CD73/NT5E is a target of miR-30a-5p and plays an important role in the pathogenesis of non-small cell lung cancer

Background

CD73 (ecto-5′-nucleotidase) is implicated in the development of many types of cancer. CD73 inhibitors are currently being tested in clinical trials for the treatment of cancer. Understanding the molecular and cellular actions of CD73 inhibitors is the key to improving this line of therapy.

Methods

Quantitative real-time PCR (qRT-PCR) was used to detect the expression of CD73 and miR-30a-5p; Western blot and immunohistochemical assays were used to investigate the levels of CD73 and other proteins. Flow cytometry was used to determine cell cycle stage and apoptosis. CCK-8 and clonogenic assays were used to investigate cell proliferation. Wound healing, migration and invasion assays were used to investigate the motility of cells. A lung carcinoma xenograft mouse model was used to investigate the in vivo effects of CD73 and miR-30a-5p.

Results

In the present study, we found that CD73 is overexpressed and miR-30a-5p is underexpressed in non-small cell lung cancer tissues compared with adjacent noncancerous. Further, we showed that CD73 is a direct target of miR-30a-5p by luciferase reporter assays, qRT-PCR and western blot analysis. We also found that overexpression of miR-30a-5p in these non-small cell lung cancer cell lines inhibited cell proliferation in vitro and in vivo. Moreover, the epithelial-to-mesenchymal phenotype was suppressed and cell migration and invasion were inhibited; these effects were brought about via the EGF signaling pathway.

Conclusions

Our findings reveal a new post-transcriptional mechanism of CD73 regulation via miR-30a-5p and EGFR-related drug resistance in non-small cell lung cancer.

Electronic supplementary material

The online version of this article (doi:10.1186/s12943-017-0591-1) contains supplementary material, which is available to authorized users.

Research progress of Tc1/Mariner superfamily

With the rapid improvement of sequencing techniques, more and more genome annotations reveal the transposons are the important components of most genomes and present on almost all organisms. Among them, the Tc1/Mariner superfamily represents the most widespread DNA transposons. Until now, fourteen active Tc1/Mariner transposons (Minos, Mos1, etc.) have been identified and some highly active artificial transposons have been created through molecular reconstruction, such as Sleeping Beauty (SB). The transposons such as SB and Mos1 have been widely used as gene transfer vectors in the fields of transgenosis, gene trapping and gene therapy. In this review, we summarize the structure, classification, distributions, transposition mechanism and excavations of active members of Tc1/Mariner as well as its application in the fields of transgenesis, gene trapping and gene therapy.

Gender determinants of smoking practice in Indigenous communities: an exploratory study

Despite the need to urgently reduce smoking rates among Indigenous Australians, in order to close-the-gap in life expectancy, little is known regarding how this can be achieved. This study aimed to explore whether a focus on gender specific determinants of smoking among Indigenous Australians could be identified, thus providing a potentially novel approach to underpin future efforts at intervention. A qualitative research design was employed. Eighty-two participants, comprised of 43 Indigenous women (mean age 32.15, SD, 12.47) and 39 Indigenous men (mean age 34.91, SD, 11.26), participated in one of 12 focus groups held in metropolitan, regional and rural locations in South Australia. Facilitators prompted discussion in response to the question: 'What is it like being a smoker these days?' Two experienced coders assessed data for themes using Attride-Stirling's (2002) method of analysis. Two global themes emerged for men and women. The first theme, 'It's Harder to Smoke Nowadays', encompassed sub-themes capturing changed smoking practices in response to tobacco control strategies implemented in Australia. Sub-themes of 'smoking in secrecy' coupled with an 'awareness of the effects of passive smoking' were identified among women. Among men, sub-themes that depicted tension between 'a desire to be a role model' and 'guilt about smoking' emerged. The second theme, 'Push and Pull Factors', identified a range of gender specific determinants of smoking. While similar reasons for smoking ('pull factors') were identified in men and women (e.g. addiction, boredom, stress, pleasure, mood stabiliser), different 'push factors' (reasons for not wanting to smoke) emerged. For men, sport, fitness and children were identified as reasons for not wanting to smoke, whereas women identified factors such as respect for non-smokers, and body image concerns. The current findings suggest that there may be fundamental differences in the determinants of smoking (pull factors) as well as reasons for wanting to quit (push factors) between Indigenous men and women. A focus on interventions that target gender specific determinants, or motivators of smoking, offers a novel, and potentially efficacious approach to reduce smoking rates among Indigenous Australians.

Dissection of H-bonding interactions in a glycolic acid–water dimer

The binding strength and collective effects of multiple H-bonds in the glycolic acid–water dimer were studied in comparison to the aromatic analog, 9-hydroxy-9-fluorene carboxylic acid (9HFCA).

MWPCR: Multiscale Weighted Principal Component Regression for High-dimensional Prediction

We propose a multiscale weighted principal component regression (MWPCR) framework for the use of high dimensional features with strong spatial features (e.g., smoothness and correlation) to predict an outcome variable, such as disease status. This development is motivated by identifying imaging biomarkers that could potentially aid detection, diagnosis, assessment of prognosis, prediction of response to treatment, and monitoring of disease status, among many others. The MWPCR can be regarded as a novel integration of principal components analysis (PCA), kernel methods, and regression models. In MWPCR, we introduce various weight matrices to prewhitten high dimensional feature vectors, perform matrix decomposition for both dimension reduction and feature extraction, and build a prediction model by using the extracted features. Examples of such weight matrices include an importance score weight matrix for the selection of individual features at each location and a spatial weight matrix for the incorporation of the spatial pattern of feature vectors. We integrate the importance score weights with the spatial weights in order to recover the low dimensional structure of high dimensional features. We demonstrate the utility of our methods through extensive simulations and real data analyses of the Alzheimer's disease neuroimaging initiative (ADNI) data set.

Digit ratio (2D:4D) and handgrip strength in a Chinese population of Han ethnicity

BACKGROUND

In humans, the relative lengths of the index finger to the ring finger (2D:4D) is a sexually dimorphic trait which correlated with prenatal sex steroids and has been increasingly used as a promising tool to evaluate the impact of prenatal hormone exposure in some traits, such as physical performance. Handgrip strength (HGS) is one potent index of physical ability and its relationship with 2D:4D ratio has been discussed in several ethnic groups.

AIMS

To investigate whether there is a correlation between 2D:4D ratio and HGS in Chinese college students of Ningxia Han ethnicity.

METHODS

608 students (211 males and 397 females) of Han ethnicity were recruited from Ningxia medical university. Photocopies and HGS of both hands were collected at Yinchuan city, in the Ningxia province of China.

RESULTS

Sexual dimorphism of 2D:4D and HGS were found, males had significantly lower 2D:4D and greater HGS than females. 2D:4D in both hands were significantly negative correlated with HGS in females and not in males.

CONCLUSIONS

2D:4D ratio is negative correlated with HGS in a Chinese population of Ningxia Han ethnicity and this association should be considered on the anthropological research within an evolutionary concept in the future.

The Statistics and Mathematics of High Dimension Low Sample Size Asymptotics

The aim of this paper is to establish several deep theoretical properties of principal component analysis for multiple-component spike covariance models. Our new results reveal an asymptotic conical structure in critical sample eigendirections under the spike models with distinguishable (or indistinguishable) eigenvalues, when the sample size and/or the number of variables (or dimension) tend to infinity. The consistency of the sample eigenvectors relative to their population counterparts is determined by the ratio between the dimension and the product of the sample size with the spike size. When this ratio converges to a nonzero constant, the sample eigenvector converges to a cone, with a certain angle to its corresponding population eigenvector. In the High Dimension, Low Sample Size case, the angle between the sample eigenvector and its population counterpart converges to a limiting distribution. Several generalizations of the multi-spike covariance models are also explored, and additional theoretical results are presented.

Increased risk of breast cancer in individuals carrying the TNRC9 rs3803662 C>T polymorphism: a meta-analysis of case-control studies

Currently, the relationship between the trinucleotide repeat containing 9 (TNRC9) rs3803662 C>T polymorphism and risk of breast cancer (BC) is uncertain. Here, we attempted to obtain a more accurate assessment of this association by conducting a meta-analysis of all eligible case-control investigations, comprising 44,820 cases and 58,316 controls. A comprehensive search was performed to identify all suitable studies involving the TNRC9 rs3803662 polymorphism and BC risk. Pooled odds ratios (ORs) and 95% confidence intervals (95%CIs) were estimated using fixed- or random-effect models. Heterogeneity, publication bias, and sensitivity analyses were also carried out. We found that the variant T allele of rs3803662 C>T greatly increases BC risk (CT vs CC: OR = 1.14, 95%CI = 1.07-1.22, P < 0.001; TT vs CC: OR = 1.38, 95%CI = 1.25-1.53, P < 0.001; CT/TT vs CC: OR = 1.19, 95%CI = 1.11-1.28, P < 0.001; TT vs

CT/CC

OR = 1.28, 95%CI = 1.19-1.38, P < 0.001). Stratified analysis based on ethnicity also revealed a markedly increased risk in Asian and Caucasian populations. Moreover, studies with hospital-based control groups showed elevated risk under the four genetic models employed, as did those using population-based controls, except under heterozygote comparison. The TNRC9 rs3803662 C>T polymorphism is greatly related to increased risk of BC, in both Asian and Caucasian populations.

A weighted scoring system to differentiate malignant liposarcomas from benign lipomas

PURPOSE

To construct a scoring system to differentiate malignant liposarcomas from benign lipomas by comparing their clinical and magnetic resonance imaging (MRI) features.

METHODS

Clinical and MRI features of 33 women and 33 men aged 17 to 83 (mean, 53) years who underwent resection of malignant liposarcomas (n=32) or benign lipomas (n=34) were reviewed.

RESULTS

The 5 strongest predictors of liposarcoma were male gender, larger tumour maximum dimension, deep to fascia, thick non-fatty septum or nodule, and internal cystic change. A weighted scoring system was constructed using the 5 strongest predictors as: Z score=10X1+X2+12X3+15X4+10X5, respectively. A cut-off score of 35 was used; all 32 malignant liposarcomas and 4 of 34 benign lipomas scored >35. The cut-off score of ≤35 could predict 30 of 66 lipomatous tumours as benign with a negative predictive value of 100% (p<0.0001).

CONCLUSION

The 5 strongest clinical and MRI features were identified to construct a scoring system to differentiate malignant from benign lipomatous tumours. Further validation in independent populations is required.

[Screening of active fractions with antithrombotic effect from Caragana jubata]

The antithrombotic effect of Caragana jubata (Pall.)Poir.ethanolic extract (TE)was evaluated by inferior vena cava thrombosis in rats and acute pulmonary thrombosis in mice. To search for the bioactive fractions of TE, comparison on acute pulmonary thrombosis was made between the two main fractions of TE (TE-1 and TE-2). Besides, pharmacological effects of TE, TE-1 and TE-2 on bleeding time and clotting time were also studied. Reference substances combined with UPLC/DAD-q-TOF-MS were applied to identify the main six compounds and other chemical constituents of the TE. The results showed that TE could significantly reduce the rat thrombosis weight in all doses (P<0.01) and improve the protective rate to mice in medium and high doses (P<0.05). TE-2 showed a stronger effect on protecting the mice from paralysis or death and prolonging the bleeding time and clotting time than TE-1. Chemical constituents in TE mainly include isoflavones, pterocarpans and stilbenoids. Constituents in TE-2 were mainly isoflavones and pterocarpans, while those in TE-1 were mainly stilbenoids, which could be inferred that all of these three kinds of constituents may be responsible for the antithrombotic effects of Caragana jubata.

Plant Aquaporin AtPIP1;4 Links Apoplastic H2O2 Induction to Disease Immunity Pathways

Hydrogen peroxide (H2O2) is a stable component of reactive oxygen species, and its production in plants represents the successful recognition of pathogen infection and pathogen-associated molecular patterns (PAMPs). This production of H2O2 is typically apoplastic but is subsequently associated with intracellular immunity pathways that regulate disease resistance, such as systemic acquired resistance and PAMP-triggered immunity. Here, we elucidate that an Arabidopsis (Arabidopsis thaliana) aquaporin (i.e. the plasma membrane intrinsic protein AtPIP1;4) acts to close the cytological distance between H2O2 production and functional performance. Expression of the AtPIP1;4 gene in plant leaves is inducible by a bacterial pathogen, and the expression accompanies H2O2 accumulation in the cytoplasm. Under de novo expression conditions, AtPIP1;4 is able to mediate the translocation of externally applied H2O2 into the cytoplasm of yeast (Saccharomyces cerevisiae) cells. In plant cells treated with H2O2, AtPIP1;4 functions as an effective facilitator of H2O2 transport across plasma membranes and mediates the translocation of externally applied H2O2 from the apoplast to the cytoplasm. The H2O2-transport role of AtPIP1;4 is essentially required for the cytoplasmic import of apoplastic H2O2 induced by the bacterial pathogen and two typical PAMPs in the absence of induced production of intracellular H2O2 As a consequence, cytoplasmic H2O2 quantities increase substantially while systemic acquired resistance and PAMP-triggered immunity are activated to repress the bacterial pathogenicity. By contrast, loss-of-function mutation at the AtPIP1;4 gene locus not only nullifies the cytoplasmic import of pathogen- and PAMP-induced apoplastic H2O2 but also cancels the subsequent immune responses, suggesting a pivotal role of AtPIP1;4 in apocytoplastic signal transduction in immunity pathways.

Tobacco TTG2 regulates vegetative growth and seed production via the predominant role of ARF8 in cooperation with ARF17 and ARF19

BACKGROUND

Plant TRANSPARENT TESTA GLABRA (TTG) proteins regulate various developmental activities via the auxin signaling pathway. Recently, we elucidated the developmental role of tobacco (Nicotiana tabacum L.) NtTTG2 in association with 12 genes that putatively encode AUXIN RESPONSIVE FACTOR (ARF) proteins, including NtARF8, NtARF17, and NtARF19. Here we show that NtTTG2 regulates tobacco growth and development by involving the NtARF8, NtARF17, and NtARF19 genes, with the NtARF8 gene playing a predominant contribution.

RESULTS

Independent silencing of the NtARF8 gene more strongly repressed tobacco growth than silencing the NtARF17 or NtARF19 gene and more effectively eradicated the growth enhancement effect of NtTTG2 overexpression. In contrast, plant growth was not affected by silencing additional nine NtTTG2-regulated NtARF genes. In double and triple gene silencing combinations, silencing the NtARF8 gene was more effective than silencing the NtARF17 or NtARF19 gene to repress growth as well as nullify growth enhancement. Therefore, the NtARF8 predominantly cooperated with the NtARF17 and NtAFR19 of the NtTTG2 functional pathway. NtARF8 also contributed to NtTTG2-regulated seed production as concurrent NtTTG2 and NtARF8 overexpression played a synergistic role in seed production quantity, whereas concurrent silencing of both genes caused more severe seed abortion than single gene silencing. In plant cells, the NtTTG2 protein facilitated the nuclear import of NtARF8 as well as increased its function as a transcription activator.

CONCLUSIONS

NtARF8 is an integral component of the NtTTG2 functional pathway, which regulates tobacco growth and development.

Repression of Smad4 by miR‑205 moderates TGF-β-induced epithelial-mesenchymal transition in A549 cell lines

The TGF-β/Smad signaling pathway plays important roles in cancer cell proliferation, apoptosis, differentiation, angiogenesis and epithelial-mesenchymal transition (EMT), which is the key event in the early stages of cancer metastasis and enhances the capability of cell migration and invasion. Smad4 acts as the only Co-Smad of TGF/Smad signaling pathway and plays the key role in TGF-β-mediated EMT. Nevertheless, the mRNA regulation mechanisms of Smad4 in human non-small cell lung cancer (NSCLC) remains largely unclear. Computational algorithms predicted that the 3'-UTR of Smad4 is a target of miR‑205. Here, we validated that miR‑205 could directly bind to 3'-UTR of Smad4 by luciferase assays. Moreover, we investigated the functional roles of miR‑205 and its molecular link to Smad4 in lung cancer cells. In this study, we confirmed that overexpression of miR‑205 suppressed the expression of Smad4, in turn, weakened the TGF-β/Smad signaling pathway and inhibited TGF-β/Smad4-induced EMT, invasion and migration ultimately. Furthermore, this study shows that miR‑205 can serve as a promising therapeutic target of highly aggressive NSCLC.

A genetic polymorphism affects the risk and prognosis of renal cell carcinoma: association with follistatin-like protein 1 expression

Few single nucleotide polymorphisms (SNPs) associated with the risk of renal cell carcinoma (RCC) have been identified, yet genetic predisposition contributes significantly to this malignancy. We previously showed that follistatin-like 1 (FSTL1) was significantly down-regulated in clear cell RCC (ccRCC), in particular metastatic ccRCC. In the present study, we systemically investigated the associations of the 6 SNPs within FSTL1-coding genomic region with RCC risk and postoperative prognosis. Age- and gender-matched case-control study (417 vs 855) indicated that rs1259293 variant genotype CC was significantly associated with an increased risk of RCC, with an odds ratio of 2.004 (95% confidence internal [CI] = 1.190-3.375). Multivariate Cox regression analysis in 309 of 417 cases showed that rs1259293 genotype (CC vs TT + CT) independently predicted an unfavorable prognosis, with a hazard ratio of 2.531 (95% CI = 1.052-6.086). Expression of FSTL1 was significantly higher in adjacent renal tissues than in tumors, and significantly higher in the tissues with rs1259293 TT genotype than in those with rs1259293 TC+CC genotypes. rs1259293 C allele might generate a CTCF binding site that blocks trans-activation of FSTL1 expression. Our results indicate that rs1259293 is associated with an increased risk and unfavorable postoperative prognosis of RCC, possibly by down-regulating FSTL1 expression in renal tissues.

ScanMe mobile

As mobile malware have increased in number and sophistication, it has become pertinent for users to have tools that can inform them of potentially malicious applications. To fulfill this need, we develop a cloud-based malware analysis service called ScanMe Mobile, for the Android platform. The objective of this service is to provide users with detailed information about Android Application Package (APK) files before installing them on their devices. With ScanMe Mobile, users are able to upload APK files from their device SD card, scan the APK in the malware detection system that could be deployed in the cloud, compile a comprehensive report, and store or share the report by publishing it to the website. ScanMe Mobile works by running the APK in a virtual sandbox to generate permission data, and analyzes the result in the machine learning detection system. Through our experimental results, we demonstrate that the proposed system can effectively detect malware on the Android platform.

Xanthomonas oryzae pv. oryzae requires H-NS-family protein XrvC to regulate virulence during rice infection

Histone-like nucleoid-structuring (H-NS) proteins, which are conserved in Gram-negative bacteria, bind DNA and act as the global transcriptional repressors. In this study, we identified and characterized the xrvC gene encoding a H-NS protein in Xathomonas oryzae pv. oryzae (Xoo) Philippines strain PXO99(A) Compared with the wild type, the xrvC-deficient mutant of PXO99(A) (named PXO99ΔxrvC) showed a reduced growth rate in both nutrient-rich and nutrient-limited media. Interestingly, PXO99ΔxrvC exhibited significantly reduced virulence on rice cultivar IRBB214, but its virulence on 31 other rice cultivars was not affected. Transcriptional analysis revealed that the expression of hrpG, hrpX and hpa1 and of 15 out of 18 tested non-TAL (transcription activator-like) effector genes was decreased significantly in the xrvC mutant compared with that in the wild type. In addition, loss of xrvC also impaired the induction of the rice susceptibility gene Os8N3 in IRBB214 by PXO99(A) Our results suggest that the xrvC gene is involved in bacterial growth, and it plays a vital role in virulence by positively regulating the expression of hrp genes and non-TAL effector genes in PXO99(A) and the susceptibility gene Os8N3 in rice.

The contribution of transposable elements to size variations between four teleost genomes

Background

Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained.

Results

In this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon). The larger genomes represent a higher diversity within each clade (superfamily) and family and a greater abundance of TEs compared with the smaller genomes; zebrafish, representing the largest genome, shows the highest diversity and abundance of TEs in its genome, followed by medaka and stickleback; while the tetraodon, representing the most compact genome, displays the lowest diversity and density of TEs in its genome. Both of Class I (retrotransposons) and Class II TEs (DNA transposons) contribute to the difference of TE accumulation of teleost genomes, however, Class II TEs are the major component of the larger teleost genomes analyzed and the most important contributors to genome size variation across teleost lineages. The hAT and Tc1/Mariner superfamilies are the major DNA transposons of all four investigated teleosts. Divergence distribution revealed contrasting proliferation dynamics both between clades of retrotransposons and between species. The TEs within the larger genomes of the zebrafish and medaka represent relatively stronger activity with an extended time period during the evolution history, in contrast with the very young activity in the smaller stickleback genome, or the very low level of activity in the tetraodon genome.

Conclusion

Overall, our data shows that teleosts represent contrasting profiles of mobilomes with a differential density, diversity and activity of TEs. The differences in TE accumulation, dominated by DNA transposons, explain the main size variations of genomes across the investigated teleost species, and the species differences in both diversity and activity of TEs contributed to the variations of TE accumulations across the four teleost species. TEs play major roles in teleost genome evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-016-0059-7) contains supplementary material, which is available to authorized users.

eHUGS: Enhanced Hierarchical Unbiased Graph Shrinkage for Efficient Groupwise Registration

Effective and efficient spatial normalization of a large population of brain images is critical for many clinical and research studies, but it is technically very challenging. A commonly used approach is to choose a certain image as the template and then align all other images in the population to this template by applying pairwise registration. To avoid the potential bias induced by the inappropriate template selection, groupwise registration methods have been proposed to simultaneously register all images to a latent common space. However, current groupwise registration methods do not make full use of image distribution information for more accurate registration. In this paper, we present a novel groupwise registration method that harnesses the image distribution information by capturing the image distribution manifold using a hierarchical graph with its nodes representing the individual images. More specifically, a low-level graph describes the image distribution in each subgroup, and a high-level graph encodes the relationship between representative images of subgroups. Given the graph representation, we can register all images to the common space by dynamically shrinking the graph on the image manifold. The topology of the entire image distribution is always maintained during graph shrinkage. Evaluations on two datasets, one for 80 elderly individuals and one for 285 infants, indicate that our method can yield promising results.