Nucleolar and spindle-associated protein 1 is a tumor grade correlated prognosis marker for glioma patients

AIMS

Despite therapeutic advances in glioma management including surgery, radiation, and chemotherapy, the improvement of patient outcome is far from satisfactory. Nucleolar and spindle-associated protein 1 (NUSAP1) is an important functional protein during mitosis, and its abnormal expression is implicated in progression of different types of tumors. However, the role of NUSAP1 in gliomas remains unclear.

METHODS

NUSAP1 expression in gliomas with different grades was investigated based on GEO glioma datasets. Kaplan-Meier survival analysis was used to evaluate its prognostic significance. In vitro assays were also performed to evaluate effects of NUSAP1 on malignant phenotypes of glioma cells by silencing NUSAP1.

RESULTS

NUSAP1 expression was correlated not only with glioma grade but also with prognosis of glioma patients. NUSAP1 depletion suppressed proliferation of U251 cells by inducing cell cycle arrest at G2/M phase and apoptosis. NUSAP1 depletion rendered U251 cells impaired migratory ability as well.

CONCLUSION

NUSAP1 is a potential prognosis marker for glioma patients and therapeutic strategies targeting NUSAP1 might hold promise in improving glioma treatment.

A Pilot Study of Circulating MicroRNA-125b as a Diagnostic and Prognostic Biomarker for Epithelial Ovarian Cancer

OBJECTIVE

Early diagnosis of epithelial ovarian cancer is critical for patient survival. The objective of this pilot study is to identify a circulating micro (mi)RNA as a potential biomarker for epithelial ovarian cancer.

METHODS

A total of 135 epithelial ovarian cancer patients and 54 benign ovarian tumor patients were recruited for this study. Using customized TaqMan low density miRNA arrays, we first screened expression levels of 48 miRNAs in sera from 18 epithelial ovarian cancer patients and 16 benign ovarian tumor patients. The most significantly and differentially expressed miRNA was then further examined in all serum samples using real-time polymerase chain reaction. Its expression was further analyzed in relationship with clinicopathological factors and patient survival.

RESULTS

Array screening data showed that expression levels of serum miRNA-20a, miRNA-125b, miRNA-126, miRNA-355, and let-7c were significantly different between malignant and benign ovarian tumor patients. Subsequent real-time polymerase chain reaction results showed that serum miRNA-125b levels were significantly higher in epithelial ovarian cancer patients compared to benign controls. Moreover, serum miRNA-125b levels were significantly higher in ovarian cancer patients in early stages I and II, and in patients having no residual tumor following surgery, but were not associated with differentiation and histological types of ovarian cancer. Notably, the higher level of miR-125b was significantly positively correlated with progression-free survival (P = 0.035) and marginally, with overall survival (P = 0.069).

CONCLUSIONS

miRNA-125b plays an important role in the pathogenesis and progression of epithelial ovarian cancer. Circulating miRNA-125b has the potential to become a novel biomarker for early diagnosis and prognosis prediction of epithelial ovarian cancer.

Correction: Boosted visible light photodegradation activity of boron doped rGO/g-C3N4 nanocomposites: the role of C–O–C bonds

Correction for ‘Boosted visible light photodegradation activity of boron doped rGO/g-C₃N₄ nanocomposites: the role of C–O–C bonds’ by Shaobo Li et al., New J. Chem., 2018, 42, 17644–17651.

Boosted visible light photodegradation activity of boron doped rGO/g-C3N4 nanocomposites: the role of C–O–C bonds

Boron doping is an effective way to promote the chemical interaction between rGO and g-C₃N₄.

Human growth hormone and human prolactin function as autocrine/paracrine promoters of progression of hepatocellular carcinoma

The death rates of hepatocellular carcinoma (HCC) are extremely high due to the paucity of therapeutic options. Animal models and anecdotal clinical evidence indicate a potential role of hGH and hPRL in HCC. However, the prognostic relevance and the functional role of tumor expression of these hormones in human HCC are not defined. Herein, we analyzed the mRNA and protein expression of hGH and hPRL in histopathological samples of non-neoplastic liver and HCC by in situ hybridization, PCR and immunohistochemistry techniques. Increased mRNA and protein expression of both hormones was observed in HCC compared with non-neoplastic liver tissues. hGH expression was significantly associated with tumor size and tumor grade. No significant association was observed between the expression of hPRL and any histopathological features. Amplification of both hGH and hPRL genes in HCC was observed when compared to non-neoplastic tissue. Expression of both hGH and hPRL was associated with worse relapse-free and overall survival in HCC patients. In vitro and in vivo functional assays performed with HCC cell lines demonstrated that autocrine expression of hGH or hPRL in HCC cells increased STAT3 activation, oncogenicity and tumor growth while functional antagonism with hGH-G120R significantly reduced these parameters. Hence, tumor expression of hGH/hPRL is associated with a worse survival outcome for patients with HCC and hGH/hPRL function as autocrine/paracrine promoters of HCC progression.

Tens of hertz narrow-linewidth laser based on stimulated Brillouin and Rayleigh scattering

We proposed and demonstrated a linewidth compression method of a laser based on stimulated Brillouin scattering (SBS) and a Rayleigh backscattering structure (RBS). The relationship between the output SBS laser linewidth and the input pump linewidth was studied theoretically and experimentally. It is shown that the narrower linewidth of the pump laser leads to the narrower bandwidth of the SBS gain and, finally, the bandwidth of the SBS will tend to its intrinsic value as the linewidth of a pump laser narrower than 10 kHz; then the linewidth of an SBS fiber ring laser would tend to 200 Hz. In order to further reduce its linewidth with low cost, RBS and a simple dual-cavity feedback structure were added and, finally, a ∼75  Hz narrow-linewidth laser with a side-mode suppression ratio of 70 dB was obtained.

MALAT1 long ncRNA promotes gastric cancer metastasis by suppressing PCDH10

EZH2, the catalytic component of polycomb repressive complex 2 (PRC2), is frequently overexpressed in human cancers and contributes to tumor initiation and progression, in part through transcriptional silencing of tumor suppressor genes. A number of noncoding RNAs (ncRNAs) recruit EZH2 to specific chromatin loci, where they modulate gene expression. Here, we used RNA immunoprecipitation sequencing (RIP-seq) to profile EZH2-associated transcripts in human gastric cancer cell lines. We identified 8,256 transcripts, including both noncoding and coding transcripts, some of which were derived from cancer-related loci. In particular, we found that long noncoding RNA (lncRNA) MALAT1 binds EZH2, suppresses the tumor suppressor PCDH10, and promotes gastric cellular migration and invasion. Our work thus provides a global view of the EZH2-associated transcriptome and offers new insight into the function of EZH2 in gastric tumorigenesis.

Co-expression of GR79 EPSPS and GAT yields herbicide-resistant cotton with low glyphosate residues

Glyphosate-resistant (GR) crops have been adopted on a massive scale by North and South American farmers. Currently, about 80% of the 120 million hectares of the global genetically modified (GM) crops are GR crop varieties. However, the adoption of GR plants in China has not occurred at the same pace, owing to several factors including, among other things, labour markets and the residual effects of glyphosate in transgenic plants. Here, we report the co-expression of codon-optimized forms of GR79 EPSPS and N-acetyltransferase (GAT) genes in cotton. We found five times more resistance to glyphosate with 10-fold reduction in glyphosate residues in two pGR79 EPSPS-pGAT co-expression cotton lines, GGCO2 and GGCO5. The GGCO2 line was used in a hybridization programme to develop new GR cottons. Field trials at five locations during three growing seasons showed that pGR79-pGAT transgenic cotton lines have the same agronomic performance as conventional varieties, but were USD 390-495 cheaper to produce per hectare because of the high cost of conventional weed management practices. Our strategy to pyramid these genes clearly worked and thus offers attractive promise for the engineering and breeding of highly resistant low-glyphosate-residue cotton varieties.

Spinal Cord is the Primary Site of Action for Skeletal Muscle Relaxation by Sevoflurane

MINI: A modified selective anesthetics delivery rabbit model was used validated to a better preferential anesthesia than previous models. Furthermore, we found evidence that primarily the spinal cord mediated the skeletal muscle relaxation action of sevoflurane.

STUDY DESIGN

A randomized, in vivo study was performed to explore the skeletal muscle relaxation action site of sevoflurane.

OBJECTIVE

The aim of this study was to investigate the skeletal muscle relaxation action of sevoflurane by a modified selective anesthetics delivery rabbit model.

SUMMARY OF BACKGROUND DATA

The action site and mechanisms of skeletal muscle relaxation caused by sevoflurane were unclear, so a modified selective anesthetics delivery model was used.

METHODS

Sixteen male New Zealand White rabbits were randomly assigned to the sevoflurane or sham group. In situ measurement of train of four, maximum single twitch, and tetanic muscle force of left tibialis anterior muscle was repeatedly measured at three time points: at the beginning of lower torso bypass (baseline value), during preferential sevoflurane delivery to the brain (brain value), during preferential sevoflurane delivery to the spinal cord (spinal cord value).

RESULTS

When 1.5MAC sevoflurane was administrated via the lungs, the arterial concentration and partial pressure of sevoflurane in the upper torso were 205.27 ± 16.23 μg/mL and 29.16 ± 1.05 mmHg, whereas in the lower torso bypass circulation were 10.39 ± 4.50 μg/mL and 1.79 ± 0.97 mmHg. Conversely, the arterial concentration and partial pressure of sevoflurane in the upper torso were 14.04 ± 5.33 μg/mL and 2.25 ± 0.84 mmHg, whereas those values were 199.38 ± 11.61 μg/mLl and 29.20 ± 1.08 mmHg in the lower torso, when 1.5MAC sevoflurane was delivered via an oxygenator. In sevoflurane group, maximum single twitch and tetanic muscle force were significantly reduced compared with baseline (single: P = 0.046; tetanic: P = 0.001) or brain values (single: P = 0.005; tetanic: P = 0.001), when spinal cord was selectively anesthetized. In the sham group, there were no significant differences among the three conditions compared.

CONCLUSION

A modified selective anesthetics delivery rabbit model has been validated, which provided evidence that the spinal cord, not the brain, was the primary site mediating the skeletal muscle relaxation action of sevoflurane.

LEVEL OF EVIDENCE

5.

Long noncoding RNA SFTA1P promoted apoptosis and increased cisplatin chemosensitivity via regulating the hnRNP-U-GADD45A axis in lung squamous cell carcinoma

Chemotherapeutic insensitivity remains one of the major obstacles in clinical treatment of lung squamous cell carcinoma (LSCC). Recently, increasing evidence has suggested that long non-coding RNAs (lncRNAs) promote tumorigenesis in many cancer types. However, the potential biological roles and regulatory mechanisms of lncRNAs in response to cisplatin treatment are poorly understood. Here, we found that lncRNA SFTA1P (surfactant associated 1, pseudogene), highly expressed in lung, was down-regulated in LSCC tissues and could be induced upon cisplatin treatment in LSCC cells. Elevated SFTA1P induced apoptosis and enhanced the sensitivity to cisplatin of LSCC cells. We further identified that hnRNP-U (heterogeneous nuclear ribonucleoprotein U) was down-regulated in LSCCs and positively correlated with patients' poor prognosis as well as SFTA1P. Mechanistic studies revealed that SFTA1P could up-regulate hnRNP-U expression. In addition, we identified that hnRNP-U enhanced cisplatin-induced apoptosis through up-regulation of GADD45A, high expression of which was correlated with good prognosis in LSCC patients. Our findings demonstrated that SFTA1P might serve as a useful biomarker for LSCC diagnosis and a predictor for cisplatin chemotherapy response in patients with LSCC.

GFF3sort: a novel tool to sort GFF3 files for tabix indexing

Background

The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse.

Results

We developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, GFF3sort can properly deal with the order of features that have the same chromosome and start position, either by remembering their original orders or by conducting parent-child topology sorting. Based on our test datasets from seven species, GFF3sort produced accurate sorting results with acceptable efficiency compared with currently available tools.

Conclusions

GFF3sort is a novel tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be useful to help with genome annotation data processing and visualization.

Electronic supplementary material

The online version of this article (10.1186/s12859-017-1930-3) contains supplementary material, which is available to authorized users.

Deletions at SLC18A1 increased the risk of CRC and lower SLC18A1 expression associated with poor CRC outcome

Copy number variations (CNVs) contribute to the development of colorectal cancer (CRC). We conducted a two-stage association study to identify CNV risk loci for CRC. We performed a gene-based rare CNV study on 694 sporadic CRC and 1641 controls using Illumina Human-OmniExpress-12v1.0 BeadChips, and further replicated in 934 CRC cases and 2680 controls for risk CNVs by using TaqMan Copy Number Assay. Tumor buddings, cancer cells in the center of primary tumor and normal intestinal epithelial cells were captured using laser capture microdissection (LCM) and were assayed using AffymetrixGeneChip® Human Genome U133 Plus 2.0 Array. In addition, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus data were assessed for the effects of risk CNVs. We found that germline deletions affecting the last six exons of SLC18A1 significantly associated with CRC with a combined P value of 6.4 × 10-5 by a two-stage analysis. Both in TCGA CRC RNA seq dataset and GDS4382, SLC18A1 was significantly down regulated in CRC tissues than in paired normal tissues (N = 32 and 17 pairs, P = 0.004 and 0.009, respectively). In LCM samples, similar observations were obtained that the expression levels of SLC18A1 in the tumor buddings, cancer cells in the center of primary tumor, and stroma of both tumor budding and cancer cells were lower than normal intestinal epithelial and stromal cells (fold change = 0.17-0.62, 0.12-0.57 and 0.37-0.68, respectively). In summary, the germline deletions at SLC18A1 contributed to the development of CRC. The role of SLC18A1 required further exploration.

An Improved Approach to Estimate Methane Emissions from Coal Mining in China

China, the largest coal producer in the world, is responsible for over 50% of the total global methane (CH₄) emissions from coal mining. However, the current emission inventory of CH4 from coal mining has large uncertainties because of the lack of localized emission factors (EFs). In this study, province-level CH4 EFs from coal mining in China were developed based on the data analysis of coal production and corresponding discharged CH4 emissions from 787 coal mines distributed in 25 provinces with different geological and operation conditions. Results show that the spatial distribution of CH₄ EFs is highly variable with values as high as 36 m3/t and as low as 0.74 m3/t. Based on newly developed CH₄ EFs and activity data, an inventory of the province-level CH4 emissions was built for 2005-2010. Results reveal that the total CH₄ emissions in China increased from 11.5 Tg in 2005 to 16.0 Tg in 2010. By constructing a gray forecasting model for CH₄ EFs and a regression model for activity, the province-level CH₄ emissions from coal mining in China are forecasted for the years of 2011-2020. The estimates are compared with other published inventories. Our results have a reasonable agreement with USEPA's inventory and are lower by a factor of 1-2 than those estimated using the IPCC default EFs. This study could help guide CH₄ mitigation policies and practices in China.

First Dark Matter Search Results from the XENON1T Experiment

We report the first dark matter search results from XENON1T, a ∼2000-kg-target-mass dual-phase (liquid-gas) xenon time projection chamber in operation at the Laboratori Nazionali del Gran Sasso in Italy and the first ton-scale detector of this kind. The blinded search used 34.2 live days of data acquired between November 2016 and January 2017. Inside the (1042±12)-kg fiducial mass and in the [5,40]  keV_{nr} energy range of interest for weakly interacting massive particle (WIMP) dark matter searches, the electronic recoil background was (1.93±0.25)×10^{-4}  events/(kg×day×keV_{ee}), the lowest ever achieved in such a dark matter detector. A profile likelihood analysis shows that the data are consistent with the background-only hypothesis. We derive the most stringent exclusion limits on the spin-independent WIMP-nucleon interaction cross section for WIMP masses above 10  GeV/c^{2}, with a minimum of 7.7×10^{-47}  cm^{2} for 35-GeV/c^{2} WIMPs at 90% C.L.

Mechanism of long non-coding RNA MALAT1 in lipopolysaccharide-induced acute kidney injury is mediated by the miR-146a/NF-κB signaling pathway

The present study aimed to examine the expression and function of the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1)/microRNA (miR)-146a/nuclear factor (NF)-κB axis in lipopolysaccharide (LPS)-induced acute kidney injury (AKI). The mRNA levels of MALAT1 and miR-146a in AKI tissues and cells were detected using reverse transcription-quantitative polymerase chain reaction analysis. The NF-κB pathway proteins and cell viability were assessed using western blot analysis and the MTT method, respectively. The secretion of inflammatory factors was determined using the ELISA method. The present study also examined effects of the abnormal expression of MALAT1 and miR-146a on cytokines and the NF-κB pathway. A potential binding region between MALAT1 and miR-146a was confirmed via RNA immunoprecipitation. The results revealed that the upregulation of MALAT1 reduced the expression of miR‑146a, and there was a negative linear correlation between MALAT1 and miR-146a in a RNA-induced silencing complex‑dependent manner. The expression levels of miR-146a were lower in the kidney injury specimens and NRK-52E cells, compared with those in the controls. MALAT1 knockdown and the overexpression of miR-146a reduced the production of phosphorylated inhibitor of NF-κB and np65 protein. miR‑146a was found to be transcriptionally induced by NF-κB, and miR-146a repressed the pro-inflammatory NF-κB pathway and downstream transcription factors. Taken together, these data indicated that the MALAT1/miR‑146a/NF-κB pathway exerted key functions in LPS-induced AKI, and provided novel insights into the mechanisms of this therapeutic candidate for the treatment of the disease.

Aberration in translation initiation and associated diseases: Role of the eukaryotic translation initiation factor 3A

Translation control in eukaryotes contributes significantly to gene expression regulation during cellular processes, which enables rapid changes of specific proteins to maintain cellular homeostasis. Eukaryotic translation is a multiple-step process that comprised of four phases: initiation, elongation, termination and ribosome recycling. The initiation phase is rate-limiting and orchestrated by a set of eukaryotic translation initiation factors (eIFs). Defects in translation initiation can result in a series of diseases. Among all eIFs, eIF3 is the largest and less-known initiation factor due to its intrinsic complexity. Aberration in eIF3A, the largest subunit of eIF3, is known to contribute to carcinogenesis and protection against evolution into higher-grade malignancy, and the altered expression or mutation of eIF3A affects the responses of cancer patients to platinum-based chemotherapy. Besides its role in cancinogenesis, eIF3A is also implicated in fibrosis, and the agents inhibiting eIF3A delay the progression of this disorder. The dual roles of eIF3A in tumorigenesis are probably due to the regulation of translation of different mRNAs at different stages of tumor progression by eIF3A. In turn the encoded products serve as pro-tumor or anti-tumor proteins at different stages.

Tumor-suppressive miRNA-135a inhibits breast cancer cell proliferation by targeting ELK1 and ELK3 oncogenes

Breast cancer is the most common malignant disease amongst women. miRNAs are small, non-coding RNAs that regulate gene expression, thus have the potential to play an important role during cancer development. Emerging evidence shows that miR-135a is down-regulated in breast cancer cells, but the functional roles of miR-135a in breast cancer cells remains unexplored. For this purpose, we investigated the expression of miR-135a in breast cancer cells and explored its functional role during breast cancer progression. In vitro study showed that miR-135a may be a novel tumor suppressor. Further studies showed that transcription factors ELK1 and ELK3 are direct target genes of miR-135a that modulates the suppressive function of miR-135a in breast cancer cells. Induced expression of miR-135a significantly downregulated the expression of ELK1 and ELK3 both at mRNA and protein levels. Furthermore, the effect of miR-135a in MCF-7 and T47D cells was investigated by the overexpression of miR-135a mimics. In vitro, induced expression of miR-135a in breast cancer cells inhibited cell Proliferation and clongenicity. Moreover, a luciferase activity assay revealed that miR-135a could directly target the 3'-untranslated region (3' UTRS) of ELK1 and ELK3 oncogenes. In addition, rescue experiment demonstrated that the promoted cell growth by transcription factors ELK1 and ELK3 was attenuated by the over-expression of miR-135a. Our study demonstrates that miR-135a regulates cell proliferation in breast cancer by targeting ELK1 and ELK3 oncogenes, and suggests that miR-135a potentially can act as a tumor suppressor.

Multi-channel mode converter based on a modal interferometer in a two-mode fiber

In this Letter, we propose a multi-channel mode converter with the concept of a modal interferometer in a two-mode fiber (TMF). Two lateral stress points in a TMF function as in-line fiber mode couplers to construct the modal interferometer, and both transmission spectra and near-field patterns confirm that the LP₀₁ mode is successfully converted into an LP₁₁ mode at the multiple channels. The measured mode conversion efficiency almost completely follows the theoretical tendency. Finally, the mode conversion is realized at 20 channels in the C+L wavelength band with conversion efficiency up to 99.5% and insertion loss as low as 0.6 dB. Furthermore, the channel spacing can be freely tailored by adjusting the distance between two stress points.

Adiposity and incident diabetes within 4 years of follow-up: the Guangzhou Biobank Cohort Study

AIM

Whether different adiposity measures predict incident diabetes differentially in general Chinese populations is unclear. We investigated this in Chinese people aged 50+ years in the Guangzhou Biobank Cohort Study.

METHODS

Waist circumference and BMI were measured at baseline, and fasting glucose was measured at both baseline and follow-up examinations. Incident diabetes was defined as fasting glucose ≥ 7.0 mmol/l, glucose after 2-h oral glucose tolerance test ≥ 11.1 mmol/l, and/or self-reported physician-diagnosed diabetes during the follow-up period.

RESULTS

Of 15 752 people without diabetes at baseline from 2003 to 2008, 1779 (11.3%) developed incident diabetes during the follow-up from 2008 to 2012 (mean = 3.6 years, sd = 1.0). After mutually adjusting each other and adjusting for other potential confounders, waist circumference showed a higher predictive value than BMI. The odds ratio (OR) (95% confidence interval (CI) was 1.50 (95% CI 1.37-1.64) for a 1 sd increment in waist circumference and 1.21 (95% CI 1.11-1.33), for a 1 sd increment in BMI. Similarly, after mutual adjustment, abdominal obesity was associated with an almost twofold odds of incident diabetes (OR 1.93, 95% CI 1.71-2.17), which was higher than that for general obesity (OR 1.76, 95% CI 1.50-2.06). The area under receiver operating characteristic curve (AUC) for waist circumference was higher than that for BMI [AUC = 0.676 (95% CI 0.660-0.686) vs. 0.665 (95% CI 0.651-0.678), P = 0.02].

CONCLUSION

Abdominal obesity predicted incident diabetes in older people better than general obesity. Our findings may be an early warning signal for local government or public health practitioners to develop and investigate more effective intervention programmes for diabetes, and should also be disseminated to the public to pay more attention to this important public health issue.