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Aims: Radiotherapy is an effective treatment for thoracic malignancies, but it can cause pulmonary injury and may lead to respiratory failure in a subset of patients. Extracellular vesicles (EVs) d...

Tumour radioresistance is a major problem for cancer radiation therapy. To identify the underlying mechanisms of this resistance, we used human non‐small cell lung cancer (NSCLC) cell lines and focused on the Inhibitor of Apoptosis Protein (IAP) family, which contributes to tumourigenesis and chemoresistance. We investigated the possible correlation between radioresistance in six NSCLC cell lines and IAP protein levels and tested the radiosensitizing effect of birinapant in vitro, a molecule that mimics the second mitochondria‐derived activator of caspase. We found that birinapant‐induced apoptosis and inhibited the proliferation of NSCLC cells after exposure to radiation. These effects were induced by birinapant downregulation of cIAP protein levels and changes of cIAP gene expression. Overall, birinapant can inhibit tumour growth of NSCLC cell lines to ironizing radiation and act as a promising strategy to overcome radioresistance in NSCLC.

Atherosclerosis (AS) is a leading cause of cardiovascular diseases (CVDs) and it results in a high rate of death worldwide, with an increased prevalence with age despite advances in lifestyle management and drug therapy. Atherosclerosis is a chronic progressive inflammatory process, and it mainly presents with lipid accumulation, foam cell proliferation, inflammatory response, atherosclerotic plaque formation and rupture, thrombosis, and vascular calcification. Therefore, there is a great need for reliable therapeutic drugs or remedies to cure or alleviate atherosclerosis and reduce the societal burden. Ginsenosides are natural steroid glycosides and triterpene saponins obtained mainly from the plant ginseng. Several recent studies have reported that ginsenosides have a variety of pharmacological activities against several diseases including inflammation, cancer and cardiovascular diseases. This review focuses on describing the different pharmacological functions and underlying mechanisms of various active ginsenosides (Rb1,-Rd, -F, -Rg1, -Rg2, and -Rg3, and compound K) for atherosclerosis, which could provide useful insights for developing novel and effective anti-cardiovascular drugs.

Lysine crotonylation (Kcrot), as a post-translational modification (PTM) originally identified at histone proteins, is involved in diverse biological processes. Several conventional machine-learning (ML) predictors were developed based on the Kcrot sites from histone proteins. Recently, thousands of Kcrot sites have been experimentally verified on non-histone proteins from multiple species. Accordingly, a few predictors have been developed for predicting the Krot sites for specific organisms (i.e. humans and papaya). Nevertheless, there is a lack of research on the comparison of the crotonylomes of different organisms. Here, we collected around 20,000 Kcrot sites experimentally identified from four different species as the benchmark data set. We present the deep-learning (DL) architecture dubbed DeepKcrot for predicting Kcrot sites on the proteomes across various species. DeepKcrot includes species-specific and general classifiers using a convolutional neural network with the word embedding (CNNWE) encoding approach. CNNWE performs better than both the traditional ML-based and other DL-based classifiers in terms of ten-fold cross-validation and independent test, independent of the size of the training set. Additionally, cross-species performance for each species-specific predictor is not as good as the self-species performance whereas the cross-species performance generally increases with the size of the training dataset. Moreover, the predictors developed based on the non-histone Kcrot sites are unsuccessful for the histone Kcrot prediction, suggesting that the Kcrot-containing peptides from non-histone and histone proteins have significantly different characteristics and data integration is required. Overall, DeepKcrot is an efficient prediction tool and freely available at http://www.bioinfogo.org/deepkcrot.

Protein engineering through directed evolution is an effective way to obtain proteins with novel functions with the potential applications as tools for diagnosis or therapeutics. Many natural proteins, largely antibodies as well as some non-antibody proteins, have undergone directed evolution in vitro in the test tubes in the laboratories around the world, resulted in the numerous protein variants with novel or enhanced functions. In this study, we constructed a Fyn SH2 variant library by randomizing the 8 variable residues in its phosphotyrosine (pTyr) binding pocket. Selection of this library by a pTyr peptide from MidT antigen led to the identification of SH2 variants with enhanced affinities to the peptide, compared to the wild type SH2, by EC50 assay. Fluorescent polarization (FP) was then applied to quantify the binding affinity of the newly identified SH2 variants. As a result, three SH2 variants, named V3, V13 and V24, have comparable binding affinities with the previously identified SH2 triple-mutant superbinder (refer to Trm). Biolayer Interferometry (BLI) assay was employed to disclose the kinetics of the binding of these SH2 superbinders, in addition to the wild type SH2, to the phosphotyrosine peptide. The results indicated that all the SH2 superbinders have two-orders increase of the dissociation rate when binding the pTyr peptide while there was no significant change in their associate rates. The previously identified SH2 superbinder Trm as well as the V13 and V24 discovered in this study have cross-reactivity with the sulfotyrosine (sTyr) containing peptide while the wild type SH2 does not. Intriguingly, though binding the pTyr peptide with comparable affinity with other SH2 superbinders, the V3 does not bind to the sTyr peptide, implying it binds to the pTyr peptide with a different pattern from the other superbinders. The newly identified superbinders could be utilized as tools for the identification of pTyr-containing proteins from tissues under different physiological or pathophysiological conditions and may have the potential in the therapeutics.

International audience; Radiotherapy is the main treatment for cancer patients. A major concern in radiotherapy is the radiation resistance of some tumors, such as human nonsmall cell lung cancer. However, the radiation dose delivered to the tumors is often limited by the possibility of collateral damage to surrounding healthy tissues. A new and efficient gadolinium-based nanoparticle, AGuIX, has recently been developed for magnetic resonance imaging-guided radiotherapy and has been proven to act as an efficient radiosensitizer. The amplified radiation effects of AGuIX nanoparticles appear to be due to the emission of low-energy photoelectrons and Auger electron interactions. We demonstrated that AGuIX nanoparticles exacerbated radiation-induced DNA double-strand break damage and reduced DNA repair in the H1299 nonsmall cell lung cancer cell line. Furthermore, we observed a significant improvement in tumor cell damage and growth suppression, under radiation therapy, with the AGuIX nanoparticles in a H1299 mouse xenograft model. This study paves the way for research into the radiosensitization mechanism of AGuIX nanoparticles and provides a scientific basis for the use of AGuIX nanoparticles as radiosensitizing drugs.

MicroRNAs (miRNAs) play a vital role in many biological processes, including cell growth, differentiation, apoptosis, development, differentiation, and carcinogenesis. Since miRNAs might play a part in cancer initiation and progression, they comprise an original class of promising diagnostic and prognostic molecular markers. In order to systematically understand the regulation of miRNA expression in cancers, the current study analyzed the miRNA expression profile in NCI-60 human cancer cell lines. Over 300 miRNAs exhibited unique expression profiles in cell lines derived from the same lineage. This study identified 9 lineage-specific miRNA expression patterns. Moreover, results indicated that miR-720 and miR-887 are expressed at relatively high levels in breast cancer cell lines compared to other types of cancer. Ultimately, matching NCI-60 drug response data to miR-720 and miR-887 expression profiles revealed that several FDA-approved drugs were inversely related to miR-720 and miR-887. Furthermore, the anti-cancer effect of perifosine was significantly enhanced by inhibiting miR-720 and decreased by miR-720 precursor treatment in breast cancer cell lines. 5-Fu treatment was enhanced by inhibiting miR-887 and decreased by miR-887 precursor treatment. The current results offer insight into the relationship between miRNA expression and their lineage types, and the approach used here represents a potential cancer therapy with the help of miRNAs.

Background According to the 2016 World Health Organization classification of central nervous system tumors, meningiomas are classified into 3 grades: I, II, and III. It has been reported that 2%–10% of meningiomas exhibit aggressive behavior, and 0.1%–1% of all patients with primary meningiomas develop distant metastases. Past studies have shown that genomic instability is strongly correlated with the risk of meningioma recurrence. Because of the rarity of this tumor, few papers have reported the prognosis and treatment of anaplastic meningioma. Under these circumstances, we present a case of multiple pulmonary and pleural metastases from a recurrent intracranial meningioma with some genetic changes. Case Description In the case, a previously healthy man aged 39 years was diagnosed with anaplastic meningioma. Postoperatively, due to multiple pulmonary and pleural metastases, adjuvant radiation, chemotherapy, and Gamma knife radiosurgery was subsequently performed. Molecular genetic examination with chromosomal microarray analysis showed that there were chromosomal abnormalities, including amplification in 1q and chr12; loss in 1p, 9p, and 22q; and catastrophe in chr8 and chr17 in both the previous brain meningioma and lung tissues, confirming the diagnosis of pulmonary metastasis of the initial grade III meningioma. Conclusions The molecular characterization of meningiomas has identified genetic biomarkers that influence tumor characteristics, such as tumor behavior, malignancy, and location. The combined analyses of genetic and epigenetic changes in meningiomas may allow researchers to unveil a more comprehensive understanding of tumor progression mechanisms.

Gut microbiota plays an important role in the high-fat diet (HFD)-induced obesity and related metabolic syndrome (MetS). Our previous study has demonstrated that unsaturated alginate oligosaccharides (UAOS) degraded by alginate lyase possess significant anti-obesity effects in HFD-fed mice. Herein, we further established that UAOS could significantly ameliorate obesity-related metabolic abnormalities, including hyperlipidemia, insulin resistance and low-grade inflammation. Particularly, the beneficial effect of UAOS on these metabolic abnormalities could be significantly reversed by antibiotic supplementation. Subsequently, the microbiological analysis has revealed that UAOS treatment can modulate the overall composition of the gut microbiota, which is highly associated with metabolic parameters. UAOS supplementation can partially reverse the gut dysbiosis induced by HFD-diet or antibiotics. Specifically, UAOS treatment selectively increased the relative abundance of beneficial intestinal bacteria (e.g. Lactobacillus and Akkermansia genus) and decreased the abundance of inflammogenic bacteria (e.g. Bacteroides and Parabacteroides). These results suggest that UAOS can attenuate the HFD-induced obesity and related abnormalities through modulating gut microbiota, indicating that UAOS can act as potent prebiotic agents in treating obesity and related metabolic diseases.

Protein lysine crotonylation (Kcr) is an important type of post-translational modification that regulates various activities. The experimental approaches to identify the Kcr sites are time-consuming and it is necessary to develop computational prediction approaches. Previously, a few classifiers were based on over 100 Kcr sites from histone proteins. Recently, thousands of Kcr sites have been experimentally verified on non-histone proteins from the plant species Papaya. We found that the previous classifiers fail to identify non-histone Kcr sites. Therefore, it is necessary to develop classifiers for non-histone proteins. Accordingly, we constructed 11 different classifiers to recognize non-histone Kcr sites by combining different features and algorithms (such as random forest and convolutional neural network (CNN)). They were compared using both ten-fold cross validation and independent test dataset. The classifier based on CNN and the word embedding approach, dubbed as pKcr, performed better than other classifiers. pKcr obtained AUC value of 0.855 and 0.853 for ten-fold cross-validation and independent data test, respectively. No statistical difference of its performances on these two tests indicates that pKcr does not overfit. In the pKcr framework, a peptide is cleaved into biological characters followed by transformation into digital vectors. These vectors are input into the CNN with participation of multiple convolution kernels to automatically extract various features and pooling layers to perform feature selection. The superior performance of pKcr suggests that this algorithm is well suited for the Kcr prediction and may be applied broadly to predicting other types of PTM sites. pKcr can be available at http://www.bioinfogo.org/pkcr.

Background: The functional dysconnectivity observed from functional magnetic resonance imaging (fMRI) studies in schizophrenia is also seen in unaffected siblings indicating its association with the genetic diathesis. We intended to apportion resting-state dysconnectivity into components that represent genetic diathesis, clinical expression or treatment effect, and resilience. Methods: fMRI data were acquired from 28 schizophrenia patients, 28 unaffected siblings, and 60 healthy controls. Based on Dosenbach’s atlas, we extracted time series of 160 regions of interest. After constructing functional network, we investigated between-group differences in strength and diversity of functional connectivity and topological properties of undirected graphs. Results: Using analysis of variance, we found 88 dysconnectivities. Post hoc t tests revealed that 62.5% were associated with genetic diathesis and 21.6% were associated with clinical expression. Topologically, we observed increased degree, clustering coefficient, and global efficiency in the sibling group compared to both patients and controls. Conclusion: A large portion of the resting-state functional dysconnectivity seen in patients represents a genetic diathesis effect. The most prominent network-level disruption is the dysconnectivity among nodes of the default mode and salience networks. Despite their predisposition, unaffected siblings show a pattern of resilience in the emergent connectomic topology. Our findings could potentially help refine imaging genetics approaches currently used in the pursuit of the pathophysiology of schizophrenia.

The anatomical structure of the human brain varies widely, as does individual cognitive behavior. It is important and interesting to study the relationship between brain structure and cognitive behavior. There has however been little previous work on the relationship between inhibitory control and brain structure. The goal of this study was to elucidate possible cortical markers related to inhibitory control using structural magnetic resonance imaging (sMRI) data. In this study, we analyzed sMRI data and inhibitory control behavior measurement values from 361 healthy adults from the Human Connectome Project (HCP). The data of all participants were divided into two datasets. In the first dataset, we first constructed individual brain morphometric similarity networks by calculating the inter-regional statistical similarity relationship of nine cortical characteristic measures (such as volume) for each brain area obtained from sMRI data. Areas that covary in their morphology are termed ‘connected’. After that, we used a brain connectome-based predictive model (CPM) to search for ‘connected’ brain areas that were significantly related to inhibitory control. This is a purely data-driven method with built-in cross-validation. Two different ‘connected’ patterns were observed for high and low inhibitory control networks. The high inhibitory control network comprised 25 ‘connections’ (edges between nodes), mostly involving nodes in the prefrontal and especially orbitofrontal cortex and inferior frontal gyrus. In the low inhibitory control network, nodes were scattered between parietal, occipital and limbic areas. Furthermore, these ‘connections’ were verified as reliable and generalizable in a cross-validation dataset. Two regions of interest, the right ventromedial prefrontal cortex including a part of medial area 10 (R.OFCmed) and left middle temporal gyrus (L.MTG) were crucial nodes in the two networks, respectively, which suggests that these two regions may be fundamentally involved in inhibitory control. Our findings potentially help to understand the relationship between areas with a correlated cortical structure and inhibitory control, and further help to reveal the brain systems related to inhibition and its disorders.\ud \ud

Resveratrol (RSV) has broad prospective applications as a radiation protection drug, but its mechanism of action is not yet clear. Here, we found that 5 μM RSV can effectively reduce the cell death caused by irradiation. Irradiation leads to G2/M phase arrest in the cell cycle, whereas RSV treatment increases S-phase cell cycle arrest, which is associated with sirtuin 1 (SIRT1) regulation. Meanwhile, RSV promotes DNA damage repair, mainly by accelerating the efficiency of homologous recombination repair. Under oxidative stress, tyrosyl-tRNA synthetase (TyrRS) is transported to the nucleus to protect against DNA damage. RSV can promote TyrRS acetylation, thus promoting TyrRS to enter the nucleus, where it regulates the relevant signaling proteins and reduces apoptosis and DNA damage. SIRT1 is a deacetylase, and SIRT1 knockdown or inhibition can increase TyrRS acetylation levels, further reducing radiation-induced apoptosis after RSV treatment. Our study revealed a new radiation protection mechanism for RSV, in which the acetylation of TyrRS and its translocation into the nucleus is promoted, and this mechanism may also represent a novel protective target against irradiation.-Gao, P., Li, N., Ji, K., Wang, Y., Xu, C., Liu, Y., Wang, Q., Wang, J., He, N., Sun, Z., Du, L., Liu, Q. Resveratrol targets TyrRS acetylation to protect against radiation-induced damage.

Aberration in the asymmetric nature of the human brain is associated with several mental disorders, including attention deficit/hyperactivity disorder (ADHD). In ADHD, these aberrations are thought to reflect key hemispheric differences in the functioning of attention, although the structural and functional bases of these defects are yet to be fully characterized. In this study, we applied a comprehensive meta-analysis to multimodal imaging datasets from 627 subjects (303 typically developing control [TDCs] and 324 patients with ADHD) with both resting-state functional and structural magnetic resonance imaging (MRI), from seven independent publicly available datasets of the ADHD-200 sample. We performed lateralization analysis and calculated the combined effects of ADHD on each of three cortical regional measures (grey matter volume - GMV, fractional amplitude of low frequency fluctuations at rest -fALFF, and regional homogeneity -ReHo). We found that compared with TDC, 68%,73% and 66% of regions showed statistically significant ADHD disorder effects on the asymmetry of GMV, fALFF, and ReHo, respectively, (false discovery rate corrected, q = 0.05). Forty-one percent (41%) of regions had both structural and functional abnormalities in asymmetry, located in the prefrontal, frontal, and subcortical cortices, and the cerebellum. Furthermore, brain asymmetry indices in these regions were higher in children with more severe ADHD symptoms, indicating a crucial pathoplastic role for asymmetry. Our findings highlight the functional asymmetry in ADHD which has (1) a strong structural basis, and thus is likely to be developmental in nature; and (2) is strongly linked to symptom burden and IQ and may carry a possible prognostic value for grading the severity of ADHD.

Oral route colon-targeted drug delivery systems (CDDSs) are desirable for the treatment of ulcerative colitis (UC). However, CDDSs are challenging owing to the physiological and anatomical barriers associated with the gastrointestinal tract (GIT). In this study, we developed an effective enzyme-triggered controlled release system using curcumin–cyclodextrin (CD–Cur) inclusion complex as core and low molecular weight chitosan and unsaturated alginate resulting nanoparticles (CANPs) as shell. The formed CD–Cur–CANPs showed a narrow particle-size distribution and a compact structure. In vitro drug release determination indicated that CD–Cur–CANPs showed pH-sensitive and α-amylase-responsive release characteristics. Furthermore, in vivo experiments demonstrated that oral administration of CD–Cur–CANPs had an efficient therapeutic efficacy, strong colonic biodistribution and accumulation, rapid macrophage uptake, promoted colonic epithelial barrier integrity and modulated production of inflammatory cytokines, reshaped the gut microbiota in mice with dextran sodium sulfate (DSS)-induced colitis. Taken together, our synthetic CD–Cur–CANPs are a promising synergistic colon-targeted approach for UC treatment.

Currently, anti-obesity drugs are limited by their high costs and numerous adverse effects. In this study, collagen peptide (CP), with molecular weights ranging from 500 to 5000, was enzymatically hydrolyzed using Walleye pollock skin. We further demonstrated the effective anti-obesity effects of CP in a High-Fat Diet-Fed Mice. The microbial analysis showed that CP treatment could regulate the overall composition of the gut microbiota. Specifically, CP intervention increased the relative abundance of Lactobacillus, Akkermansia, Parabacteroides, and Odoribacter spp. CP intervention decreased the abundance of intestinal inflammation bacteria, such as Erysipelatoclostridium and Alistipes. To the best of our knowledge, this study was the first of its kind to provide evidence that CP could restore the composition of the gut microbiota destroyed in the HFD mouse model. These results indicate that CP from Walleye pollock skin is a potential agent for further development as an adjuvant treatment for obesity and related metabolic diseases.

As a novel type of post-translational modification, lysine 2-Hydroxyisobutyrylation (Khib) plays an important role in gene transcription and signal transduction. In order to understand its regulatory mechanism, the essential step is the recognition of Khib sites. Thousands of Khib sites have been experimentally verified across five different species. However, there are only a couple traditional machine-learning algorithms developed to predict Khib sites for limited species, lacking a general prediction algorithm. We constructed a deep-learning algorithm based on convolutional neural network with the one-hot encoding approach, dubbed CNNOH. It performs favorably to the traditional machine-learning models and other deep-learning models across different species, in terms of cross-validation and independent test. The area under the ROC curve (AUC) values for CNNOH ranged from 0.82 to 0.87 for different organisms, which is superior to the currently-available Khib predictors. Moreover, we developed the general model based on the integrated data from multiple species and it showed great universality and effectiveness with the AUC values in the range of 0.79 to 0.87. Accordingly, we constructed the on-line prediction tool dubbed DeepKhib for easily identifying Khib sites, which includes both species-specific and general models. DeepKhib is available at http://www.bioinfogo.org/DeepKhib.

Cysteine S-sulphenylation (CSO), as a novel post-translational modification (PTM), has emerged as a potential mechanism to regulate protein functions and affect signal networks. Because of its functional significance, several prediction approaches have been developed. Nevertheless, they are based on a limited dataset from Homo sapiens and there is a lack of prediction tools for the CSO sites of other species. Recently, this modification has been investigated at the proteomics scale for a few species and the number of identified CSO sites has significantly increased. Thus, it is essential to explore the characteristics of this modification across different species and construct prediction models with better performances based on the enlarged dataset. In this study, we constructed several classifiers and found that the long short-term memory model with the word-embedding encoding approach, dubbed LSTMWE, performs favorably to the traditional machine-learning models and other deep-learning models across different species, in terms of cross-validation and independent test. The area under the receiver operating characteristic (ROC) curve for LSTMWE ranged from 0.82 to 0.85 for different organisms, which was superior to the reported CSO predictors. Moreover, we developed the general model based on the integrated data from different species and it showed great universality and effectiveness. We provided the on-line prediction service called DeepCSO that included both species-specific and general models, which is accessible through http://www.bioinfogo.org/DeepCSO.

Oligoalginate lyases catalyze the degradation of alginate polymers and oligomers into monomers, a prerequisite for biotechnological utilizing alginate. In this study, we report the cloning, expression and biochemical characterization of a new polysaccharide lyase (PL) family 17 oligoalginate lyase, OalV17, from the marine bacterium Vibrio sp. SY01. The recombinant OalV17 showed metal ion independent and detergent resistant properties. Furthermore, OalV17 is an exo-type enzyme that yields alginate monomers as the main product and recognizes alginate disaccharides as the minimal substrate. Site-directed mutagenesis followed by kinetic analysis indicates that the residue Arg231 plays a key role in substrate specificity. Furthermore, a rapid and efficient alginate monomer-producing method was developed directly from Laminaria japonica. These results suggest that OalV17 is a potential candidate for saccharification of alginate.

Ionizing radiation (IR) can act as a negative factor for human homeostasis, by causing and even aggravating a series of pathological conditions. To protect the intactness of normal tissues, effective anti-radiation drugs are urgently needed for alleviating the outcomes of radioactive damage. In this study, we demonstrate that atractylenolide II (ATR II), a sesquiterpenoid monomer extracted from traditional Chinese medicine atractylodes macrocephala, can markedly suppress IR damage by promoting the expression of antioxidant factors heme oxygenase-1 (HO-1) and NAD(P)H dehydrogenase quinone oxido-reductase 1 (NQO-1), which are mediated by nuclear factor-erythroid 2-like 2 (Nrf2) signaling pathway. Furthermore, here we reveal that ATR II effectively upregulates the expression of mitogen-activated protein kinase p38 (MAPKp38), which also acts as a regulator of Nrf2 signaling cascade. Indeed, treatment with a MAPKp38 inhibitor can significantly downregulate the expression of Nrf2 and its downstream target genes HO-1 and NQO-1 and, consequently, abolish the protective effect of ATR II against IR. Consistently, ATR II also has a protective function against IR-induced damage in animal models. In conclusion, our study provides an unexpected function of ATR II in preventing IR-induced damage by modulating MAPKp38/Nrf2 signaling pathway.

As a newly-identified protein post-translational modification, malonylation is involved in a variety of biological functions. Recognizing malonylation sites in substrates represents an initial but crucial step in elucidating the molecular mechanisms underlying protein malonylation. In this study, we constructed a deep learning (DL) network classifier based on long short-term memory (LSTM) with word embedding (LSTMWE) for the prediction of mammalian malonylation sites. LSTMWE performs better than traditional classifiers developed with common pre-defined feature encodings or a DL classifier based on LSTM with a one-hot vector. The performance of LSTMWE is sensitive to the size of the training set, but this limitation can be overcome by integration with a traditional machine learning (ML) classifier. Accordingly, an integrated approach called LEMP was developed, which includes LSTMWE and the random forest classifier with a novel encoding of enhanced amino acid content. LEMP performs not only better than the individual classifiers but also superior to the currently-available malonylation predictors. Additionally, it demonstrates a promising performance with a low false positive rate, which is highly useful in the prediction application. Overall, LEMP is a useful tool for easily identifying malonylation sites with high confidence. LEMP is available at http://www.bioinfogo.org/lemp. Keywords: Deep learning, Recurrent neural network, LSTM, Malonylation, Random forest

Background/Aims: Circular RNAs (circRNAs) make up a large class of non-coding RNAs and play important roles in a variety of diseases, including nervous system diseases and cancers. The intestinal epithelium is sensitive to ionizing radiation, radiotherapy of abdominal or pelvic tumors or nuclear accident exposure can lead to high radiation toxicity, which can result in radiation-induced intestinal injury. The goal of this present study was to analyze the potential roles of circRNAs in radiation-induced intestinal injury. Methods: Mice were divided into two groups: control group and irradiated group. Irradiated group was 3.5 days after 14Gy abdominal irradiation (ABI) group. We started with RNA-seq of circRNA changes in mouse jejuna after radiation and validated by RT-PCR in the following experimental. miRNAs targeted mRNAs were predicted using proprietary software based on target scan and Miranda. The network of circRNA-miRNA-mRNA was illustrated by cytoscape software. Results: 2751 circRNAs were detected in the two groups. At day 3.5 post-radiation, 42 and 48 circRNAs were found to be significantly upregulated and downregulated, respectively, compared to the control (p≤0.05, Fold Change ≥2). Further, the altered expression of 10 circRNAs (chr18: 35610871-35613502+, chr15: 95864225-95894541+, chr3: 96041338-96042928-, chr5: 64096979-64108263+, chr19: 16705875-16710941-, chr5: 134491893-134500149-, chr19: 42562552-42564341+, chr5: 32640331-32664400+, chr3: 72958113-72960367- and chr8: 79343654-79372364-) were verified by RT-PCR. Compared the miRNA-targeted mRNAs with our mRNAs sequencing data, we found 14 upregulated circRNA-targeted mRNAs were also unregulated and 22 downregulated circRNAs-targeted mRNAs were also downregulated. Gene ontology and KEGG pathway analyses indicated the predicted genes were mainly involved in the MAPK signaling pathway. Conclusions: This study reveals that expression of circRNAs was altered in the jejuna of mice post-irradiation and provides a resource for the study of circRNAs in radiation-induced intestinal injury and repair.

N6-methyladenosine (m6A) is a prevalent RNA methylation modification involved in several biological processes. Hundreds or thousands of m6A sites identified from different species using high-throughput experiments provides a rich resource to construct in-silico approaches for identifying m6A sites. The existing m6A predictors are developed using conventional machine-learning (ML) algorithms and most are species-centric. In this paper, we develop a novel cross-species deep-learning classifier based on bidirectional Gated Recurrent Unit (BGRU) for the prediction of m6A sites. In comparison with conventional ML approaches, BGRU achieves outstanding performance for the Mammalia dataset that contains over fifty thousand m6A sites but inferior for the Saccharomyces cerevisiae dataset that covers around a thousand positives. The accuracy of BGRU is sensitive to the data size and the sensitivity is compensated by the integration of a random forest classifier with a novel encoding of enhanced nucleic acid content. The integrated approach dubbed as BGRU-based Ensemble RNA Methylation site Predictor (BERMP) has competitive performance in both cross-validation test and independent test. BERMP also outperforms existing m6A predictors for different species. Therefore, BERMP is a novel multi-species tool for identifying m6A sites with high confidence. This classifier is freely available at http://www.bioinfogo.org/bermp.

Diffusion tensor imaging and its distinct capability to detect micro-structural changes in vivo allows the exploration of white matter (WM) abnormalities in patients who have been diagnosed with schizophrenia; however, the results regarding the anatomical positions and degree of abnormalities are inconsistent. In order to obtain more robust and stable findings, we conducted a multi-level analysis to investigate WM disruption in a relatively large sample size (142 schizophrenia patients and 163 healthy subjects). Specifically, we evaluated the univariate fractional anisotropy (FA) in voxel level; the bivariate pairwise structural connectivity between regions using deterministic tractography as the network node defined by the Human Brainnetome Atlas; and the multivariate network topological properties, including the network hub, efficiency, small-worldness, and strength. Our data demonstrated callosal and subcortical WM alterations in patients with schizophrenia. These disruptions were evident in both voxel and connectivity levels and further supported by associations between FA values and illness duration. Based on the findings regarding topological properties, the structural network showed weaker global integration in patients with schizophrenia than in healthy subjects, while brain network hubs showed decreased functionality. We replicated these findings using an automated anatomical labeling atlas to define the network node. Our study indicates that callosal and subcortical WM disruptions are biomarkers for chronic schizophrenia., Highlights • Combine voxel-based analysis and diffusion tractography methods to detect white matter abnormalities in schizophrenia. • We find schizophrenia white matter disruption in voxel level, connectivity level and network level. • Callosal and subcortical white matter disruptions could be the biomarkers for chronic schizophrenia.

To ensure the safety of clinical applications of MSCs, thorough understanding of their impacts on tumor initiation and progression is essential. Here, to further explore the complex dialog between MSCs and tumor cells, umbilical cord-derived mesenchymal stem cells (UC-MSCs) were employed to be cocultured with either breast or ovarian cancer cells. Though having no obvious influence on proliferation or apoptosis, UC-MSCs exerted intense stem cell-like properties promoting effects on both cancer models. Cocultured cancer cells showed enriched side population, enhanced sphere formation ability, and upregulated pluripotency-associated stem cell markers. Human cytokine array and real-time PCR revealed a panel of MSC-derived prostemness cytokines CCL2, CXCL1, IL-8, and IL-6 which were induced upon coculturing. We further revealed IL-1β, a well-characterized proinflammatory cytokine, to be the inducer of these prostemness cytokines, which was generated from inflammatory UC-MSCs in an autocrine manner. Additionally, with introduction of IL-1RA (an IL-1 receptor antagonist) into the coculturing system, the stem cell-like characteristics promoting effects of inflammatory UC-MSCs were partially blocked. Taken together, these findings suggest that transduced inflammatory MSCs work as a major source of IL-1β in tumor microenvironment and initiate the formation of prostemness niche via regulating their secretome in an IL-1β-dependent manner.

MUC1, a type I transmembrane glycoprotein, mediates tumor growth and cellular differentiation in various types of cancers. However, the mechanism of MUCI in ovarian cancer has not been fully clarified. In our study, we have observed that MUC1 can play a crucial role in the development and progression of ovarian cancer and act as a predictive marker. We also found that MUC1 could increase the expression of EGFR, and MUC1-EGFR co-administration could promote the cellular growth via the AKT pathway. Taxol is an important drug for treating ovarian cancer, which can prevent cancer recurrence and reduce mortality. Our data have collectively reflected that Taxol can prevent ovarian cancer with abnormal expression of MUC1.

Background: Tumor derived vascular endothelial growth factor (VEGF) can stimulate proliferation and migration of endothelial cells and recruit endothelial progenitor cells into tumors for vascular formation via a paracrine manner. Now increasing evidence suggests that VEGF also serves as an autocrine factor promoting cell survival and tumor angiogenesis. Real time visualization of VEGF activity in the early stages of tumor formation using molecular imaging will provide unprecedented insight into the biological processes of cancer. Methods: The mouse breast cancer cell line 4T1 was transfected with an inducible, bidirectional tetracycline (Bi-Tet) promoter driving VEGF and renilla luciferase (Rluc). This was used to quantitatively image conditional switching of VEGF by bioluminescence imaging (BLI) under the control of systemic administration of doxycycline. Simultaneously, 4T1 cells were labelled with the double fusion reporter gene (Fluc-eGFP) to establish a breast cancer model. Results: We found that inducible VEGF could promote proliferation and attenuate apoptosis due to oxidative stress in an autocrine manner in vitro. In vivo studies revealed that induction of VEGF expression during early tumor development not only dramatically enhanced tumor growth but also increased tumor angiogenesis as visualized by BLI. Finally, immunohistochemistry staining confirmed that inducing VEGF expression promoted cell survival and tumor neovascularization. Conclusion: Together the inducible bidirectional tetracycline (Bi-Tet) co-expression system combined with the dual bioluminescence imaging (BLI) system provides a platform to investigate a target gene’s role in the pathologic process of cancer and facilitates noninvasive monitoring of biological responses in real time.

// Dan Wang 1, 3, * , Hui Sang 1, 3, * , Kaiyue Zhang 2 , Yan Nie 2 , Shuang Zhao 1, 3 , Yan Zhang 2, 3 , Ningning He 2 , Yuebing Wang 2 , Yang Xu 2 , Xiaoyan Xie 4 , Zongjin Li 1, 2 , Na Liu 1, 2 1 Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China 2 School of Medicine, Nankai University, Tianjin, China 3 College of Life Sciences, Nankai University, Tianjin, China 4 Stem Cells and Regenerative Medicine Lab, Beijing Institute of Transfusion Medicine, Beijing, China * These authors contributed equally to this work Correspondence to: Na Liu, email: liuna@nankai.edu.cn Zongjin Li, email: zongjinli@nankai.edu.cn Keywords: embryonic stem cell, ground state, Stat3 signal pathway, imaging Received: November 24, 2016 Accepted: March 01, 2017 Published: March 10, 2017 ABSTRACT Embryonic stem cells (ES cells) can be maintained its undifferentiated state with feeder cells or LIF, which can activate Jak/Stat3 pathway. Recently, it has been reported a new culture condition comprising serum-free medium with ERK and GSK3β inhibitors (2i) could drive ES cells into a state of pluripotency more like inner cell mass (ICM) in mouse blastocysts called ground state. However, although 2i could sustain ES cells self-renewal, LIF is routinely added. The roles of Stat3 activation are still unclear now. Here we investigated whether Jak/Stat3 might also contribute to the induction of ground state pluripotency. We introduced a lentiviral construct with 7-repeat Stat3-binding sequence to drive Renilla luciferase into ES cells, which can be used as a reporter to detect Stat3 activation by noninvasive bioluminescence imaging. Using this ES cells, we investigated the role of Stat3 activation in ground state maintenance. The results showed that Stat3 could be activated by 2i. Stattic, a chemical inhibitor of Stat3 phosphorylation, could effectively inhibit Stat3 activation in ES cells. When Stat3 activation was suppressed, ground state related genes were down regulated, and ES cells could not be maintained the ground state pluripotency even in 2i medium. All of these results indicate Stat3 activation is required in ground state maintenance.

Mesenchymal stem cells (MSCs) derived from different tissues may aid in the regeneration of radiation-induced organ lesions; however, the radiation responses of human MSCs from different sources are unknown. In our study, a comparison of the results from cell proliferation, apoptosis, cell cycle, DNA damage, and DNA repair assays consistently showed that MSCs derived from adipose tissue possess a significantly stronger radiation resistance capacity than MSCs derived from umbilical cord and gingival, which is accompanied by a higher level of phosphorylated signal transducer and activator of transcription 3 (Stat3) expression. This reminds us Stat3 could be a potential biomarker of radiation resistance. These findings provide a better understanding of radiation-induced biologic responses in MSCs and may lead to the development of better strategies for stem cell treatment and cancer therapy.

Maintenance of genome integrity is critical for faithful propagation of genetic information and the prevention of the mutagenesis induced by various DNA damage events. RecQ-mediated genome instability protein 1 (RMI1), together with Bloom syndrome protein and topoisomerase IIIα, form an evolutionarily conserved complex that is critical for the maintenance of genomic stability. Herein, we report that RMI1 depletion increases cell sensitivity to camptothecin treatment, as shown by an elevation of genotoxic stress-induced DNA double-strand breaks, a stronger activation of the DNA damage response, and a greater G2/M cell cycle delay. Our findings support that, upon DNA damage, RMI1 forms nuclear foci at the damaged regions, interacts with RAD51, and facilitates the recruitment of RAD51 to initiate homologous recombination. Our data reveal the importance of RMI1 in response to DNA double-strand breaks and shed light on the molecular mechanisms by which RMI1 contributes to maintain genome stability.-Fang, L., Sun, X., Wang, Y., Du, L., Ji, K., Wang, J., He, N., Liu, Y., Wang, Q., Zhai, H., Hao, J., Xu, C., Liu, Q. RMI1 contributes to DNA repair and to the tolerance to camptothecin.

Radiation therapy is one of the most common cancer treatments. It is important to understand how cells respond to ionizing radiation (IR) to improve therapeutic efficacy. Circular RNAs (circRNAs) recently have been found to regulate a variety of cellular processes. However, it is poorly defined that their expression pattern and their identity in cells following IR exposure. Here, we performed high-throughput sequencing and comprehensive analysis of circRNA expression in human embryonic kidney (HEK) 293T cells before and after irradiation. We identified totally 5592 circRNAs and discovered 1038 new circRNAs. We found 158 circRNAs with significantly differential expression after IR exposure. Among them, there were 61 upregulated and 97 downregulated circRNAs. Using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and circRNA-microRNA-messenger RNA network analyses, we found the differentially expressed circRNAs might be involved in the signal pathways of oxidative phosphorylation, epithelial growth factor receptor (EGFR) tyrosine kinase inhibitor resistance, and mammalian target of rapamycin (mTOR) signaling.

Low cell retention and engraftment after transplantation limit the successful application of stem cell therapy for AKI. Engineered microenvironments consisting of a hydrogel matrix and growth factors have been increasingly successful in controlling stem cell fate by mimicking native stem cell niche components. Here, we synthesized a bioactive hydrogel by immobilizing the C domain peptide of IGF-1 (IGF-1C) on chitosan, and we hypothesized that this hydrogel could provide a favorable niche for adipose-derived mesenchymal stem cells (ADSCs) and thereby enhance cell survival in an AKI model. In vitro studies demonstrated that compared with no hydrogel or chitosan hydrogel only, the chitosan-IGF-1C hydrogel increased cell viability through paracrine effects. In vivo, cotransplantation of the chitosan-IGF-1C hydrogel and ADSCs in ischemic kidneys ameliorated renal function, likely by the observed promotion of stem cell survival and angiogenesis, as visualized by bioluminescence imaging and attenuation of fibrosis. In conclusion, IGF-1C immobilized on a chitosan hydrogel provides an artificial microenvironment for ADSCs and may be a promising therapeutic approach for AKI.

With the extensive application of radiotherapy in various cancers, its side effects in tissues adjacent to cancers are garnering much attention. Intestines are sensitive to irradiation due to its rapid proliferation, and irradiation-induced enteric inflammation is common in patients with pelvic peritoneal tumors. Sirt1, class III protein deacetylase, could lead to transcriptional repression of various inflammation-associated genes, and our previous study has proved its relationship with interleukin (IL)-1β. Here we show that resveratrol, the activator of Sirt1, could alleviate the bowel inflammation induced by irradiation and the expression of Sirt1 is consistent with the inflammation level. We further identified in vivo that Sirt1 repress the expression of IL-1β by the repression of NLR Family, Pyrin Domain Containing protein 3 (NLRP3) expression. In conclusion, this study confirms resveratrol acts against radiation-induced inflammatory bowel disease via NLRP-3 inflammasome repression in mice and supports Sirt1 as a potential biomarker and therapy target in intestinal radiation protection.

Human are exposed to ionizing radiation from natural and artificial sources, which consequently poses a possible risk to human health. However, accumulating evidence indicates that the biological effects of low-dose radiation (LDR) are different from those of high-dose radiation (HDR). Low-dose radiation–induced hormesis has been extensively observed in different biological systems, including immunological and hematopoietic systems. Adaptive responses in response to LDR that can induce cellular resistance to genotoxic effects from subsequent exposure to HDR have also been described and researched. Bystander effects, another type of biological effect induced by LDR, have been shown to widely occur in many cell types. Furthermore, the influence of LDR-induced biological effects on certain diseases, such as cancer and diabetes, has also attracted the interest of researchers. Many studies have suggested that LDR has the potential antitumor and antidiabetic complications effects. In addition, the researches on whether LDR could induce stochastic effects were also debated. Studies on the biological effects of LDR in China started in 1970s and considerable progress has been made since. In the present article, we provide an overview of the research progress on the biological effects of LDR in China.

Background Cytokine-based cancer therapies have attracted a great deal of attention in recent years. Unfortunately, resistance to treatment limits the efficacy of these therapeutics. Therefore, the aim of our study was to explore the mechanism of IL-2-based therapy for hepatocellular carcinoma in an attempt to increase the efficiency of this treatment option. Methods HepG2 cells were treated with IL-2. Then, siRNA against TZA was used to transfected into HepG2 cells. Cellular apoptosis was measured via MTT assay, TUNEL assay and caspase-3 activity. Cellular proliferation was evaluated via EdU assay and western blotting. Cellular migration was detected via Transwell assay. Mitochondrial function was monitored by mitochondrial potential analysis, ROS staining, immunofluorescence and western blotting. Pathway blocker and activator were used to establish the role of JNK/F-actin/mitochondrial fission signaling pathway in HepG2 cells stress response. Results Our study found that IL-2 treatment significantly reduced the viability, mobility and proliferation of HepG2 cells in vitro. We also demonstrated that IL-2 treatment was accompanied by an increase in the expression of transcriptional co-activator with PDZ-binding motif (TAZ). Interestingly, genetic ablation of TAZ in the presence of IL-2 further promoted apoptosis, inhibited mobility, and arrested proliferation in HepG2 cells. At the molecular level, IL-2 administration activated excessive mitochondrial fission via the JNK/F-actin pathway; these effects were further enhanced by TAZ deletion. Mechanistically, TAZ knockdown further increased the expression of mitochondrial fission-related proteins such as Drp1, Mff and Fis. The augmented mitochondrial fission stimulated ROS overproduction, mediated redox imbalance, interrupted mitochondrial energy generation, reduced mitochondrial membrane potential, promoted leakage of the pro-apoptotic molecule cyt-c into the nucleus, and initiated caspase-9-related mitochondrial death. Further, we demonstrated that the anti-proliferative and anti-metastatic effects of IL-2 in HepG2 cells were enhanced by TAZ deletion, suggesting that IL-2 sensitizes HepG2 cells to IL-2-based cytokine therapy. However, JNK/F-actin pathway blockade could abrogate the inhibitory effects of TAZ deletion on HepG2 migration, proliferation and survival. Conclusions Taken together, our data indicate that the anti-tumor effects of IL-2-based therapies may be enhanced by TAZ deletion in a JNK/F-actin pathway-dependent manner. This finding provides a novel combinatorial therapeutic approach for treating hepatocellular carcinoma that might significantly increase the efficacy of cytokine-based therapies in a clinical setting. Electronic supplementary material The online version of this article (10.1186/s12935-018-0615-y) contains supplementary material, which is available to authorized users.

Radiotherapy resistance in patient with non‑small cell lung cancer (NSCLC) reduces patient survival and remains a significant challenge for the treatment of NSCLC. Radiation resistance has been demonstrated to be affected by secreted factors, yet it remains unclear how autocrine secretions affect the radioresistance of NSCLC cells. In the present study, the NSCLC cell line, NCI‑H460, was irradiated with γ‑rays (4 Gy) and then cultured in medium from H460 cells or normal medium to examine the potential influence of cell secretions on the radiation resistance of H460 cells. Cell viability, accumulation of reactive oxygen species and DNA repair capacity were all markedly improved in the irradiated H460 cells that were cultured in conditioned medium (CM), compared with those cells cultured in normal medium. In addition, G2/M cell cycle arrest and upregulation of homologous recombination repair proteins were observed in the CM‑treated cells, while exosomes secreted by H460 cells had no influence on the radiation resistance of H460 cells. Taken together, these results indicate that autocrine secretions enhance the radiation resistance of γ‑irradiated H460 cells and that these secretions mainly affect the DNA repair process.

The acquisition of radioresistance by breast cancer cells during radiotherapy may lead to cancer recurrence and poor survival. Signal transducer and activator of transcription 3 (Stat3) is activated in breast cancer cells and, therefore, may be an effective target for overcoming therapeutic resistance. Mesenchymal stem cells (MSCs) have been investigated for use in cancer treatment. Here, we investigated the potential of MSC conditioned medium (MSC-CM) in sensitizing breast cancer to radiotherapy. It was found that MSC-CM could inhibit the level of activated Stat3, suppress cancer growth, and exhibit synergetic effects with radiation treatment in vitro and in vivo. Furthermore, MSC-CM reduced the ALDH-positive cancer stem cells (CSCs) population, modulated several potential stem cell markers, and decreased tumor migration, as well as metastasis. These results demonstrate that MSC-CM suppresses breast cancer cells growth and sensitizes cancer cells to radiotherapy through inhibition of the Stat3 signaling pathway, thus, providing a novel strategy for breast cancer therapy by overcoming radioresistance.

Background/Aims: SirT1, a conserved NAD+-dependent deacetylase, has been implicated in modulating cell survival and stress responses, and it appears to play an important role in tumorigenesis and cancer resistance to chemoradiotherapy. The mechanism of SirT1 in cancer chemoradiotherapy remains to be further elucidated, which could provide potential targets for cancer therapy. Methods: We performed colony formation, immunofluorescence microscopy, flow cytometry, RNA interference, and western blotting assays to determine whether SirT1 regulates radiation sensitization and which mechanisms and/or pathways it takes in lung cancer cell lines A549 and H460. Results: Initially, the expression of SirT1 was found to be negatively correlated with radiosensitivity in lung cancer cell lines A549 and H460. RNA interference with siSirT1 against SirT1 specifically reduced SirT1 expression and induced radiosensitivity both in A549 and H460 cell lines. In contrast, the radiosensitivity was significantly reduced once SirT1 was activated by resveratrol. Immunofluorescence assay and apoptosis analysis indicated that the effect of SirT1 on the radiosensitivity observed in the A549 and H460 cell lines was mainly achieved by regulating DNA damage repair and apoptosis processes. Furthermore, the expression of SirT1 negatively modulated the expression of apoptosis-related protein NF-κB and its downstream regulator of Smac. Conclusion: Our results indicate that SirT1 regulates apoptosis and radiation sensitization in lung cancer cell lines A549 and H460 via the SirT1/NF-κB/Smac pathway.

Tolerance of glucose deprivation is an important factor for cancer proliferation, survival, migration and progression. To systematically understand adaptive responses under glucose starvation in cancers, we analyzed reverse phase protein array (RPPA) data of 115 protein antibodies across a panel of approximately 170 heterogeneous cancer cell lines, cultured under normal and low glucose conditions. In general, glucose starvation broadly altered levels of many of the proteins and phosphoproteins assessed across the cell lines. Many mTOR pathway components were selectively sensitive to glucose stress, although the change in their levels still varied greatly across the cell line set. Furthermore, lineage- and genotype-based classification of cancer cell lines revealed mutation-specific variation of protein expression and phosphorylation in response to glucose starvation. Decreased AKT phosphorylation (S473) was significantly associated with PTEN mutation under glucose starvation conditions in lung cancer cell lines. The present study (see TCPAportal.org for data resource) provides insight into adaptive responses to glucose deprivation under diverse cellular contexts.

Colorectal cancer is one of the most common types of malignancies worldwide, and as it is often diagnosed at an advanced stage, it is a serious threat to human health. MicroRNAs are important regulators of the growth and metastasis of colon cancer (CC). In the present study, the results demonstrated that kallikrein‑related peptidase 6 (KLK6) plays a critical role in suppressing colon carcinoma progression. To further investigate whether microRNAs affect the impact of KLK6, a bioinformatics approach was employed, which indicated that let‑7i‑5p may directly target KLK6. Furthermore, the expression level of let‑7i‑5p was significantly negatively correlated with the expression of KLK6 at the mRNA and protein levels in CC. Functionally, overexpression of let‑7i‑5p inhibited the proliferation and invasion of CC cells, and suppressed the growth of CC in vitro. The luciferase reporter assays revealed that let‑7i‑5p targeted the KLK6 3'‑untranslated region. Collectively, these results indicated that let‑7i‑5p inhibited the proliferation and metastasis of CC cells by targeting KLK6, thereby blocking the cell cycle and promoting apoptosis in colon cells. Therefore, the present study revealed that the let‑7i‑5p/KLK6 axis may be a potential target for new therapeutic strategies to treat colon tumors.

With the abilities of self-renewal and differentiation, embryonic stem (ES) cells provide an unlimited source for stem cell-based therapeutics. However, the maintenance of ES cells with mouse embryonic fibroblasts (MEFs) can limit the clinical translation of ES cells. In the present study, we synthesized a fusion protein of the immunoglobulin G (IgG) fragment crystallizable region and vascular endothelial cadherin (VE-cadherin) extracellular domain (VE-cad-Fc) as a substrate for mouse ES cell culture, and we hypothesized that VE-cadherin could enhance the pluripotency and self-renewal of ES cells. Furthermore, we introduced a Stat3 reporter imaging system into ES cells and investigated the mechanism of the pluripotency enhancement mediated by VE-cadherin through cultured ES cells on VE-cad-Fc-coated plates using molecular imaging techniques. The resulting data revealed that VE-cad-Fc could activate the Stat3 signaling pathway, leading to the upregulation of stemness-related markers SSEA-1 and alkaline phosphatase (ALP). Moreover, VE-cad-Fc recovered the expression of Oct4, c-Myc, Nanog, Sox2, Tbx3 and Klf4 in differentiated ES cells, as well as enhanced the pluripotency of ES cells. In conclusion, VE-cadherin fusion protein coating methods provide an alternative towards feeder free culture of ES cells, and the strategy developed in the present study may benefit the clinical translation of ES cell-based therapeutics.

Cellular functions are frequently regulated by protein-protein interactions involving the binding of a modular domain in one protein to a specific peptide sequence in another. This mechanism may be explored to identify binding partners for proteins harboring a peptide-recognition domain. Here we report a proteomic strategy combining peptide and protein microarray screening with biochemical and cellular assays to identify modular domain-mediated protein-protein interactions in a systematic manner. We applied this strategy to Numb, a multi-functional protein containing a phosphotyrosine-binding (PTB) domain. Through the screening of a protein microarray, we identified >100 protein kinases, including both Tyr and Ser/Thr kinases, that could potentially interact with the Numb PTB domain, suggesting a general role for Numb in regulating kinase function. The putative interactions between Numb and several tyrosine kinases were subsequently validated by GST pull-down and/or co-immunoprecipitation assays. Furthermore, using the Oriented Peptide Array Library approach, we defined the specificity of the Numb PTB domain which, in turn, allowed us to predict binding partners for Numb at the genome level. The combination of the protein microarray screening with computer-aided prediction produced the most expansive interactome for Numb to date, implicating Numb in regulating phosphorylation signaling through protein kinases and phosphatases. Not only does the data generated from this study provide an important resource for hypothesis-driven research to further define the function of Numb, the proteomic strategy described herein may be employed to uncover the interactome for other peptide-recognition domains whose consensus motifs are known or can be determined.

Obesity and its related complications have become one of the leading problems affecting human health. However, current anti-obesity treatments are limited by high cost and numerous adverse effects. In this study, we investigated the use of a non-toxic green food additive, known as unsaturated alginate oligosaccharides (UAOS) from the enzymatic degradation of Laminaria japonicais, which showed effective anti-obesity effects in a high-fat diet (HFD) mouse model. Compared with acid hydrolyzed saturated alginate oligosaccharides (SAOS), UAOS significantly reduced body weight, serum lipid, including triacylglycerol (TG), total cholesterol (TC) and free fatty acids (FFA), liver weight, liver TG and TC, serum alanine aminotransferase (ALT), and aspartate aminotransferase (AST) levels, adipose mass, reactive oxygen species (ROS) formation, and accumulation induced in HFD mice. Moreover, the structural differences in &beta, d-mannuronate (M) and its C5 epimer &alpha, l-guluronate (G) did not cause significant functional differences. Meanwhile, UAOS significantly increased both AMP-activated protein kinase &alpha, (AMPK&alpha, ) and acetyl-CoA carboxylase (ACC) phosphorylation in adipocytes, which indicated that UAOS had an anti-obesity effect mainly through AMPK signaling. Our results indicate that UAOS has the potential for further development as an adjuvant treatment for many metabolic diseases such as fatty liver, hypertriglyceridemia, and possibly diabetes.

Background Microenvironment is being increasingly recognized as a critical determinant in tumor progression and metastasis. However, the appropriate regulatory mechanism to maintain the normal balance between differentiation and self-renewal of the cancer cell in microenvironment is not well known. Methods 4T1 breast cancer cells were treated with embryonic stem (ES) cell conditioned medium which was collected from mouse ES cells. Inhibition of tumor cell growth was based on the reduction of cell proliferation and viability, and inhibition of aggressive properties of tumor cells were examined using the wound-healing and mammosphere assays. The expression of stem cell-associated genes was detected by quantitative RT-PCR. Results We used a real-time imaging system to investigate the effect of the mouse ES cell microenvironment on aggressive breast cancer cells in vitro and in vivo. Exposure of breast cancer cells in mouse ES cell conditioned medium resulted in inhibition of growth, migration, metastasis, and angiogenesis of cancer cells. For many tumors, aggressive properties were tightly related to Stat3 signaling activation. We specifically discovered that the ES cell microenvironment sufficiently suppressed Stat3 signaling pathway activation in aggressive tumor cells, leading to a reduction in tumorigenesis and invasiveness. Conclusions We identified important functions of Stat3 and their implications for antitumor effects of ES cell conditioned medium. Some factors secreted by ES cells could efficiently suppress Stat3 pathway activation in breast cancer cells, and were then involved in cancer cell growth, survival, invasion, and migration. This study may act as a platform to understand tumor cell plasticity and may offer new therapeutic strategies to inhibit breast cancer progression.

Glioblastoma (GBM), the most common type of primary tumor in the central nervous system, is a very aggressive brain tumor with poor prognosis and a high recurrence rate. Increasing evidence suggests that human cytomegalovirus (HCMV) infection is related to GBM and leads to GBM cell growth and metastasis. MicroRNAs are important regulators in the growth and metastasis of glioblastoma. This study aimed to demonstrate the role of miR-144-3p in HCMV-positive glioblastoma. We found that, after HCMV infection, the expression of miR-144-3p decreased, whereas the expression of TOP2A increased. Bioinformatics analyses indicated that miR-144-3p directly targets the TOP2A 3&prime, UTR (Untranslated Region). We discovered that the overexpression of miR-144-3p downregulated the overexpression of TOP2A and inhibited the proliferation, clone formation, and invasion of HCMV-positive glioma in vitro. Taken together, these results show that miR-144-3p inhibited growth and promoted apoptosis in glioma cells by targeting TOP2A.