AC010168.2, MIR200CHG, and AC098613.1) showed valuable prognostic effects in BLCA patients. More importantly, the four-DEL-based risk score had the potential to become an independent marker for the survival status prediction of BLCA patients. Distinct co-expressed genes and signaling pathways were identified when BLCA was categorized into low- and high-risk groups. Furthermore, a protein-coding gene, HIST4H4 was found only 68 bp from the AC010168.2 DEL. HIST4H4 expression level was evidently up-regulated and positively correlated with AC010168.2 in BLCA patients.

CONCLUSION

This in silico investigation pioneers the future investigation of the utility of prognostic lncRNAs for BLCA.

Epidemiologic Association of Nonalcoholic Fatty Liver Disease and Urinary Calculi: a Population-based Cross-sectional Study in Southern China

INTRODUCTION

Nonalcoholic fatty liver disease (NAFLD) has been reported to have effects on kidney diseases; however, a link between NAFLD and urinary calculi remains to be confirmed. This study was conducted on a male population based on our previous Fangchenggang Area Male Health and Examination Survey in Guangxi, China in order to estimate the frequency of urinary calculi and assess the association between NAFLD and urinary calculi while controlling for possible confounders.

MATERIALS AND METHODS

This was a population-based cross-sectional study conducted in the Fangchenggang region in Guangxi, China. The diagnoses of NAFLD and urinary calculi were made by ultrasonography. Clinical and laboratory findings were analyzed to investigate whether NAFLD was a risk factor for urinary calculi.

RESULTS

A total of 3719 men were enrolled (age range, 17 to 88 years). Slightly more than a quarter (26.5%) of the participants were diagnosed with NAFLD. The percentage of urinary calculi in all participants was 6.9%, and the percentage of NAFLD patients with urinary calculi (8.4%) was significantly higher than that among patients without NAFLD (6.4%, P < .05). Advanced age; high body mass index; elevated levels of blood glucose, cholesterol, triglycerides, and low-density lipoprotein cholesterol; low education; lower or higher physical activity; and NAFLD were independent risk factors for urinary calculi (P < .05).

CONCLUSIONS

Our results showed that NAFLD was associated with a higher incidence of urinary calculi in this cohort and NAFLD might represent a risk factor for urinary calculi.

Analysis of microarrays of miR-34a and its identification of prospective target gene signature in hepatocellular carcinoma

BACKGROUND

Currently, some studies have demonstrated that miR-34a could serve as a suppressor of several cancers including hepatocellular carcinoma (HCC). Previously, we discovered that miR-34a was downregulated in HCC and involved in the tumorigenesis and progression of HCC; however, the mechanism remains unclear. The purpose of this study was to estimate the expression of miR-34a in HCC by applying the microarray profiles and analyzing the predicted targets of miR-34a and their related biological pathways of HCC.

METHODS

Gene expression omnibus (GEO) datasets were conducted to identify the difference of miR-34a expression between HCC and corresponding normal tissues and to explore its relationship with HCC clinicopathologic features. The natural language processing (NLP), gene ontology (GO), pathway and network analyses were performed to analyze the genes associated with the carcinogenesis and progression of HCC and the targets of miR-34a predicted in silico. In addition, the integrative analysis was performed to explore the targets of miR-34a which were also relevant to HCC.

RESULTS

The analysis of GEO datasets demonstrated that miR-34a was downregulated in HCC tissues, and no heterogeneity was observed (Std. Mean Difference(SMD) = 0.63, 95% confidence intervals(95%CI):[0.38, 0.88], P < 0.00001; P_{heterogeneity} = 0.08 I² = 41%). However, no association was found between the expression value of miR-34a and any clinicopathologic characteristics. In the NLP analysis of HCC, we obtained 25 significant HCC-associated signaling pathways. Besides, we explored 1000 miR-34a-related genes and 5 significant signaling pathways in which CCND1 and Bcl-2 served as necessary hub genes. In the integrative analysis, we found 61 hub genes and 5 significant pathways, including cell cycle, cytokine-cytokine receptor interaction, notching pathway, p53 pathway and focal adhesion, which proposed the relevant functions of miR-34a in HCC.

CONCLUSION

Our results may lead researchers to understand the molecular mechanism of miR-34a in the diagnosis, prognosis and therapy of HCC. Therefore, the interaction between miR-34a and its targets may promise better prediction and treatment for HCC. And the experiments in vivo and vitro will be conducted by our group to identify the specific mechanism of miR-34a in the progress and deterioration of HCC.

The impact of atosiban on pregnancy outcomes in women undergoing in vitro fertilization-embryo transfer: A meta-analysis

Background

Atosiban is administered to women undergoing in vitro fertilization-embryo transfer (IVF-ET) to improve pregnancy outcomes. However, the results of this treatment were controversial. We conducted this meta-analysis to investigate whether atosiban improves pregnancy outcomes in the women undergoing in vitro fertilization (IVF).

Methods

Databases of PubMed, EMBASE, Web of Science, China BioMedicine, and Google Scholar were systematically searched. Meta-analyses were performed to investigate whether atosiban improves pregnancy outcomes in the women undergoing IVF.

Results

Our results showed that atosiban was associated with higher implantation (OR = 1.63, 95% CI: 1.17–2.27; P = 0.004) and clinical pregnancy (OR = 1.84, 95% CI: 1.31–2.57; P < 0.001) rates. However, atosiban showed no significant association with the miscarriage, live birth, multiple pregnancy or ectopic pregnancy rates. When a further subgroup analysis was performed in the women undergoing repeated implantation failure (RIF), implantation (OR = 1.93, 95% CI: 1.45–2.57; P < 0.001), clinical pregnancy (OR = 2.48, 95% CI: 1.70–3.64; P <0.001) and the live birth (OR = 2.89, 95% CI: 1.78–4.67; P < 0.001) rates were significantly higher in the case group. Nevertheless, no significant difference was detected in the miscarriage and multiple pregnancy rates between the case and control groups.

Conclusion

Atosiban may be more appropriate for women undergoing RIF and play only a limited role in improving pregnancy outcomes in the general population of women undergoing IVF. These conclusions should be verified in large and well-designed studies.

Evaluation and clinical significance of cyclin-dependent kinase5 expression in cervical lesions: a clinical research study in Guangxi, China

Background

Studies have been reported that cyclin-dependent kinase5 (CDK5) was associated with the development of several cancers. However, the relationship between CDK5 level and clinicopathological factors is still poorly understood in cervical diseases. The aim of the current study was to investigate the expression of CDK5 and its clinical significance in variant cervical lesions.

Methods

Immunohistochemistry (IHC) was used to detect CDK5 expression in 54 cases of chronic cervicitis, 42 cases of condyloma acuminate (CA), 38 cases of carcinoma in situ, and 360 cases of cervical cancers [adenocarcinoma, n = 63; squamous cell carcinoma (SCC), n = 263; adenosquamous carcinoma, n = 34]. The clinicopathological characteristics in relation to CDK5 were examined by Pearson’s Chi-square test.

Results

The positive rates of CDK5 were 27.8, 31.0, 50, 54.0, 58.8, and 62.7 % in chronic cervicitis, CA, carcinoma in situ, adenocarcinoma, adenosquamous carcinoma and SCC, respectively. Statistically analysis showed that CDK5 expression in cervical cancer tissues was higher than non-cervical cancer tissues (inflammation and CA) (P < 0.001). The overexpression of CDK5 was significantly correlated with lymph node metastasis (r = 0.317; P < 0.001), histological type (r = 0.198; P < 0.001), FIGO stage (r = 0.358; P < 0.001), TNM stage (r = 0.329; P < 0.001) and pathological grade (r = 0.259; P < 0.001) in cervical lesions evaluated by Pearson’s Chi-square test. Furthermore, the positive relationships were found between CDK5 and lymph node metastasis (P < 0.001), FIGO stage (P < 0.001), TNM stage (P < 0.001) and pathological grade (P < 0.001) in SCC. CDK5 was positively interrelated to TNM stage (P = 0.017) in adenosquamous carcinoma.

Conclusions

CDK5 may play a vital role in the development of cervical cancer, which may be a marker for the diagnosis, therapy and prognosis of cervical cancer.

Development and characterization of microsatellite markers in Prunus sibirica (Rosaceae)

PREMISE OF THE STUDY

Microsatellite loci were developed for Prunus sibirica to investigate genetic diversity, population genetic structure, and marker-assisted selection of late-blooming cultivars in the breeding of P. sibirica. •

METHODS AND RESULTS

Using a magnetic bead enrichment strategy, 19 primer pairs were developed and characterized across 40 individuals from three P. sibirica wild populations and six individuals of P. armeniaca. The number of alleles per locus varied from three to 11 and the observed and expected heterozygosities ranged from 0.063 to 0.917 and 0.295 to 0.876, respectively, in the three P. sibirica wild populations. All primer pairs could be successfully amplified in six individuals of P. armeniaca. •

CONCLUSIONS

These microsatellite primer pairs should be useful for population genetics, germplasm identification, and marker-assisted selection in the breeding of P. sibirica and related species.

Phenanthrene and pyrene uptake by arbuscular mycorrhizal maize and their dissipation in soil

Polycyclic aromatic hydrocarbons (PAHs) commonly found in soils can be degraded in rhizosphere, but may also be taken up by plants. The effects of arbuscular mycorrhizal (AM) fungi on uptake of phenanthrene (PHE) and pyrene (PYR) in maize and on their dissipation in soil were investigated using the three-compartmentalized rhizoboxes. Inoculation of Glomus mosseae significantly (p<0.01) increased PHE and PYR concentrations in maize roots and significantly (p<0.05) enhanced PYR translocation from roots to stems in the soil treatments of the PHE+PYR spiked-soils added into the central compartment of the rhizoboxes. There was a significant (p<0.05) dissipation gradient of PHE and PYR observed away from the maize roots, with the highest dissipation rates recorded in rhizosphere zone in the central compartments of the rhizoboxes, followed by near rhizosphere zone and bulk soil zone in the outer compartments. However, G. mosseae only exerted minimal impacts on dissipation of PHE and PYR in the rhizosphere. The present study suggested that the hyphae and extraradical mycelium of AM fungi could play important roles in the uptake and translocation of PHE and PYR in plants. The present results indicated that there is a potential for the use of AM fungi and plant for remediating PAHs contaminated soils.

The study of the tumor stem cell properties of CD133+CD44+ cells in the human lung adenocarcinoma cell line A549

We studied the tumor stem cell properties of the CD133+CD44+ subpopulation in the human lung adenocarcinoma cell line A549. A549 cells were classified into subpopulations based on differential expression patterns for CD133 and CD44. Cells from different subpopulations were cultured and subcutaneously injected into 32 nude mice. Our results as following, (1) The majority of A549 cells died, whereas only about 4.11% of cells divided and proliferated to form cell clones. (2) The expression of CD133 and CD44 in proliferative cancer cells was statistically significantly different from that in normal A549 cells (p < 0.001). (3) Cell proliferation in group A (CD133+CD44+) was the fastest among all groups. Cell proliferation in A549 cells was slower than in group A but faster than in groups B (CD133-CD44-), C (CD133-CD44+), and D (CD133+CD44-). (4) The tumorigenic capacity in cells from group A was significantly higher than that in cells from groups B (p<0.001), C (p<0.001) and D (p<0.04). In conclusion, CD133+CD44+ cells in the adenocarcinoma cell line A549 have expressive significant cancer stem cell properties with continuous proliferative capacity and differentiation potential.

Ancient paddy soils from the Neolithic age in China’s Yangtze River Delta

Identifying prehistoric irrigated rice fields and characterizing the beginning of paddy soil development are important for a better understanding of human development and agricultural history. In 2003, paddy soils and irrigated rice fields buried at a depth of 100-130 cm were excavated at Chuo-dun-shan in the Yangtze River Delta, close to Suzhou, China. The fields of sizes between 1.4 and 16 m(2) were surrounded with ridges that were connected to ditches/ponds via outlets to control the water level within the fields. Many carbonized and partly carbonized rice grains with an age of 3,903 B.C. (measured (14)C age 5,129+/-45 a BP) were recovered. The surface layers of these buried paddy fields showed a high content of soil organic matter and a considerable high density of rice opals. The latter were identified to derive from Oryza spp. Solid-state (13)C nuclear magnetic resonance spectroscopy revealed aromatic carbon (C) as the predominant organic C form in the fossil surface layer. This is expected, if the major source represents burnt rice and straw. In summary, our data are in agreement with new evidences indicating that in China, paddy soils and irrigated rice cultivation were initiated and developed more than 6,000 years ago.

Changes of soil microbiological properties caused by land use changing from rice-wheat rotation to vegetable cultivation

A survey was done recently in Jiaxing city of Zhejiang Province in the Yangtze River Delta to compare the differences of soil microbiological properties among paddy soils with different land use including continuous open-field vegetable cultivation (OFVC), plastic-greenhouse vegetable cultivation (PGVC) and traditional rice-wheat rotation (RWR). The soil types included are percolating, permeable and waterlogged paddy soils. The results indicate that the microbial flora was markedly changed as the land use changed for all the three soil types. In continuous vegetable cultivation soils, especially in PGVC soils, the bacteria amounts decreased dramatically, but the fungal and actinomyce amounts increased as compared with RWR soils. The dehydrogenase activities decreased significantly in vegetable soils, especially in PGVC soils as compared with RWR soils. The microbial biomass C and the total phospholipid contents (TPL) in vegetable cultivation soil greatly decreased as compared with RWR soils. Biolog analysis indicated that the kinds of carbon sources that could be metabolized by native microbes in PGVC soils greatly decreased as compared with OFVC soils and RWR soils, revealing that microbial diversity had decreased since land use change. The activities of some soil enzymes including urease, invertase and phosphase were all lower in OFVC soils than those in RWR soils, and those in PGVC soils were the lowest. The degradation of microbiological activities in continuous vegetable cultivation soils, especially in PGVC soils, as compared with RWR soils might have been caused by soil acidification and accumulation of salts due to overuse of both organic and inorganic fertilizers in vegetable cultivation.

Interactions between arbuscular mycorrhizae and heavy metals under sand culture experiment

A sand culture experiment was established to determine interactions between arbuscular mycorrhizae and heavy metals. Mycorrhizal infection rates, spore densities, maize root and shoot weights, and heavy metal contents in maize were as indexes of responses of arbuscular mycorrhizal fungi (Acaulospora laevis, Glomus caledonium and Glomus manihotis) to heavy metals (Cu and Cd). The mycorrhizal infection rates of G. caledonium were the highest among these three mycorrhizal fungi, but the sporulating ability of G. caledonium was the poorest in the heavy metal treatments. The shoot and root weights of non-mycorrhizal plants were usually greater than those of mycorrhizal plants when the Cu concentrations in solutions are less than 3 mg l(-1) or Cd concentrations less than 1 mg l(-1). When Cd concentrations were 0.5 and 1 mg(-1), the root and shoot weights of plants inoculated with A. laevis were significantly (p < 0.05) lower than those of other treatments. Copper concentrations in shoots of mycorrhizal plants were higher than those of non-mycorrhizal ones at all Cu concentrations in solution, especially at low Cu concentrations. As to A. laevis, Cu concentrations in roots and shoots of the host were higher than those of non-mycorrhizal plants in these treatments. Thus A. laevis was sensitive to Cu and Cd, especially Cd, and G. caledonium was more tolerant to these two heavy metals. It is suggested that G. caledonium might be a promising mycorrhizal fungus for bioremediation of heavy metal contaminated soil.

Effect of DBP/DEHP in vegetable planted soil on the quality of capsicum fruit

Field experiment was conducted to investigate the di-n-butyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP) contamination in Capsicum annum fruit grown in DBP and DEHP contaminated soil, and to evaluate the effect of DBP and DEHP on the quality of capsicum fruit. The top layer soil (0-10 cm) of plots was treated with a mixture of DBP and DEHP (1:1 w/w) and capsicum seedlings were transplanted. After 90 days, capsicum fruit, shoot and root samples were collected. DBP and DEHP concentration in various parts of the samples were determined by gas chromatography. Vitamin C and capsaicin contents in fruit were determined using 2,4-dinitrophenylhydrazine colorimetric analysis and sodium nitrite-sodium molybdate colorimetric analysis, respectively. The results showed that DBP concentration in fruit, shoot and root increased with the increase of soil-applied DBP/DEHP concentration, but DEHP was not detected in all samples. When the soil-applied DBP/DEHP concentration was 5, 10, 20, 40, 80 and 160 mg kg(-1) soil, compared with control, vitamin C and capsaicin content in capsicum fruit decreased by 1.6%, 5.9%, 10.6%/o, 18.2%, 19.2%, 22.6% and 1.6%, 2.5%, 12.9%, 20.1%, 22.2%, respectively. Pearson correlation analysis demonstrated that the decrease of vitamin C and capsaicin content was negatively correlated to the increase of DBP concentration in capsicum fruit, which suggested that DBP uptake by the plant might be mainly responsible for quality degradation of capsicum fruit.