SNNRice6mA: A Deep Learning Method for Predicting DNA N6-Methyladenine Sites in Rice Genome

DNA N6-methyladenine (6mA) is an important epigenetic modification, which is involved in many biology regulation processes. An accurate and reliable method for 6mA identification can help us gain a better insight into the regulatory mechanism of the modification. Although many experimental techniques have been proposed to identify 6mA sites genome-wide, these techniques are time consuming and laborious. Recently, several machine learning methods have been developed to identify 6mA sites genome-wide. However, there is room for the improvement on their performance for predicting 6mA sites in rice genome. In this paper, we developed a simple and lightweight deep learning model to identify DNA 6mA sites in rice genome. Our model needs no prior knowledge of 6mA or manually crafted sequence feature. We built our model based on two rice 6mA benchmark datasets. Our method got an average prediction accuracy of ∼93% and ∼92% on the two datasets we used. We compared our method with existing 6mA prediction tools. The comparison results show that our model outperforms the state-of-the-art methods.

Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate

Genes are not randomly distributed on eukaryotic chromosomes. Some neighboring genes show order conservation among species, while some neighboring genes separate during evolution even though their neighborhoods are conserved in some species. Here, I investigated whether after-separation gene repositioning is under natural selection for evolutionary conserved gene neighborhoods compared with nonconserved neighborhoods. After separation, genes with conserved neighborhoods show low-expression divergence between the after-separation species and the before-separation species. After genes separate from their conserved gene neighbors, their after-separation gene neighbors tend to show coexpression and coprotein complex with their before-separation gene neighbors. These results indicate evolutionary constraints on the selection of neighboring genes after evolutionary conserved gene neighborhoods separate.

P1643An exploratory analysis for the optimal monitoring interval of N-terminal pro-B-type natriuretic peptide in patients with stable heart failure

Background

N-terminal pro-B-type natriuretic peptide (NT-proBNP) is a potential biomarker for monitoring the status of heart failure. However, the optimal monitoring interval is unknown. This study aims to investigate minimal informative monitoring interval of NT-proBNP in patients with stable chronic heart failure.

Methods

In this retrospective open cohort study, adult patients followed up at a tertiary hospital for chronic heart failure with NT-proBNP measurements were included if they had been previously admitted due to acute heart failure and were free from readmission over 6 months after discharge. We analyzed NT-proBNP measured between 6 months after discharge and the timepoint of an alteration of medication regimen or readmission due to worsening of heart failure. To distinguish actual progression of the disease from biological variability and measurement error, the signal-to-noise ratio method was applied with a random-effects model. Stratified analysis was performed according to underlying risks.

Results

In this analysis, 368 patients were included with NT-proBNP measured between July 2009 and December 2017. The patients had 6.0 times of NT-proBNP measurements in median (interquartile range [IQR] 4.0–10.0) during the follow-up period (median 12.0 months [IQR 6.0–27.0]). In the estimates of the random-effects model, signal (i.e. actual progression of the disease) exceeded noise (i.e. biological variability and measurement error) at 8.1 months (95% confidence interval [CI]: 5.7–10.1) after the index measurement. In a subgroup analysis according to the AHEAD risk score, the minimal informative monitoring interval was shortened as the risk score increased (0–1 point: 12.3 months [95% CI: 10.3–14.5]; 2–3 points: 8.0 months [95% CI: 6.8–9.7]; 4–5 points: 3.3 months [95% CI: 3.0–3.8]; Figure).

Informative intervals stratified by risk

Conclusion

In patients with stable chronic heart failure, the overall minimal informative monitoring interval of NT-proBNP measurement was 8.1 months, which varies by underlying risk. The optimal monitoring interval could be lengthened especially for patients at lower risk.

Identification of key pathways and genes changes in pancreatic cancer cells (BXPC-3) after cross-talk with primary pancreatic stellate cells using bioinformatics analysis

Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors with poor prognosis, and the interaction between activated pancreatic stellate cells (PSCs) and PDAC cells plays an important role in the development of PDAC. The aim of this study was to identify gene changes in BXPC-3 after cross-talk with PSCs and reveal their potential mechanisms. The gene expression profiling analysis of BXPC-3 was completed after co-culture with primary PSCs for 48 h. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and the differentially expressed genes (DEGs) were identified by Agilent GeneSpring GX software. In total, 3657 DEGs were identified in BXPC-3, including 1881 up-regulated genes and 1776 downregulated genes. GO analysis results showed that upregulated DEGs were significantly enriched in biological processes (BP), including peptide metabolic process, response to stress and electron transport chain; the downregulated DEGs were significantly enriched in biological processes, including signaling, multicellular organism development and anatomical structure development. KEGG pathway analysis revealed that 19 pathways were upregulated and 32 pathways were downregulated, and that upregulated DEGs were enriched in protein export and glutathione metabolism, while the downregulated DEGs were enriched in axon guidance and focal adhesion. The top 10 upregulated genes and the top 10 downregulated genes were identified. By constructing PPI network, we selected out 10 key genes (TP53, SRC, IL6, JUN, ISG15, CAD, STAT1, OAS3, OAS1, VIM) and significant pathways. The associated survival analysis was performed and the SRC, IL-6, ISG15, STAT1, OAS3, OAS1 and VIM were proved to be related to worse overall survival time of PDAC patients. In conclusion, the present study indicated that the identified DEGs promote our understanding of the molecular mechanisms underlying the interaction between pancreatic cancer cells and PSCs and might be used as molecular targets in the future to study the role of tumor microenvironment in the progression of PDAC.

Kaempferol attenuates imiquimod-induced psoriatic skin inflammation in a mouse model

Psoriasis is an immune-mediated inflammatory skin disease that mainly affects the skin barrier. Treatment for psoriasis mainly includes conventional immunosuppressive drugs. However, long-term treatment with global immunosuppressive agents may cause a variety of side effects, including nephrotoxicity and infections. Kaempferol, a natural flavonol present in various plants, is known to possess potent anti-inflammatory, anti-oxidant and anti-cancerous properties. However, it is unknown whether kaempferol is also anti-psoriatic. Here we established an imiquimod (IMQ)-induced psoriatic mouse model to explore the potential therapeutic effects of kaempferol on psoriatic skin lesions and inflammation. In this study, we demonstrated that treatment with kaempferol protected mice from developing psoriasis-like skin lesions induced by topical administration of IMQ. Kaempferol reduced CD3⁺ T cell infiltration and gene expression of major proinflammatory cytokines, including interleukin (IL)-6, IL-17A and tumor necrosis factor (TNF)-α, in the psoriatic skin lesion. It also down-regulated proinflammatory nuclear factor kappa B (NF-κB) signaling in the skin. The therapeutic effects were associated with a significant increase in CD4⁺ forkhead box protein 3 (FoxP3)⁺ regulatory T cell (T_reg ) frequency in the spleen and lymph nodes as well as FoxP3-positive staining in the skin lesion. Conversely, depletion of CD4⁺ CD25⁺ T_regs reversed the therapeutic effects of kaempferol on the skin lesion. Kaempferol also lowered the percentage of IL-17A⁺ CD4⁺ T cells in the spleen and lymph nodes of IMQ-induced psoriatic mice. Finally, kaempferol suppressed the proliferation of T cells in vitro and their mTOR signaling. Thus, our findings suggest that kaempferol may be a therapeutic drug for treating human psoriasis in the near future.

[A survey of attitudes to and demands on internship in graduates majoring in preventive medicine in 6 colleges and universities in China]

Objective: To understand the internship of students majoring in preventive medicine in 6 colleges and universities in China, and provide reference suggestions for the improvement of internship arrangement. Methods: By using the method of combined clustering and convenient sampling, the fifth grades students majoring in preventive medicine in six universities in the eastern, central and western China were surveyed by using questionnaires to collect the information of their attitudes (to) and suggestions for clinical and public health internships. Results: A total of 596 students were surveyed. In terms of the benefits of clinical internship and public health internship, students who thought that the internship was fruitful accounted for >88%, and more students thought that reform is needed in clinical internship compared with public health internship. In clinical internship, the students through that the time arrangement was not appropriate enough (95, 39.58%), the content should be more detailed and in-depth (73, 30.42%) and the content did not conform to the professional direction (54, 22.50%). In public health internship, the students thought that the time arrangement was not appropriate (77, 45.56%), the content should be more detailed and standardized (65, 38.46%) and the types of internship bases should be more diversified (20, 11.83%). Conclusions: The undergraduates majoring in preventive medicine felt to be benefited from clinical practice and public health internships and thought they are of necessity. At the same time, there are still many problems which needs to be improved in the two types of internships. It is necessary to make joint efforts from students, teachers, colleges and practice bases to promote the continuous improvement of undergraduate internship.

Aptamer-Based Fluorescent Sensor Array for Multiplexed Detection of Cyanotoxins on a Smartphone

Developing easy-to-use and miniaturized detectors is essential for in-field monitoring of environmentally hazardous substances, such as the cyanotoxins. We demonstrated a differential fluorescent sensor array made of aptamers and single-stranded DNA (ssDNA) dyes for multiplexed detection and discrimination of four common cyanotoxins with an ordinary smartphone within 5 min of reaction. The assay reagents were preloaded and dried in a microfluidic chip with a long shelf life over 60 days. Upon the addition of analyte solutions, competitive binding of cyanotoxin to the specific aptamer-dye conjugate occurred. A zone-specific and concentration-dependent reduction in the green fluorescence was observed as a result of the aptamer conformation change. The aptasensors are fully optimized by quantification of their dissociation constants, tuning the stoichiometric ratios of reaction mixtures, and implementation of an internal intensity correction step. The fluorescent sensor array allowed for accurate identification and measurement of four important cyanotoxins, including anatoxin-a (ATX), cylindrospermopsin (CYN), nodularin (NOD), and microcystin-LR (MC-LR), in parallel, with the limit of detection (LOD) down to a few nanomolar (<3 nM), which is close to the World Health Organization's guideline for the maximum concentration allowed in drinking water. The smartphone-based sensor platform also showed remarkable chemical specificity against potential interfering agents in water. The performance of the system was tested and validated with real lake water samples that were contaminated with trace levels of individual cyanotoxins as well as binary, ternary, and quaternary mixtures. Finally, a smartphone app interface has been developed for rapid on-site data processing and result display.

Pan-cancer analysis identifies telomerase-associated signatures and cancer subtypes

Background

Cancer cells become immortalized through telomere maintenance mechanisms, such as telomerase reverse transcriptase (TERT) activation. In addition to maintaining telomere length, TERT activates manifold cell survival signaling pathways. However, telomerase-associated gene signatures in cancer remain elusive.

Methods

We performed a systematic analysis of TERT high (TERT^high) and low (TERT^low) cancers using multidimensional data from The Cancer Genome Atlas (TCGA). Multidimensional data were analyzed by propensity score matching weight algorithm. Coexpression networks were constructed by weight gene coexpression network analysis (WGCNA). Random forest classifiers were generated to identify cancer subtypes.

Results

The TERT^high-specific mRNA expression signature is associated with cell cycle-related coexpression modules across cancer types. Experimental screening of hub genes in the cell cycle module suggested TPX2 and EXO1 as potential regulators of telomerase activity and cell survival. MiRNA analysis revealed that the TERT^high-specific miR-17-92 cluster can target biological processes enriched in TERT^low cancer and that its expression is negatively correlated with the tumor/normal telomere length ratio. Intriguingly, TERT^high cancers tend to have mutations in extracellular matrix organization genes and amplify MAPK signaling. By mining the clinical actionable gene database, we uncovered a number of TERT^high-specific somatic mutations, amplifications and high expression genes containing therapeutic targets. Finally, a random forest classifier integrating telomerase-associated multi-omics signatures identifies two cancer subtypes showed profound differences in telomerase activity and patient survival.

Conclusions

In summary, our results depict a telomerase-associated molecular landscape in cancers and provide therapeutic opportunities for cancer treatment.

Electronic supplementary material

The online version of this article (10.1186/s12943-019-1035-x) contains supplementary material, which is available to authorized users.

Identification of key pathways and genes changes in pancreatic cancer cells (BXPC-3) after cross-talked with primary pancreatic stellate cells using bioinformatics analysis

Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors with poor prognosis, and the interaction between activated pancreatic stellate cells (PSCs) and PDAC cells plays an important role in the development of PDAC. The aim of this study was to identify gene changes in BXPC-3 after cross-talked with PSCs and reveal their potential mechanisms. The gene expression profiling analysis of BXPC-3 was completed after co-cultured with primary PSCs for 48 h. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and the differentially expressed genes (DEGs) were identified by Agilent GeneSpring GX software. In total, 3657 DEGs were identified in BXPC-3, including 1881 up-regulated genes and 1776 downregulated genes. GO analysis results showed that up-regulated DEGs were significantly enriched in biological processes (BP), including peptide metabolic process, response to stress, and electron transport chain; the down-regulated DEGs were significantly enriched in biological processes, including signaling, multicellular organismal development, and anatomical structure development. KEGG pathway analysis revealed that 19 pathways were upregulated and 32 pathways were downregulated, and that up-regulated DEGs were enriched in protein export and glutathione metabolism, while the down-regulated DEGs were enriched in axon guidance and focal adhesion. The top 10 up-regulated genes, and the top 10 down-regulated genes were identified. By constructing PPI network, we selected out 10 key genes (TP53, SRC, IL6, JUN, ISG15, CAD, STAT1, OAS3, OAS1, VIM) and significant pathways. The associated survival analysis was performed and the SRC, IL-6, ISG15, STAT1, OAS3, OAS1 and VIM were proved to be related to worse overall survival time of PDAC patients. In conclusion, the present study indicated that the identified DEGs promote our understanding of the molecular mechanisms underlying the interaction between pancreatic cancer cells and PSCs and might be used as molecular targets in the future to study the role of tumor microenvironment in the progression of PDAC.

Identification of key pathways and gene changes in primary pancreatic stellate cells after cross-talk with pancreatic cancer cells (BXPC-3) using bioinformatics analysis

It is well known that as the king of cancer, pancreatic ductal adenocarcinoma (PDAC) has relatively malignant biological behavior and poor prognosis. The interaction between pancreatic stellate cells and PDAC cells promotes the development of PDAC. The aim of this study was to describe gene characteristics in pancreatic stellate cell (PSCs) after cross-talked with BXPC-3 and unravel their underlying mechanisms. The expression profiling analysis of genes in PSCs was completed after co-cultured with primary BXPC-3 for 48h. The Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis and gene ontology (GO) analysis were performed, and the differentially expressed genes (DEGs) were identified by Agilent GeneSpring GX program. In total, 1804 DEGs were filtered out in PSCs, including 958 up-regulated genes and 846 downregulated genes. GO analysis showed that the up-regulated DEGs were significantly enriched in biological processes (BP) such as defense response, immune system process and immune response; the down-regulated DEGs were significantly enriched in biological regulation and cytoskeleton organization. KEGG pathway analysis showed that 28 pathways were upregulated and 5 were downregulated. By constructing PPI network, we selected out 10 key genes (IL6，IL8, IL1B, BCL2, CCL2, CSF2, KIT, ICAM1, PTPRC and IGF1) and significant enriched pathways. In conclusion, the current study suggests that the filtered DEGs contribute to our understanding of the molecular mechanisms underlying the interaction between PSCs and pancreatic cancer cells, and might be used as molecular targets to further the study the role of tumor microenvironment in the progression of PDAC.

Prophage Diversity of 'Candidatus Liberibacter asiaticus' Strains in California

Huanglongbing (HLB) is a highly destructive citrus disease and is associated with a nonculturable bacterium, 'Candidatus Liberibacter asiaticus'. 'Ca. L. asiaticus' in the United States was first found in Florida in 2005 and is now endemic there. In California, 'Ca. L. asiaticus' was first detected in Hacienda Heights in Los Angeles County in 2012 and has now been detected in multiple urban locations in southern California. Knowledge of 'Ca. L. asiaticus' strain diversity in California is important for HLB management. In this study, genomic diversity among 10 'Ca. L. asiaticus' strains from six California locations were analyzed using a next-generation sequencing (NGS) (Illumina MiSeq and HiSeq) approach. Draft genome sequences of 'Ca. L. asiaticus' strains were assembled. Sequences of the 16S ribosomal RNA gene and nrdB confirmed 'Ca. L. asiaticus' identity. Prophages were detected in all 'Ca. L. asiaticus' strains. The California 'Ca. L. asiaticus' strains formed four prophage typing groups (PTGs): PTG1, with type 1 prophage only (strains from Anaheim, San Gabriel, and Riverside); PTG2, with type 2 prophage only (strains from Hacienda Heights); PTG1-3, with both type 1 and 3 prophages (a strain from Cerritos); and PTG1-2, with both type 1 and type 2 prophages (a strain from La Habra). Analyses of the terL sequence showed that all California 'Ca. L. asiaticus' strains were not introduced from Florida but likely from locations in Asia. Miniature inverted-repeat transposable elements were found in all 'Ca. L. asiaticus' strains, yet, a jumping-out event was detected in the 'Ca. L. asiaticus' strain from Cerritos. Altogether, this study demonstrated that the NGS approach focusing on prophage variation was sensitive and effective in revealing diversity of 'Ca. L. asiaticus' strains in California.

[Differential expressions analysis of piwi-interacting RNAs in hepatocellular carcinoma]

Objective: To investigates the role of piwi-interacting RNAs (piRNA) in the occurrence and development of hepatocellular carcinoma. Methods: Second-generation small RNA sequencing was performed on cancer and paracancerous tissues, metastatic and non-metastatic liver cancer tissues of patients with liver cancer, and the sequencing data were filtered out for the common RNA sequences to be repeated. The piRNA predictor was used to forecast the possible new piRNA merged with the downloaded known piRNA to screen out distinction. A miRanda algorithm was used to predict the corresponding target genes and functional enrichment analysis. piRNA was selected for experimental functional (migration) analysis. An independent t-test was used to compare means between the two groups. Results: 66 772 piRNAs (known 149) were obtained by sequencing. 241 piRNAs were found in cancer and paracancerous tissues, and 1 634 piRNAs were found in metastatic and non-metastatic tumors. Analysis of the GO and KEGG pathways of the target genes of differential piRNAs revealed that they were mainly involved in cell adhesion. An experimental functional analysis was performed on the selected Pirna (PIR1/97), which showed that it promoted the migration of hepatoma cells (LM3: t = 8.829, P < 0.05; PLC: t = 7.318, P < 0.05). Conclusion: The expression levels of piRNA in hepatocellular carcinoma patients with cancer and paracancerous tissues, metastasis and non-metastatic liver cancer tissues are different and it could be entailed in the metastasis process of hepatocellular carcinoma. Hence, experimental functional analysis is required for research and experimental confirmation.

The Impact of lncRNA Dysregulation on Clinicopathology and Survival of Breast Cancer: A Systematic Review and Meta-analysis

Dysregulation of multiple long non-coding RNAs (lncRNAs) was reported to play major roles in breast cancer (BC). Here we aimed to collect most of the relevant literature to assess the prognostic value of lncRNAs in BC. To this end, we systematically searched PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang to identify published articles on the associations of lncRNAs with clinicopathology and/or survival of BC. Via this searching, we identified 70 articles involving 9,307 BC patients and regarding 48 lncRNAs. The expression of 41 lncRNAs was related to one or more clinicopathological parameters of BC, including tumor size; lymph node metastasis; histological grade; TNM stage; and estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2) statuses (p < 0.05). Dysregulation of 28 lncRNAs was associated with overall survival, and abnormal expression of 9 lncRNAs was linked to disease-free survival. Furthermore, the expression level of 3 lncRNAs was correlated with metastasis-free survival, 3 lncRNAs with relapse-free survival, and 3 lncRNAs with progression-free survival. Our analysis showed that multiple lncRNAs were significantly associated with BC clinicopathology and survival. A large-scale study is needed to verify the prognostic value of these lncRNAs in BC.

Association between body mass index and breast cancer risk: evidence based on a dose-response meta-analysis

Introduction

Breast cancer is the most common cancer in women worldwide. The association between body mass index (BMI) and breast cancer risk has been paid more attention in the past few years, but the findings are still controversial. To obtain a more reliable conclusion, we performed a dose–response meta-analysis on 12 prospective cohort studies comprising 22,728,674 participants.

Methods

Linear and nonlinear trend analyses were conducted to explore the dose–response relationship between BMI and breast cancer risk. The summary relative risk (SRR) and 95% confidence intervals (CIs) were used to evaluate the cancer risk.

Results

The overall results showed a weak positive association between a 5-unit increase in BMI and breast cancer risk, indicating that a 5 kg/m² increase in BMI corresponded to a 2% increase in breast cancer risk (SRR: 1.02, 95% CI: 1.01–1.04, p<0.001). Notably, further subgroup meta-analysis found that higher BMI could be a protective factor of breast cancer risk for premenopausal women (SRR: 0.98, 95% CI: 0.96–0.99, p<0.001). In addition, the dose–response result demonstrated that there was a linear association between BMI and breast cancer risk (P_nonlinearity=0.754).

Conclusion

In summary, this dose–response meta-analysis of prospective cohort studies showed that every 5 kg/m² increase in BMI corresponded to a 2% increase in breast cancer risk in women. However, higher BMI could be a protective factor in breast cancer risk for premenopausal women. Further studies are necessary to verify these findings and elucidate the pathogenic mechanisms.

pgRNAFinder: a web-based tool to design distance independent paired-gRNA

SUMMARY

The CRISPR/Cas System has been shown to be an efficient and accurate genome-editing technique. There exist a number of tools to design the guide RNA sequences and predict potential off-target sites. However, most of the existing computational tools on gRNA design are restricted to small deletions. To address this issue, we present pgRNAFinder, with an easy-to-use web interface, which enables researchers to design single or distance-free paired-gRNA sequences. The web interface of pgRNAFinder contains both gRNA search and scoring system. After users input query sequences, it searches gRNA by 3' protospacer-adjacent motif (PAM), and possible off-targets, and scores the conservation of the deleted sequences rapidly. Filters can be applied to identify high-quality CRISPR sites. PgRNAFinder offers gRNA design functionality for 8 vertebrate genomes. Furthermore, to keep pgRNAFinder open, extensible to any organism, we provide the source package for local use.

AVAILABILITY AND IMPLEMENTATION

The pgRNAFinder is freely available at http://songyanglab.sysu.edu.cn/wangwebs/pgRNAFinder/, and the source code and user manual can be obtained from https://github.com/xiexiaowei/pgRNAFinder.

CONTACT

songyang@bcm.edu or daizhim@mail.sysu.edu.cn.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Infusion of leukocytes from HLA haplo-identical familial donors as an adjuvant in the HLH-2004 protocol to treat the virus-associated adult hemophagocytic lymphohistiocytosis: a retrospective study of 26 patients

Adult hemophagocytic lymphohistiocytosis (HLH) is a fatal disease with poor survival and a limited role of drug therapies. To help to recognize virus and enhance survival, we infused leukocytes derived from human leukocyte antigen (HLA) haplo-identical familial donors to patients. We retrospectively investigated 26 adult virus-associated hemophagocytic syndrome (VAHS) patients' medical records from 2006-2017. Eleven of the 26 patients accepted relatives' derived leukocytes infusions in addition to drug therapies recommended in the HLH-2004 protocol. The leukocyte doses ranged from 0.75 to 3.30×10⁸ per kilogram of body weight. The other 15 patients accepted immunosuppressive and supportive therapies referred to in the HLH-2004 protocol. We compared the treatment outcomes of the two groups of patients. Patients in the cell infusion group had a lower viral load (P = 0.023) and better laboratory results and prolonged overall survival (60.44 vs. 20.18 weeks, P = 0.047). A factor that might relate to overall survival is platelet count (P = 0.032), except for the leukocyte infusions (P = 0.012). For patients without acceptable donors, infusions of leukocytes from HLA haplo-identical familial donors could be a feasible treatment to prolong overall survival as an adjuvant to drug therapies.

Validation of EORTC QLQ-OES18 for Chinese patients with esophageal cancer

The aim of this study is to evaluate the reliability, validity, and acceptability of the Chinese version of the EORTC QLQ-OES18 in patients with esophageal cancer. The questionnaire was translated according to the guideline of the EORTC. One hundred and forty-nine patients with esophageal cancer from Tianjin Medical University Cancer Institute and Hospital completed the Karnofsky performance scale (KPS) and the simplified Chinese EORTC QLQ-C30/OES18 scales during July 2013 to January 2014. The results were statistically analyzed by Cronbach's α coefficient, Spearman correlation test with multiple strengthen analysis, and Wilcoxon Rank Sum test. The internal consistency (Cronbach's α coefficient) of all four scales (dysphagia, eating, reflux, and pain) was 0.689-0.822, which were satisfactory or near satisfactory. The absolute values of correlation of each scale between EORTC QLQ-OES18 and EORTC QLQ-C30 were 0.002-0.750 while there was no significant difference between groups divided by KPS scores. We confirmed the Chinese version of EORTC QLQ-OES18 appears to be a reliable, valid, and acceptable instrument for measuring the health-related quality of life of patients with esophageal cancer in mainland China.

Prognostic and predictive values of PD-L1 expression in patients with digestive system cancer: a meta-analysis

BACKGROUND

PD-L1 has been reported to be expressed in diverse human malignancies. However, the prognostic value of PD-L1 in digestive system cancers remains inconclusive. Therefore, we conducted this meta-analysis to evaluate the prognostic impact of PD-L1 expression in digestive system cancers.

MATERIALS AND METHODS

We searched the PubMed, Embase, and the Chinese National Knowledge Infrastructure for publications concerning PD-L1 expression in digestive system cancers. Correlations of PD-L1 expression level with overall survival (OS), disease-free survival (DFS), and recurrence-free survival (RFS) were analyzed.

RESULTS

Finally, 32 studies with 7,308 patients were included. Our results show that PD-L1 expression was significantly associated with poorer OS (hazard ratio [HR] =1.44, 95% confidence interval [CI] =1.18-1.76, P<0.001), but not DFS (HR =0.91, 95% CI =0.61-1.37, P=0.657) or RFS (HR =1.27, 95% CI =0.75-2.14, P=0.368). Moreover, in the subgroup analysis, significant associations between PD-L1 expression and OS were found in Asians (HR =1.50, 95% CI =1.19-1.89, P=0.001), gastric cancer (HR =1.43, 95% CI =1.05-1.94, P=0.021), and pancreatic carcinoma (HR =2.64, 95% CI =1.78-3.93, P<0.001).

CONCLUSION

These results suggest that the expression of PD-L1 is associated with worse OS in digestive system cancers, especially in gastric cancer and pancreatic cancer. In addition, PD-L1 may act as a new parameter for predicting poor prognosis and a promising target for anticancer therapy in digestive system cancers.

[High expression of hnRNPAB/Kap1 together promote poor prognosis in HCC]

Objective: To further understand the interaction protein spectrum of heterogeneous ribonucleoprotein AB (hnRNP AB), and to investigate their clinical significance in hepatocellular carcinoma (HCC). Methods: We carried out mass spectrometry to reveal the specific peptides of KRAB-associated protein 1 (Kap1) and hnRNPAB, and verified their interaction by immunocoprecipitation and western blotting. Expression of hnRNPAB/Kap1 proteins were detected by immunohistochemical staining in the tissue microarrays. Categorical data were analyzed by the chi square test or Fisher exact test; enumeration data between groups were compared using Student t-test or Wilcocon signed rank test; the cumulative recurrence and survival rates were evaluated using the Kaplan-Meier method and the differences were assessed using the log-rank test. Results: We identified Kap1 as a molecular partner for hnRNPAB in HCCLM3 cells and HepG2 cells as well. We found that the 5-year survival rate of the Kap1high patients was significantly lower than the survival rate of those of the Kap1low group (36% vs 59% , HR = 1.67, P < 0.001). Similarly, Kap1high HCC patients had the poorest prognosis at 5-years, with higher cumulative recurrence rate than Kap1low patients (72% vs 54%, HR = 1.66, P = 0.001). Univariate and Multivariate analyses revealed that hnRNPAB /Kap1 alone (HR = 1.35 /1.28, P = 0.001) or in combination with Kap1 (HR =1.24 /1.27, P < 0.05) were independent prognostic indicators for overall survival and time to recurrence. Conclusion: In HCC cells, hnRNPAB and Kap1 form protein complexes. The expression levels of hnRNPAB alone or in combination with Kap1 in HCC patients are important because they provide not only a predictor for HCC prognosis but also a therapeutic target for future studies.

The effect of Qing Huan Ling on the hypoglutamatergic schizophrenia model in mice

Objective

To investigate the effect of Qing Huan Ling and (or) risperidone on activity and preferences behavior of the hypoglutamatergic schizophrenia model in mice.

Methods

Seventy kunming mice were randomly divided into 5 groups, one group as placebo group. The rest groups intraperitoneal injection MK-801 continuously 14 day, then randomly numbered: model group, Qing Huan Ling group, risperidone groupand Qing Huan Ling combined risperidone group. Intragastric administration give corresponding drugs for each group one month, at the same time observe high activities and changes in the preferences of five groups.

Results

Compared with the blank group, activity of the rest model groups induced by MK-801 was increased (P < 0.05). After intragastric administration one month, model groups of high activity was decreased, especially risperidone combined Qing Huan Ling group. There was no statistical meaning in inquiry activity of five groups (P > 0.05). Compared with model group, latent period of step-through test was prolonged 35.5 s (P < 0.05), of step-down test was prolonged 11.4 s in risperidone combined Qing Huan Ling group.

Conclusion

The combination of Qing Huan Ling and risperidone can suppress the high activity; also can protect harmed memory of the preference behavior in the hypoglutamatergic schizophrenia model in mice.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

CTLA-4 polymorphisms associate with breast cancer susceptibility in Asians: a meta-analysis

Previous studies have investigated the association between cytotoxic T-lymphocyte antigen-4 (CTLA-4) polymorphisms and breast cancer susceptibility, but the results remained inconsistent. Therefore, we evaluated the relationship between four common CTLA-4 polymorphisms and breast cancer risk by a meta-analysis, aiming to derive a comprehensive and precise conclusion. We searched EMBASE, Pubmed, Web of Science, CNKI, and Wanfang databases until July 18th, 2016. Finally, ten eligible studies involving 4,544 breast cancer patients and 4,515 cancer-free controls were included; all these studies were from Asia. Odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the breast cancer risk in five genetic models. The results indicated that the CTLA-4 +49A>G (rs231775) polymorphism had a significant association with decreased breast cancer risk in allelic, homozygous, dominant and recessive models. Also, the +6230G>A (rs3087243) polymorphism reduced breast cancer risk especially in the Chinese population under homozygous and recessive models. In contrast, the -1661A>G (rs4553808) polymorphism increased breast cancer risk in allelic, heterozygous and dominant models, whereas -1722 T>C (rs733618) did not relate to breast cancer risk. In conclusion, CTLA-4 polymorphisms significantly associate with breast cancer susceptibility in Asian populations, and different gene loci may have different effects on breast cancer development. Further large-scale studies including multi-racial populations are required to confirm our findings.

Association of genetic polymorphisms in MIF with breast cancer risk in Chinese women

Macrophage migration inhibitory factor (MIF) has been reported to associate with increased cancer risk in several cancers. However, the role of MIF in breast cancer (BC) susceptibility remains unknown. For the first time, we conducted a case-control study to assess the potential association of three common MIF gene variants (rs755622, rs1803976, rs11548059) with BC susceptibility in Chinese women. Total 560 breast cancer patients and 583 age- and sex-matched healthy individuals were recruited from Northwest China, and the DNA was genotyped by Sequenom MassARRAY. Odds ratios (OR) and 95% confidence intervals (95% CI) were computed to estimate the associations. We found that C/G, C/C, and C/G-C/C genotype carriers in MIF rs755622 have a significantly increased risk of BC (C/G vs. G/G: OR = 1.36, 95% CI = 1.07-1.75, P = 0.014; C/C vs. GG: OR = 2.01, 95% CI = 1.06-3.79, P = 0.029; C/G-C/C vs. G/G: OR = 1.42 95% CI = 1.11-1.80, P = 0.004). Further analyses indicate that the BC risk is associated with Ki-67 status, and the rs755622 polymorphism increases breast cancer risk among elder patients (≥49 years). There is no association between BC risk and other two polymorphisms (rs1803976 and rs11548059) by overall analysis and stratified analysis. In conclusion, MIF rs755622 polymorphism increases BC susceptibility in Chinese population, especially among elder patients.

Plasma Mitochondrial DNA Levels as a Biomarker of Lipodystrophy Among HIV-infected Patients Treated with Highly Active Antiretroviral Therapy (HAART)

Lipodystrophy is a common complication in HIV-infected patients taking highly active antiretroviral therapy. Its early diagnosis is crucial for timely modification of antiretroviral therapy. We hypothesize that mitochondrial DNA in plasma may be a potential marker of LD in HIV-infected individuals. In this study, we compared plasma mitochondrial DNA levels in HIV-infected individuals and non-HIV-infected individuals to investigate its potential diagnostic value. Total plasma DNA was extracted from 67 HIV-infected patients at baseline and 12, 24 and 30 months after initiating antiretroviral therapy. Real-time quantitative PCR was used to determine the mitochondrial DNA levels in plasma. Lipodystrophy was defined by the physician-assessed presence of lipoatrophy or lipohypertrophy in one or more body regions. The mitochondrial DNA levels in plasma were significantly higher at baseline in HIV-infected individuals than in non-HIV-infected individuals (p<0.05). At month 30, 33 out of 67 patients (49.2%) showed at least one sign of lipodystrophy. The mean plasma mitochondrial DNA levels in lipodystrophy patients were significantly higher compared to those without lipodystrophy at month 24 (p<0.001). The receiver operating curve analysis demonstrated that using plasma mitochondrial DNA level (with cut-off value <5.09 log10 copies/ml) as a molecular marker allowed identification of patients with lipodystrophy with a sensitivity of 64.2% and a specificity of 73.0%. Our data suggest that mitochondrial DNA levels may help to guide therapy selection with regards to HIV lipodystrophy risk.

Dissecting Embryonic Stem Cell Self-Renewal and Differentiation Commitment from Quantitative Models

To model quantitatively embryonic stem cell (ESC) self-renewal and differentiation by computational approaches, we developed a unified mathematical model for gene expression involved in cell fate choices. Our quantitative model comprised ESC master regulators and lineage-specific pivotal genes. It took the factors of multiple pathways as input and computed expression as a function of intrinsic transcription factors, extrinsic cues, epigenetic modifications, and antagonism between ESC master regulators and lineage-specific pivotal genes. In the model, the differential equations of expression of genes involved in cell fate choices from regulation relationship were established according to the transcription and degradation rates. We applied this model to the Murine ESC self-renewal and differentiation commitment and found that it modeled the expression patterns with good accuracy. Our model analysis revealed that Murine ESC was an attractor state in culture and differentiation was predominantly caused by antagonism between ESC master regulators and lineage-specific pivotal genes. Moreover, antagonism among lineages played a critical role in lineage reprogramming. Our results also uncovered that the ordered expression alteration of ESC master regulators over time had a central role in ESC differentiation fates. Our computational framework was generally applicable to most cell-type maintenance and lineage reprogramming.

DNA signals at isoform promoters

Transcriptional heterogeneity is extensive in the genome, and most genes express variable transcript isoforms. However, whether variable transcript isoforms of one gene are regulated by common promoter elements remain to be elucidated. Here, we investigated whether isoform promoters of one gene have separated DNA signals for transcription and translation initiation. We found that TATA box and nucleosome-disfavored DNA sequences are prevalent in distinct transcript isoform promoters of one gene. These DNA signals are conserved among species. Transcript isoform has a RNA-determined unstructured region around its start site. We found that these DNA/RNA features facilitate isoform transcription and translation. These results suggest a DNA-encoded mechanism by which transcript isoform is generated.

[Current status on management and needs related to education and training programs set for new employees at the provincial Centers for Disease Control and Prevention, in China]

OBJECTIVE

In order to understand the current management status on education/training and needs for training among new employees working at the provincial CDC in China during 2012-2014, so as to provide basis for setting up related programs at the CDC levels.

METHODS

Based on data gathered through questionnaire surveys run by CDCs from 32 provincial and 5 specifically-designated cities, microsoft excel was used to analyze the current status on management of education and training, for new employees.

RESULTS

There were 156 management staff members working on education and training programs in 36 CDCs, with 70% of them having received intermediate or higher levels of education. Large differences were seen on equipment of training hardware in different regions. There were 1 214 teaching staff with 66 percent in the fields or related professional areas on public health, in 2014. 5084 new employees conducted pre/post training programs, from 2012 to 2014 with funding as 750 thousand RMB Yuan. 99.5% of the new employees expressed the needs for further training while. 74% of the new staff members expecting a 2-5 day training program to be implemented. 79% of the new staff members claimed that practice as the most appropriate method for training.

CONCLUSIONS

Institutional programs set for education and training at the CDCs need to be clarified, with management team organized. It is important to provide more financial support on both hardware, software and human resources related to training programs which are set for new stuff members at all levels of CDCs.

Effects of zoledronic acid on bone fusion in osteoporotic patients after lumbar fusion

Treatment with zoledronic acid in osteoporotic patients with spinal fusion shortens the duration of time to fusion, improves the fusion rate, prevents the subsequent adjacent vertebral compression fractures, improves the clinical outcomes, and prevents immobilization-induced bone loss in the hip.

INTRODUCTION

The objective of the study was to explore the effects of zoledronic acid on the healing process in osteoporotic patients following spinal fusion in a randomized, placebo-controlled, and triple-blinded study.

METHODS

Seventy-nine osteoporotic patients with single-level degenerative spondylolisthesis were randomly assigned to receive either zoledronic acid infusion (zoledronic acid group) or saline infusion (controls) after spinal fusion. Functional radiography and CT scans were used to evaluate fusion status. Bone formation was graded into three categories: Grade A (bridging bone bonding with adjacent vertebral bodies), Grade B (bridging bone bonding with either superior or inferior vertebral body), or Grade C (incomplete bony bridging). A solid fusion was defined as less than 5° of angular motion with Grade A or B bone formation. Adjacent vertebral compression fractures (VCF) were assessed on MRI at 12 months after surgery. Serum level of carboxy terminal cross-linked telopeptide of type I collagen (β-CTX) and amino-terminal propeptide of type I procollagen (PINP) was measured. Bone mineral density (BMD) was measured by DXA. Oswestry Disability Index (ODI) was used to assess the clinical outcomes.

RESULTS

Grade A or B bridging bone was more frequently observed in zoledronic acid group at 3, 6, and 9 months post-operation compared to the control group (p < 0.05). At 12 -months post-operation, bridging bone and solid fusion were not significantly different between groups. No patients in zoledronic acid group showed aVCF, whereas six patients (17 %) in the control group did (p < 0.05). Both β-CTX and PINP were suppressed in zoledronic acid group. BMD at the femoral neck decreased rapidly and did not return to the preoperative level in the controls at 3 (-1.4 %), 6 (-2.5 %), and 12 (-0.8 %) months after surgery. Zoledronic acid prevented this immobilization-induced bone loss and increased BMD. ODI showed the improved clinical outcomes compared with controls at 9 and 12 months post-surgery.

CONCLUSION

Treatment with zoledronic acid in osteoporotic patients with spinal fusion shortens the time to fusion, improves the fusion rate, prevents subsequent aVCFs, and improves clinical outcomes.