A prognostic biomarker NRG1 promotes U-87 MG glioblastoma cell malignancy by inhibiting autophagy via ERBB2/AKT/mTOR pathway.

Glioblastoma (GBM) is the most common and aggressive primary brain malignancy. Studies have shown that autophagy-related (ATG) genes play important roles in regulating GBM malignancy. However, the mechanism still needs to be fully elucidated. Based on clinical and gene expression information of GBM patients downloaded from The The Cancer Genome Atlas database, Kaplan-Meier, univariate Cox regression, least absolute shrinkage and selection operator regression and multivariate Cox regression were applied to construct a risk signature for GBM prognosis, followed by validation using receiver operating characteristic analysis. Next, Cell Counting Kit-8, wound healing assay, flow cytometry, monodansyl cadaverine autophagy staining assay, immunofluorescence staining and western blot, either in the absence or presence of ERBB2/AKT/mTOR inhibitors, were carried out in GBM U87 cell line to explore molecular pathway underlying GBM malignancy. A three-ATG-gene signature (HIF1A, ITGA3, and NGR1) was constructed for GBM prognosis with the greatest contribution from NRG1. In vitro experiments showed that NRG1 promoted U87 cell migration and proliferation by inhibiting autophagy, and ERBB2/AKT/mTOR is a downstream pathway that mediates the autophagy-inhibitory effects of NRG1. We constructed an ATG gene prognostic model for GBM and demonstrated that NRG1 inhibited autophagy by activating ERBB2/AKT/mTOR, promoting GBM malignancy, thus providing new insights into the molecular contribution of autophagy in GBM malignancy.

A risk signature of three autophagy-related genes for predicting lower grade glioma survival is associated with tumor immune microenvironment.

Treatment for lower-grade gliomas (LGG) has been challenging. Though emerging approaches such as immunotherapy is promising, it is still faced with immune tolerance, an obstacle that may be overcome by targeting autophagy-related (ATG) genes. After identifying three differentially expressed ATG genes (RIPK2, MUL1 and CXCR4), we constructed an ATG gene risk signature by Kaplan-Meier, univariate Cox regression, least absolute shrinkage and selection operator regression and multivariate Cox regression, followed by internal and external validation using K-M and ROC analysis. Since gene set enrichment analysis (GSEA) suggested that the signature was strongly associated with immune cell functions, CIBERSORT, LM22 matrix and Pearson correlation were further performed, showing that the risk signature was significantly correlated with immune cell infiltration and immune checkpoint genes. In conclusion, we identified and independently validated an ATG gene risk signature for LGG patients, as well as discovering its significant association with LGG immune microenvironment.

Identification and validation of a six-lncRNA prognostic signature with its ceRNA networks and candidate drugs in lower-grade gliomas.

Gliomas account for 75% of the primary malignant brain tumors and a majority of lower-grade gliomas (LGG) inevitably develop into glioblastoma. The dysregulation of lncRNAs play a crucial role in LGG. In the present study, we first screened out six differentially expressed lncRNAs (AC021739.2, AL031722.1, AL354740.1, FGD5-AS1, LINC00844, and NEAT1) based on TCGA and GTEx RNA-seq databases. LncRNA prognostic signature was then established by Kaplan-Meier and multivariate Cox proportional hazards regression, with its predictive value validated by time-dependent receiver operating characteristic (ROC) curves. After lncRNA-miRNA-mRNA regulatory networks were established by Cytoscape 3.7.2, Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, with results enriched in various malignancy-related functions and pathways. Finally, six putative drugs (irinotecan, camptothecin, mitoxantrone, azacitidine, mestranol, and enilconazole) were predicted by Connectivity Map. In conclusion, we identified a 6-lncRNA prognostic signature with its ceRNA networks, and six candidate drugs against LGG.

[Retracted] Association between vascular endothelial growth factor gene polymorphisms and the risk of osteonecrosis of the femoral head: Systematic review.

[This retracts the article DOI: 10.3892/br.2015.527.].

Quantum Sensing of Free Radicals in Primary Human Granulosa Cells with Nanoscale Resolution.

Cumulus granulosa cells (cGCs) and mural granulosa cells (mGCs), although derived from the same precursors, are anatomically and functionally heterogeneous. They are critical for female fertility by supporting oocyte competence and follicular development. There are various techniques used to investigate the role of free radicals in mGCs and cCGs. Yet, temporospatial resolution remains a challenge. We used a quantum sensing approach to study free radical generation at nanoscale in cGCs and mGCs isolated from women undergoing oocyte retrieval during in vitro fertilization (IVF). Cells were incubated with bare fluorescent nanodiamonds (FNDs) or mitochondria targeted FNDs to detect free radicals in the cytoplasm and mitochondria. After inducing oxidative stress with menadione, we continued to detect free radical generation for 30 min. We observed an increase in free radical generation in cGCs and mGCs from 10 min on. Although cytoplasmic and mitochondrial free radical levels are indistinguishable in the physiological state in both cGCs and mGCs, the free radical changes measured in mitochondria were significantly larger in both cell types, suggesting mitochondria are sites of free radical generation. Furthermore, we observed later occurrence and a smaller percentage of cytoplasmic free radical change in cGCs, indicating that cGCs may be more resistant to oxidative stress.

Three Oxidative Stress-Related Genes That Associate Endometrial Immune Cells Are Considered as Potential Biomarkers for the Prediction of Unexplained Recurrent Implantation Failure.

Recurrent implantation failure (RIF) represents a new challenge in the field of assisted reproductive technology (ART). Considering the known effects of immune cell regulation on embryo implantation process, as well as our gene set variation analysis (GSVA) results that suggested the association between RIF and pathways of oxidative stress and immune responses, we hypothesized that oxidative stress- related genes (OSGs) associated with aberrant immunological factor may represent novel biomarkers for unexplained RIF. We therefore screened out the immune cell coexpressed OSGs by performing CIBERSORT, LM22 matrix and Pearson correlation, followed by constructing an OSG signature by least absolute shrinkage and selection operator (LASSO) regression. Three OSGs (AXL, SLC7A11 and UBQLN1) were then identified to establish a RIF risk signature, which showed high ability to discriminating RIF from fertile control. A nomogram was established, with a free online calculator for easier clinical application. Finally, Chilibot, protein-protein interaction analysis and BioGPS were sequentially applied for the investigation of functional relationships of these three genes with RIF and other OSGs, as well as their expression abundance across different human tissues. In conclusion, we identified an OSG signature that are relevant novel markers for the occurrence of unexplained RIF.

Identification of long non-coding RNA biomarkers and signature scoring, with competing endogenous RNA networks- targeted drug candidates for recurrent implantation failure.

Recurrent implantation failure (RIF) remains a source of frustration and presents challenges to clinicians in the practice of assisted reproductive technology (ART). Long non-coding RNAs (lncRNAs) are increasingly recognised as potential biomarkers in various diseases. In this study, eight differentially expressed lncRNAs (LINC00645, LINC00844, LINC02349, AC010975.1, AC022034.1, AC096719.1, AC104072.1 and DLGAP1-AS3) to distinguish RIF from fertile women were identified by RobustRankAggreg (RRA). A two-lncRNA signature for predicting RIF was established by least absolute shrinkage and selection operator (LASSO) regression, with accuracy confirmed by receiver operating characteristic (ROC) curves. After lncRNA-microRNA-mRNA regulatory networks were established by Cytoscape 3.7.2, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses were performed, suggesting that the lncRNA-miRNA-mRNA regulatory networks were associated with biological processes involved in endometrial receptivity. Finally, three putative drugs (miconazole, terfenadine and STOCK1N-35215) for RIF were predicted by a Connectivity Map. In conclusion, we identified eight lncRNA biomarkers and a two-lncRNA signature for predicting RIF, as well as proposing three candidate drugs against RIF by targeting the ceRNA networks.

An Oxidative Stress-Related Gene Signature in Granulosa Cells Is Associated with Ovarian Aging.

Ovarian aging is associated with a decrease in fecundity. Increased oxidative stress of granulosa cells (GCs) is an important contributor. We thus asked whether there is an oxidative stress-related gene signature in GCs associated with ovarian aging. Public nonhuman primate (NHP) single-cell transcriptome was processed to identify GC cluster. Then, a GC signature for ovarian aging was established based on six oxidative stress-related differentially expressed genes (MAPK1, STK24, AREG, ATG7, ANXA1, and PON2). Receiver operating characteristic (ROC) analysis confirmed good discriminating capacity in both NHP single-cell and human bulk transcriptome datasets. Gene expression levels were investigated using qPCR in the human ovarian granulosa-like tumor cell line (KGN) and mouse GCs. In an oxidative stress model, KGN cells were treated with menadione (7.5 µM, 24 h) to induce oxidative stress, after which upregulation of MAPK1, STK24, ATG7, ANXA1, and PON2 and downregulation of AREG were observed (p < 0.05). In an aging model, KGN cells were continuously cultured for 3 months, leading to increased expressions of all genes (p < 0.05). In GCs of reproductively aged (8-month-old) Kunming mice, upregulated expression of Mapk1, Stk24, Atg7, and Pon2 and downregulated expression of Anxa1 and Areg were observed (p < 0.01). We therefore here identify a six-gene GC signature associated with oxidative stress and ovarian aging.

The emerging role of the chondroitin sulfate proteoglycan family in neurodegenerative diseases.

Chondroitin sulfate (CS) is a kind of linear polysaccharide that is covalently linked to proteins to form proteoglycans. Chondroitin sulfate proteoglycans (CSPGs) consist of a core protein, with one or more CS chains covalently attached. CSPGs are precisely regulated and they exert a variety of physiological functions by binding to adhesion molecules and growth factors. Widely distributed in the nervous system in human body, CSPGs contribute to the major component of extracellular matrix (ECM), where they play an important role in the development and maturation of the nervous system, as well as in the pathophysiological response to damage to the central nervous system (CNS). While there are more than 30 types of CSPGs, this review covers the roles of the most important ones, including versican, aggrecan, neurocan and NG2 in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and multiple sclerosis. The updated reports of the treatment of neurodegenerative diseases are involving CSPGs.

Identification and validation of a five-lncRNA signature for predicting survival with targeted drug candidates in ovarian cancer.

The dysregulation of long non-coding RNAs (lncRNAs) plays a crucial role in ovarian cancer (OC). In this study, we screened out five differentially expressed lncRNAs (AC092718.4, AC138035.1, BMPR1B-DT, RNF157-AS1, and TPT1-AS1) between OC and normal ovarian based on TCGA and GTEx RNA-seq databases by using Kaplan-Meier analysis and univariate Cox, LASSO, and multivariate Cox regression. Then, a risk signature was constructed, with 1, 3, 5-year survival prediction accuracy confirmed by ROC curves, and an online survival calculator for easier clinical use. With lncRNA-microRNA-mRNA regulatory networks established, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, suggesting the involvement of a variety of cancer-related functions and pathways. Finally, five candidate small-molecule drugs (thioridazine, trifluoperazine, loperamide, LY294002, and puromycin) were predicted by Connectivity Map. In conclusion, we identified a 5-lncRNA signature of prognostic value with its ceRNA networks, and five candidate drugs against OC.[Figure: see text].

Association between vascular endothelial growth factor gene polymorphisms and the risk of osteonecrosis of the femoral head: Systematic review.

Emerging evidence has shown that vascular endothelial growth factor (VEGF) gene polymorphisms are the key initiators that regulate the expression of the VEGF protein, which has a vital role in osteonecrosis of the femoral head (ONFH). The aim of the present study was to investigate whether polymorphisms of the VEGF genes are associated with the occurrence of ONFH. A comprehensive search was performed on MEDLINE, Embase, Web of Science and China National Knowledge Infrastructure databases before June 2015. Meta-analyses were carried out for the VEGF gene -634G/C polymorphisms (single-nucleotide polymorphism with 3 eligible studies). The pooled odds ratios with 95% confidence intervals (CIs) were used to evaluate the strength of the association. All the eligible studies, involving 1,564 individuals, were identified. According to the inclusion criteria, 3 case-control studies were finally included in the meta-analysis. The present meta-analysis indicates that the VEGF gene -634G/C polymorphism [CC+GC vs. GG: Response rate (RR)=0.79; 95% CI, 0.67-0.92; GG vs. GC: RR=0.83; 95% CI, 0.72-0.97; GG vs. CC: RR=0.82; 95% CI, 0.72-0.93] is associated with the occurrence of ONFH, and the association with the male subgroup (RR=0.78; 95% CI, 0.65-0.94; P=0.009) is more evident. In conclusion, the present meta-analysis suggests that the VEGF gene -634G/C polymorphism has a significant association with ONFH occurrence among the investigated patients (P<0.01).