Enrichment Analysis Identifies Functional MicroRNA-Disease Associations in Humans

Substantial evidence has shown that microRNAs (miRNAs) may be causally linked to the occurrence and progression of human diseases. Herein, we conducted an enrichment analysis to identify potential functional miRNA-disease associations (MDAs) in humans by integrating currently known biological data: miRNA-target interactions (MTIs), protein-protein interactions, and gene-disease associations. Two contributing factors to functional miRNA-disease associations were quantitatively considered: the direct effects of miRNA that target disease-related genes, and indirect effects triggered by protein-protein interactions. Ninety-nine miRNAs were scanned for possible functional association with 2223 MeSH-defined human diseases. Each miRNA was experimentally validated to target ≥ 10 mRNA genes. Putative MDAs were identified when at least one MTI was confidently validated for a disease. Overall, 19648 putative MDAs were found, of which 10.0% was experimentally validated. Further results suggest that filtering for miRNAs that target a greater number of disease-related genes (n ≥ 8) can significantly enrich for true MDAs from the set of putative associations (enrichment rate = 60.7%, adjusted hypergeometric p = 2.41×10⁻⁹¹). Considering the indirect effects of miRNAs further elevated the enrichment rate to 72.6%. By using this method, a novel MDA between miR-24 and ovarian cancer was found. Compared with scramble miRNA overexpression of miR-24 was validated to remarkably induce ovarian cancer cells apoptosis. Our study provides novel insight into factors contributing to functional MDAs by integrating large quantities of previously generated biological data, and establishes a feasible method to identify plausible associations with high confidence.     

Disparities between Ophthalmologists and Patients in Estimating Quality of Life Associated with Diabetic Retinopathy

Background

This study aimed to evaluate and compare the utility values associated with diabetic retinopathy (DR) in a sample of Chinese patients and ophthalmologists.

Methods

Utility values were evaluated by both the time trade-off (TTO) and rating scale (RS) methods for 109 eligible patients with DR and 2 experienced ophthalmologists. Patients were stratified by Snellen best-corrected visual acuity (BCVA) in the better-seeing eye. The correlations between the utility values and general vision-related health status measures were analyzed. These utility values were compared with data from two other studies.

Results

The mean utility values elicited from the patients themselves with the TTO (0.81; SD 0.10) and RS (0.81; SD 0.11) methods were both statistically lower than the mean utility values assessed by ophthalmologists. Significant predictors of patients’ TTO and RS utility values were both LogMAR BCVA in the affected eye and average weighted LogMAR BCVA. DR grade and duration of visual dysfunction were also variables that significantly predicted patients’ TTO utility values. For ophthalmologists, patients’ LogMAR BCVA in the affected eye and in the better eye were the variables that significantly predicted both the TTO and RS utility values. Patients’ education level was also a variable that significantly predicted RS utility values. Moreover, both diabetic macular edema and employment status were significant predictors of TTO and RS utility values, whether from patients or ophthalmologists. There was no difference in mean TTO utility values compared to our American and Canadian patients.

Conclusions

DR caused a substantial decrease in Chinese patients’ utility values, and ophthalmologists substantially underestimated its effect on patient quality of life.     

MiR-133a Is Functionally Involved in Doxorubicin-Resistance in Breast Cancer Cells MCF-7 via Its Regulation of the Expression of Uncoupling Protein 2

The development of novel targeted therapies holds promise for conquering chemotherapy resistance, which is one of the major hurdles in current breast cancer treatment. Previous studies indicate that mitochondria uncoupling protein 2 (UCP-2) is involved in the development of chemotherapy resistance in colon cancer and lung cancer cells. In the present study we found that lower level of miR133a is accompanied by increased expression of UCP-2 in Doxorubicin-resistant breast cancer cell cline MCF-7/Dox as compared with its parental cell line MCF-7. We postulated that miR133a might play a functional role in the development of Doxorubicin-resistant in breast cancer cells. In this study we showed that: 1) exogenous expression of miR133a in MCF-7/Dox cells can sensitize their reaction to the treatment of Doxorubicin, which is coincided with reduced expression of UCP-2; 2) knockdown of UCP-2 in MCF-7/Dox cells can also sensitize their reaction to the treatment of Doxorubicin; 3) intratumoral delivering of miR133a can restore Doxorubicin treatment response in Doxorubicin-resistant xenografts in vivo, which is concomitant with the decreased expression of UCP-2. These findings provided direct evidences that the miR133a/UCP-2 axis might play an essential role in the development of Doxorubicin-resistance in breast cancer cells, suggesting that the miR133a/UCP-2 signaling cohort could be served as a novel therapeutic target for the treatment of chemotherapy resistant in breast cancer.     

Integrative Analysis of mRNA and miRNA Expression Profiles of the Tuberous Root Development at Seedling Stages in Turnips

The tuberous root of Brassica rapa L. (turnip) is an important modified organ for nutrition storage. A better understanding of the molecular mechanisms involved in the process of tuberous root development is of great value in both economic and biological context. In this study, we analyzed the expression profiles of both mRNAs and miRNAs in tuberous roots at an early stage before cortex splitting (ES), cortex splitting stage (CSS), and secondary root thickening stage (RTS) in turnip based on high-throughput sequencing technology. A large number of differentially expressed genes (DEGs) and several differentially expressed miRNAs (DEMs) were identified. Based on the DEG analysis, we propose that metabolism is the dominant pathway in both tuberous root initiation and secondary thickening process. The plant hormone signal transduction pathway may play a predominant role in regulating tuberous root initiation, while the starch and sucrose metabolism may be more important for the secondary thickening process. These hypotheses were partially supported by sequential DEM analyses. Of all DEMs, miR156a, miR157a, and miR172a exhibited relatively high expression levels, and were differentially expressed in both tuberous root initiation and the secondary thickening process with the expression profiles negatively correlated with those of their target genes. Our results suggest that these miRNAs play important roles in tuberous root development in turnips.     

Association between BMP15 Gene Polymorphism and Reproduction Traits and Its Tissues Expression Characteristics in Chicken

BMP15 (Bone morphogenetic protein 15) is an oocyte-secreted growth factor required for ovarian follicle development and ovulation in mammals, but its effects on reproduction in chickens are unclear. In this study, the association between BMP15 polymorphisms and reproduction traits were analyzed, and its expression characteristics in different tissues were explored in LaiWu Black chickens. Three single nucleotide polymorphisms (SNPs) were identified in four hundred LaiWu Black chickens. One SNP (NC_006091.3:g.1773T>C) located in exon 2 which was significantly associated with egg weight at first egg (EWFE) (P = 0.0389), was novel. Diplotypes based on the three SNPs were found to be significantly associated with egg weight at age of 43W (EW43) (P = 0.0058). The chickens with H3H3 diplotype had their first egg 0.57 days later than chickens with H5H5 diplotype and 1.21 days-3.96 days earlier than the other five diplotype chickens. The egg production at age of 43W (E43), egg production at age of 46W (E46) and egg production at age of 48W (E48) for chickens with H3H3 diplotype were the highest among all the chickens, and the E48 of chickens with H3H3 diplotype had 11.83 eggs higher than chickens with H1H5 diplotype. RT-qPCR results showed that the expression level of BMP15 gene in ovarian follicle was in the order of 4 mm>6 mm -8 mm> 15 mm -19 mm> 23 mm -29 mm > 33 mm -34 mm in diameter. The mRNA level in follicles of 4 mm and 6–8 mm in diameter were significantly higher than that in the other follicles (P<0.01). In the same week, the highest mRNA level was found in the ovary, and it was significantly different from that found in the liver and oviduct (P<0.01). Our results indicate that BMP15 plays a vital role in the development of ovary and follicles, especially in the development of primary follicles. H3H3 may be an potential advantageous molecular marker for improving reproduction traits in chickens.     

Mental Health Functioning in the Human Rights Field: Findings from an International Internet-Based Survey

Human rights advocates play a critical role in promoting respect for human rights world-wide, and engage in a broad range of strategies, including documentation of rights violations, monitoring, press work and report-writing, advocacy, and litigation. However, little is known about the impact of human rights work on the mental health of human rights advocates. This study examined the mental health profile of human rights advocates and risk factors associated with their psychological functioning. 346 individuals currently or previously working in the field of human rights completed an internet-based survey regarding trauma exposure, depression, posttraumatic stress disorder (PTSD), resilience and occupational burnout. PTSD was measured with the Posttraumatic Stress Disorder Checklist-Civilian Version (PCL-C) and depression was measured with the Patient History Questionnaire-9 (PHQ-9). These findings revealed that among human rights advocates that completed the survey, 19.4% met criteria for PTSD, 18.8% met criteria for subthreshold PTSD, and 14.7% met criteria for depression. Multiple linear regressions revealed that after controlling for symptoms of depression, PTSD symptom severity was predicted by human rights-related trauma exposure, perfectionism and negative self-appraisals about human rights work. In addition, after controlling for symptoms of PTSD, depressive symptoms were predicted by perfectionism and lower levels of self-efficacy. Survey responses also suggested high levels of resilience: 43% of responders reported minimal symptoms of PTSD. Although survey responses suggest that many human rights workers are resilient, they also suggest that human rights work is associated with elevated rates of PTSD and depression. The field of human rights would benefit from further empirical research, as well as additional education and training programs in the workplace about enhancing resilience in the context of human rights work.     

Age-Based Differences in the Genetic Determinants of Glycemic Control: A Case of FOXO3 Variations

BackgroundGlucose homeostasis is a trait of healthy ageing and is crucial to the elderly, but less consideration has been given to the age composition in most studies involving genetics and hyperglycemia.MethodsSeven variants in FOXO3 were genotyped in three cohorts (n = 2037; LLI, MI_S and MI_N; mean age: 92.5±3.6, 45.9±8.2 and 46.8±10.3, respectively) to compare the contribution of FOXO3 to fasting hyperglycemia (FH) between long-lived individuals (LLI, aged over 90 years) and middle-aged subjects (aged from 35–65 years).ResultsA different genetic predisposition of FOXO3 alleles to FH was observed between LLI and both of two middle-aged cohorts. In the LLI cohort, the longevity beneficial alleles of three variants with the haplotype “AGGC” in block 1 were significantly protective to FH, fasting glucose, hemoglobin A_1C and HOMA-IR. Notably, combining multifactor dimensionality reduction and logistic regression, we identified a significant 3-factor interaction model (rs2802288, rs2802292 and moderate physical activity) associated with lower FH risk. However, not all of the findings were replicated in the two middle-aged cohorts.ConclusionOur data provides a novel insight into the inconsistent genetic determinants between middle-aged and LLI subjects. FOXO3 might act as a shared genetic predisposition to hyperglycemia and lifespan.     

Remediation of Nitrobenzene Contaminated Soil by Combining Surfactant Enhanced Soil Washing and Effluent Oxidation with Persulfate

The combination of surfactant enhanced soil washing and degradation of nitrobenzene (NB) in effluent with persulfate was investigated to remediate NB contaminated soil. Aqueous solution of sodium dodecylbenzenesulfonate (SDBS, 24.0 mmol L^-1) was used at a given mass ratio of solution to soil (20:1) to extract NB contaminated soil (47.3 mg kg^-1), resulting in NB desorption removal efficient of 76.8%. The washing effluent was treated in Fe²⁺/persulfate and Fe²⁺/H₂O₂ systems successively. The degradation removal of NB was 97.9%, being much higher than that of SDBS (51.6%) with addition of 40.0 mmol L^-1 Fe²⁺ and 40.0 mmol L^-1 persulfate after 15 min reaction. The preferential degradation was related to the lone pair electron of generated SO₄•⁻, which preferably removes electrons from aromatic parts of NB over long alkyl chains of SDBS through hydrogen abstraction reactions. No preferential degradation was observed in •OH based oxidation because of its hydrogen abstraction or addition mechanism. The sustained SDBS could be reused for washing the contaminated soil. The combination of the effective surfactant-enhanced washing and the preferential degradation of NB with Fe²⁺/persulfate provide a useful option to remediate NB contaminated soil.