Genome-wide targets identification of "core" pluripotency transcription factors with integrated features in human embryonic stem cells

Embryonic stem cells (ESCs) play an important role in developmental biology which is still lacking clear molecular mechanisms. The "core" transcription factors (TFs) including OCT4, SOX2 and NANOG are essential for maintaining the stemness of ESCs. But the downstream targets of these "core" TFs are still ambiguous. Based on support vector machine (SVM) technology, this study develops a label method algorithm (LMA) for genome-wide target identification of "core" TFs in humans, which eliminates the need for negative training samples. This method integrates histone modifications and TF binding motifs as identification features. Compared with a previous mapping-convergence (M-C) algorithm, the LMA can provide more stable and reliable predictions. 4796, 3166 and 4384 target genes of OCT4, SOX2 and NANOG, respectively, were identified with the LMA model. Then verifications of the predicted targets were carried out based on their functional consistency and their connection degree in networks from a computational system biology perspective. The results showed that the targets of "core" TFs present higher gene functional similarity and closer connection distance than background levels.

Nodal ratio of positive to excised nodes, but not number of positive lymph nodes is better to predict group to avoid chemotherapy among postmenopausal ER-positive, lymph node-positive T1-T2 breast cancer patients

AIM OF STUDY

To identify whether nodal ratio (NR) of positive to excised nodes is superior to number of positive lymph nodes to predict group to avoid chemotherapy among postmenopausal ER-positive, lymph node-positive, T1-T2 breast cancer patients.

MATERIALS AND METHODS

Postmenopausal estrogen receptor (ER)-positive, lymph node-positive patients who received endocrine therapy (n = 173) with complete baseline data in our hospital between 2000 and 2006 were included. The disease-free survival (DFS) was compared. Survival analysis was performed using Kaplan-Meier method. Cox proportional hazard models were used to evaluate the prognostic value of chemotherapy with different NR for DFS. P--values less than 0.05 were regarded as significant.

RESULTS

The median follow-up was 72 months. Three of 13 variables analyzed remained significantly prognostic for survival in the Cox proportional hazards model. These included age (hazard ratio (HR) =1.642, 95% confidence interval (CI) =1.154-2.337, P = 0.006); histological grade (HR = 2.463,95% CI = 1.389-4.367, P = 0.002); and NR (HR = 2.280, 95% CI = 1.113-4.671, P = 0.024). Subgroup analysis by NR status showed that in patients with NR ≥ 0.20, chemotherapy significantly improves DFS (HR = 0.360, 95% CI = 0.195-0.663, P = 0.001); while in patients with NR < 0.20, chemotherapy did not significantly affect DFS (HR = 0.677, 95% CI = 0.227-2.107, P = 0.493). Radiotherapy is an important factor that improves DFS in lymph node-positive patients, so it is considered in all analysis.

CONCLUSION

This retrospective analysis demonstrates that NR of positive to excised nodes, but not number of positive lymph nodes is better to predict group to avoid chemotherapy among postmenopausal ER-positive, lymph node-positive T1-T2 breast cancer patients.

Inverse associations of outdoor activity and vitamin D intake with the risk of Parkinson's disease

Early studies had suggested that vitamin D intake was inversely associated with neurodegenerative diseases, such as Alzheimer's disease and multiple sclerosis. However, the associations of vitamin D intake and outdoor activities with Parkinson's disease (PD) are still unclear, so this study is to evaluate these relationships from a case-control study in elderly Chinese. The study population involved 209 cases with new onsets of PD and 210 controls without neurodegenerative diseases. The data on dietary vitamin D and outdoor activities were collected using a food-frequency questionnaire and self-report questionnaire. Multivariable logistic regressions were used to examine the associations between dietary outdoor activities, vitamin D intake and PD. Adjustment was made for sex, age, smoking, alcohol use, education, and body mass index (BMI). Adjusted odds ratios (ORs) for PD in quartiles for outdoor physical activity were 1 (reference), 0.739 (0.413, 1.321), 0.501 (0.282, 0.891), and 0.437 (0.241, 0.795), respectively (P=0.002 for trend). Adjusted ORs for PD in quartiles for total vitamin D intake were 1 (reference), 0.647 (0.357, 1.170), 0.571 (0.318, 1.022), and 0.538 (0.301, 0.960), respectively (P=0.011 for trend). Our study suggested that outdoor activity and total vitamin D intake were inversely associated with PD, and outdoor activity seems to be more significantly associated with decreased risk for PD.

Differential expression of COX-2 in osteoarthritis and rheumatoid arthritis

In this study, we investigated the differential expression profiles of cyclooxygenase-2 (COX-2) mRNA and proteins in osteoarthritis (OA) and rheumatoid arthritis (RA) patients to elucidate the role of COX-2 expression in the pathogenesis and development of these diseases and to provide novel drug targets for treating arthritis. A total of 60 patients who received arthroscopic surgeries for treating OA (N = 30) or RA (N = 30) were examined. Fifteen normal synovial tissue samples were included as the control group. Fibroblastic synovial cells in all samples were cultured in vitro and COX-2 mRNA, protein expression levels, and COX-2 levels were detected in synovial fluids by real-time polymerase chain reaction, western blotting, and enzyme-linked immunosorbent assay methods, respectively. The mRNA level of COX-2 was significantly elevated in synovial cells from OA and RA patients compared to that in control samples (P < 0.05). COX-2 mRNA level was significantly higher in synovial cells from OA patients than in those from RA patients (P < 0.05). Consistent results were obtained for COX-2 protein expression levels from patients' synovial samples. In synovial fluids, OA (P < 0.05), but not RA (P > 0.05), patients showed significantly higher COX-2 levels compared to the control group. Elevated synovial COX-2 expression facilitates the pathogenesis of OA and RA, and thus this index reflects the condition of these 2 diseases.

[Phenylpropanoids and phenylethanol from flowers of Rosa rugosa]

A new phenylpropanoid (1), together with seven known ones (2-8), has been isolated from the flowers of Rosa rugosa collected from Shanxi province by using various chromatographic techniques. Compound 1 is a new compound, and it displayed cytotoxicity against NB4, SH-SY5Y, PC3, A549 and MCF7 cell lines with IC₅₀ values of 8.2, 6.2, 4.3, 2.8, and 9.6 µmol · L⁻¹ respectively.

CR1 rs3818361 Polymorphism Contributes to Alzheimer's Disease Susceptibility in Chinese Population

Recent genome-wide association studies (GWAS) reported CR1 rs3818361 polymorphism to be an Alzheimer's disease (AD) susceptibility variant in European ancestry. Three independent studies investigated this association in Chinese population. However, these studies reported weak or no significant association. Here, we reinvestigated the association using all the samples from three independent studies in Chinese population (N = 4047, 1244 AD cases and 2803 controls). We also selected three independent studies in European ancestry population (N = 11787, 3939 AD cases and 7848 controls) to evaluate the effect of rs3818361 polymorphism on AD risk in different ethnic backgrounds. In Chinese population, we did not identified significant heterogeneity using additive, recessive, and dominant genetic models. Meta-analysis showed significant association between rs3818361 and AD with P = 6.00E-03 and P = 5.00E-03. We further identified no heterogeneity of rs3818361 polymorphism between Chinese and European populations. We found that rs3818361 polymorphism contributed to AD with similar genetic risk in Chinese and European populations. In summary, this is the first study to show significant association between rs3818361 polymorphism and AD in Chinese population by a meta-analysis method. Our findings indicate that the effect of CR1 rs3818361 polymorphism on AD risk in Chinese cohorts is consistent with the increased risk observed in European AD cohorts.

Genetic Variant rs10757278 on Chromosome 9p21 Contributes to Myocardial Infarction Susceptibility

Large-scale genome-wide association studies (GWAS) have revealed that rs10757278 polymorphism (or its proxy rs1333049) on chromosome 9p21 is associated with myocardial infarction (MI) susceptibility in individuals of Caucasian ancestry. Following studies in other populations investigated this association. However, some of these studies reported weak or no significant association. Here, we reevaluated this association using large-scale samples by searching PubMed and Google Scholar databases. Our results showed significant association between rs10757278 polymorphism and MI with p = 6.09 × 10-22, odds ratio (OR) = 1.29, 95% confidence interval (CI) 1.22-1.36 in pooled population. We further performed a subgroup analysis, and found significant association between rs10757278 polymorphism and MI in Asian and Caucasian populations. We identified that the association between rs10757278 polymorphism and MI did not vary substantially by excluding any one study. However, the heterogeneity among the selected studies varies substantially by excluding the study from the Pakistan population. We found even more significant association between rs10757278 polymorphism and MI in pooled population, p = 3.55 × 10-53, after excluding the study from the Pakistan population. In summary, previous studies reported weak or no significant association between rs10757278 polymorphism and MI. Interestingly, our analysis suggests that rs10757278 polymorphism is significantly associated with MI susceptibility by analyzing large-scale samples.

Polymorphisms in the SIRT5 gene and their association with body measurement and ultrasound traits in Qinchuan cattle

Silent information regulator 5 (SIRT5), a member of the Sirtuin family class III nicotinamide adenine dinucleotide-dependent protein deacetylases, plays an important role in metabolic and aging processes in mammals. We identified 4 single-nucleotide polymorphisms (SNPs) (G22010A, G22052A, G22119T, and G22245C) in the 3' untranslated regions of the SIRT5 gene from 572 Qinchuan cattle by sequencing and investigating their association with growth and ultrasound traits. The frequencies of genotype GG and allele G were high at the 4 SNPs. Based on the X(2) test, the genotypic distributions of the 4 SNPs were not in Hardy-Weinberg equilibrium (P < 0.05 or P < 0.01). Association analysis of individual SNPs and haplotype combinations revealed that the 4 loci were significantly associated with some body measurement and ultrasound traits in Qinchuan cattle, and the H1H5 (AG-GA-GG-GG) diplotypes had better performance than other combinations in Qinchuan cattle. Our results demonstrate that SIRT5 may be a candidate for marker-assisted selection in future breeding programs for Qinchuan cattle.

Retinal nerve fiber layer and macular thinning in systemic lupus erythematosus: an optical coherence tomography study comparing SLE and neuropsychiatric SLE

OBJECTIVE

Due to the lack of reliable biomarkers in diagnosing and monitoring neuropsychiatric systemic lupus erythematosus (NPSLE), the aim of this study was to examine the utility of measurements obtained through spectral domain optical coherence tomography (SD-OCT) as a biomarker for NP involvement in SLE.

METHODS

Retinal nerve fiber layer (RNFL) and macula scans were performed using SD-OCT on 15 NPSLE patients, 16 SLE patients without NP symptoms (non-NP SLE), and 16 healthy controls. Macular volume and thickness of the central macula and peripapillary RNFL were compared between the groups and to scores on two validated cognitive tests.

RESULTS

NPSLE patients did not differ significantly from non-NP SLE patients in retinal thickness or macular volume. However, SLE patients as a whole showed significant RNFL and macular thinning compared to controls. Scores on the Trail Making Test B, a test of complex attention, showed significant correlation to temporal superior and temporal inferior RNFL thickness.

CONCLUSION

Our results demonstrate RNFL thinning in SLE, and confirm the previous finding of high incidence of abnormal brain scans in SLE. These findings suggest that OCT measurements may be indicative of neurodegeneration in SLE and may be a useful biomarker for early cognitive impairment in SLE.

Clinical research of persimmon leaf extract and ginkgo biloba extract in the treatment of vertebrobasilar insufficiency

This paper aims to compare the curative effects of persimmon leaf extract and ginkgo biloba extract in the treatment of headache and dizziness caused by vertebrobasilar insufficiency. Sixty patients were observed, who underwent therapy with persimmon leaf extract and ginkgo biloba extract based on the treatment of nimodipine and aspirin. After 30 days, 30 patients treated with persimmon leaf extract and 30 patients with ginkgo biloba extract were examined for changes in hemodynamic indexes and symptoms, such as headache and dizziness. The results showed statistically significant differences of 88.3% for the persimmon leaf extract and 73.1% for the ginkgo biloba extract, P < 0.05. Compared to the group of ginkgo biloba extract, the group of persimmon leaf extract had more apparent improvement in the whole blood viscosity, plasma viscosity, fibrinogen, hematokrit, and platelet adhesion rate, and the difference was statistically significant (P < 0.05 or P < 0.01). Based on these analyses, it can be concluded that persimmon leaf extract is better than ginkgo biloba extract in many aspects, such as cerebral circulation improvement, cerebral vascular expansion, hypercoagulable state lowering and vertebrobasilar insufficiency-induced headache and dizziness relief.

LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression

Long non-coding RNAs (lncRNAs) have emerged as critical regulators of genes at epigenetic, transcriptional and post-transcriptional levels, yet what genes are regulated by a specific lncRNA remains to be characterized. To assess the effects of the lncRNA on gene expression, an increasing number of researchers profiled the genome-wide or individual gene expression level change after knocking down or overexpressing the lncRNA. Herein, we describe a curated database named LncRNA2Target, which stores lncRNA-to-target genes and is publicly accessible at http://www.lncrna2target.org. A gene was considered as a target of a lncRNA if it is differentially expressed after the lncRNA knockdown or overexpression. LncRNA2Target provides a web interface through which its users can search for the targets of a particular lncRNA or for the lncRNAs that target a particular gene. Both search types are performed either by browsing a provided catalog of lncRNA names or by inserting lncRNA/target gene IDs/names in a search box.

Identifying the Association Between Alzheimer's Disease and Parkinson's Disease Using Genome-Wide Association Studies and Protein-Protein Interaction Network

Alzheimer's disease (AD) and Parkinson's disease (PD) are the first and second most common neurodegenerative diseases in the elderly. Shared clinical and pathological features have been reported. Recent large-scale genome-wide association studies (GWAS) have been conducted and reported a number of AD and PD variants. Until now, the underlying genetic mechanisms for all these newly identified PD variants as well as the association between AD and PD are still unclear exactly. We think that PD variants may contribute to AD and PD by influence on brain gene expression. Here, we conducted a systems analysis using (1) AD and PD variants (P < 5.00E-08) identified by the published GWAS; (2) four brain expression GWAS datasets using expression quantitative trait loci from the cerebellum and temporal cortex; (3) large-scale AD GWAS from the Alzheimer Disease Genetics Consortium (ADGC); (4) a protein-protein interaction network. Our results indicated that PD variants around the 17q21 were associated with gene expression and suggestive AD risk. We also identified significant interaction among AD and PD susceptibility genes. We believe that our findings may explain the underlying genetic mechanisms for newly identified PD variants in PD and AD, as well as the association between AD and PD, which may be very useful for future genetic studies for both diseases.

Pathway analysis of genome-wide association study and transcriptome data highlights new biological pathways in colorectal cancer

Colorectal cancer (CRC) is a common malignancy that meets the definition of a complex disease. Genome-wide association study (GWAS) has identified several loci of weak predictive value in CRC, however, these do not fully explain the occurrence risk. Recently, gene set analysis has allowed enhanced interpretation of GWAS data in CRC, identifying a number of metabolic pathways as important for disease pathogenesis. Whether there are other important pathways involved in CRC, however, remains unclear. We present a systems analysis of KEGG pathways in CRC using (1) a human CRC GWAS dataset and (2) a human whole transcriptome CRC case-control expression dataset. Analysis of the GWAS dataset revealed significantly enriched KEGG pathways related to metabolism, immune system and diseases, cellular processes, environmental information processing, genetic information processing, and neurodegenerative diseases. Altered gene expression was confirmed in these pathways using the transcriptome dataset. Taken together, these findings not only confirm previous work in this area, but also highlight new biological pathways whose deregulation is critical for CRC. These results contribute to our understanding of disease-causing mechanisms and will prove useful for future genetic and functional studies in CRC.

RADB: a database of rheumatoid arthritis-related polymorphisms

Rheumatoid arthritis (RA) is an autoimmune disease that has a complex genetic basis. Therefore, it is important to explore the genetic background of RA. The extensive recent application of polymorphic genetic markers, especially single nucleotide polymorphisms, has presented us with a large quantity of genetic data. In this study, we developed the Database of Rheumatoid Arthritis-related Polymorphisms (RADB), to integrate all the RA-related genetic polymorphisms and provide a useful resource for researchers. We manually extracted the RA-related polymorphisms from 686 published reports, including RA susceptibility loci, polymorphisms associated with particular clinical features of RA, polymorphisms associated with drug response in RA and polymorphisms associated with a higher risk of cardiovascular disease in RA. Currently, RADB V1.0 contains 3235 polymorphisms that are associated with 636 genes and refer to 68 countries. The detailed information extracted from the literature includes basic information about the articles (e.g. PubMed ID, title and abstract), population information (e.g. country, geographic area and sample size) and polymorphism information (e.g. polymorphism name, gene, genotype, odds ratio and 95% confidence interval, P-value and risk allele). Meanwhile, useful annotations, such as hyperlinks to dbSNP, GenBank, UCSC, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway, are included. In addition, a tool for meta-analysis was developed to summarize the results of multiple studies. The database is freely available at http://www.bioapp.org/RADB.

Database URL:http://www.bioapp.org/RADB.