Search

BackgroundSeveral high-throughput technologies can measure in parallel the abundance of many mRNA transcripts within a sample. These include the widely-used microarray as well as the more recently developed methods based on sequence tag abundances such as the Massively Parallel Signature Sequencing (MPSS) technology. A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms.ResultsWe compared transcript abundance (gene expression) measurement data obtained using Affymetrix and Agilent microarrays with MPSS data. All three technologies were used to analyze the same set of mRNA samples; these samples were extracted from various wild type Arabidopsis thaliana tissues and floral mutants. We calculated correlations and used clustering methodology to compare the normalized expression data and expression ratios across samples and technologies. Abundance expression measurements were more similar between different samples measured by the same technology than between the same sample measured by different technologies. However, when expression ratios were employed, samples measured by different technologies were found to cluster together more frequently than with abundance expression levels.Furthermore, the two microarray technologies were more consistent with each other than with MPSS. We also investigated probe-position effects on Affymetrix data and tag-position effects in MPSS. We found a similar impact on Affymetrix and MPSS measurements, which suggests that these effects were more likely a characteristic of the RNA sample rather than technology-specific biases.ConclusionComparisons of transcript expression ratios showed greater consistency across platforms than measurements of transcript abundance. In addition, for measurements based on abundances, technology differences can mask the impact of biological differences between samples and tissues.

Background: Oral squamous cell carcinoma (OSCC) is a malignant cancer, the survival rate of patients is disappointing. Therefore, it is necessary to identify the driven-genes and prognostic biomarkers in OSCC. Methods: Four Gene Expression Omnibus (GEO) datasets were integratedly analyzed using bioinformatics approaches, including identification of differentially expressed genes (DEGs), GO and KEGG analysis, construction of protein-protein interaction (PPI) network, selection of hub genes, analysis of prognostic information and genetic alterations of hub genes. ONCOMINE, The Cancer Genome Atlas (TCGA) and Human Protein Atlas databases were used to evaluate the expression and prognostic value of hub genes. Tumor immunity was assessed to investigate the functions of hub genes. Finally, Cox regression model was performed to construct a multiple-gene prognostic signature. Results: Totally 261 genes were found to be dysregulated. 10 genes were considered to be the hub genes. The Kaplan-Meier analysis showed that upregulated SPP1, FN1, CXCL8, BIRC5, PLAUR, and AURKA were related to poor outcomes in OSCC patients. FOXM1 and TPX2 were considered as the potential immunotherapeutic targets with future clinical significance. Moreover, we constructed a nine-gene signature (TEX101, DSG2, SCG5, ADA, BOC, SCARA5, FST, SOCS1, and STC2), which can be utilized to predict prognosis of OSCC patients effectively. Conclusion: These findings may provide new clues for exploring the molecular mechanisms and targeted therapy in OSCC. The hub genes and risk gene signature are helpful to the personalized treatment and prognostic judgement. [ABSTRACT FROM AUTHOR]

Osteosarcoma (OS), a malignant primary bone tumor often seen in young adults, is highly aggressive. The improvements in high-throughput technologies have accelerated the identification of various prognostic biomarkers for cancer survival prediction. However, only few studies focus on the prediction of prognosis in OS patients using gene expression data due to small sample size and the lack of public datasets. In the present study, the RNA-seq data of 82 OS samples, along with their clinical information, were collected from the TARGET database. To identify the prognostic genes for the OS survival prediction, we selected the top 50 genes of contribution as the initial candidate genes of the prognostic risk model, which were ranked by random forest model, and found that the prognostic model with five predictors including CD180, MYC, PROSER2, DNAI1, and FATE1 was the optimal multivariable Cox regression model. Moreover, based on a multivariable Cox regression model, we also developed a scoring method and stratified the OS patients into groups of different risks. The stratification for OS patients in the validation set further demonstrated that our model has a robust performance. In addition, we also investigated the biological function of differentially expressed genes between two risk groups and found that those genes were mainly involved with biological pathways and processes regarding immunity. In summary, the identification of novel prognostic biomarkers in OS would greatly assist the prediction of OS survival and development of molecularly targeted therapies, which in turn benefit patients' survival. [ABSTRACT FROM AUTHOR]

Licochalcone A (LCA) exhibited anticancer activity through modulating reactive oxygen species (ROS) levels in some cancer cells and has been evidenced to suppress colorectal cancer (CRC) formation and progression. However, whether LCA mediates the progression of CRC by regulating ROS production remains unclear. To address this, HCT-116 cells were treated with LCA, resulting in G0/G1 phase arrest, apoptosis, and high ROS generation, which were attenuated by N-acetyl-L-cysteine, a ROS inhibitor. In addition, LCA suppressed the expression of thioredoxin reductase 1 (TrxR1) in HCT-116 cells, leading to high ROS levels and apoptosis. Moreover, LCA administration combined with TrxR1 inhibition further enhanced the production of ROS and apoptosis in HCT-116 cells compared to LCA administration or TrxR1 inhibition alone. These results demonstrated that LCA might enhance the production of ROS by targeting TrxR1, leading to apoptosis in HCT-116 cells, which provides potential insight for the interventional treatment of CRC. [ABSTRACT FROM AUTHOR]

Background/Aims: Long non-coding RNAs (lncRNAs) play vital roles in carcinogenesis as oncogenes or tumor suppressor genes. This study explored the biological function of lncRNA gastric adenocarcinoma predictive long intergenic non-coding RNA (GAPLINC) in human non-small cell lung cancer (NSCLC). Methods: GAPLINC expression in NSCLC specimens and cell lines was detected by qRT-PCR and Western blot. The effect of GAPLINC on cell proliferation was investigated using CCK8-assay, colony formation assay, and xenograft model. The effects of GAPLINC on apoptosis and cell cycle were determined using flow cytometry. The mechanism of GAPLINC involved in NSCLC was explored using Western blot, luciferase reporter assay, and RNA fluorescence in situ hybridization. Results: We found that GAPLINC expression was up-regulated in NSCLC tissues and cell lines. Overexpression of GAPLINC was associated with poor prognosis in patients with NSCLC. Silencing of GAPLINC significantly inhibited cell proliferation, promoted apoptosis, and induced cell cycle arrest in the G0/G1 phase. Results from xenograft transplantation showed that GAPLINC silencing inhibited the tumor growth in vivo. Interestingly, GAPLINC silencing decreased the expression of eukaryotic elongation factor-2 kinase (eEF2K) protein both in vivo and in vitro. Bioinformatic analysis and luciferase reporter confirmed that miR-661 targeted GAPLINC and eEF2K 3'-UTR and was negatively correlated with the expression of GAPLINC and eEF2K. Conclusion: Our findings indicate that GAPLINC promotes NSCLC tumorigenesis by regulating miR-661/eEF2K cascade and provide new insights for the pathogenesis underlying NSCLC and potential targets for therapeutic strategy. [ABSTRACT FROM AUTHOR]

Notch-regulated ankyrin-repeat protein (NRARP) has recently been reported to be involved in a number of malignant cancers; however, its role in non-small lung cancer (NSCLC) remains unclear. The present study aimed to identify whether NRARP could be applied as a novel prognostic marker for NSCLC. A total of 108 NSCLC patients were enrolled in the present study and their lung tissues were collected. Reverse-transcription quantitative polymerase chain reaction and immunohistochemical staining were used to assess the mRNA and protein levels of NRARP. Appropriate statistical tests were performed to evaluate the associations between NRARP protein expression and clinicopathological features and prognosis in NSCLC patients. The results revealed that NRARP expression was significantly associated with tumor differentiation (P=0.001), Tumor-Node-Metastasis stage (P=0.004) and cigarette smoking (P<0.001). Furthermore, patients with higher NRARP protein expression had signifi- cantly shorter overall survival times (P<0.001). Multivariate analysis indicated that overexpression of NRARP protein could be applied as an independent prognostic biomarker for NSCLC. In summary, the present study demonstrated that NRARP protein is overexpressed in NSCLC and that high NRARP expression is correlated with tumor progression and overall survival time. These data indicated the potential value of NRARP as a novel therapeutic target for the treatment of NSCLC. [ABSTRACT FROM AUTHOR]

Castration plays a regulatory role in growth and carcass traits, particularly in fat deposition, but its molecular mechanisms are still not clear. The present study showed that castration significantly reduced the serum growth hormone and the responses of the growth hormone receptor ( GHR), insulin-like growth factor 1 ( IGF-I), IGF-IR and peroxisome proliferator-activated receptor gamma ( PPARγ) to castration were similar in different adipose tissues. However, the GHR expression trends were opposite between the liver and the adipose tissues; bisulfite sequencing PCR (BSP) showed that its methylation in these two tissues was different. In particular, the GHR methylation rate in the liver of castrated and intact pigs were 93.33% and 0, respectively, which was consistent with its higher expression level in the intact group. It was predicted that there were potential binding sites for 11 transcription factors in the ninth CpG site (which was methylated and demethylated in subcutaneous adipose tissue of the intact and castrated groups, respectively), including androgen receptor ( AR), CCAAT/enhancer binding protein-α ( C/EBPα) and C/EBPβ, all of which are important factors in lipid metabolism. These results indicate that DNA methylation may participate in castration-induced fat deposition. [ABSTRACT FROM AUTHOR]

Unlike the genomes of many mammals that have a single NK-lysin gene, the cattle genome contains a family of four genes, one of which is expressed preferentially in the lung. In this study, we compared the expression of the four bovine NK-lysin genes in healthy animals to animals challenged with pathogens known to be associated with bovine respiratory disease (BRD) using transcriptome sequencing (RNA-seq). The expression of several NK-lysins, especially NK2C, was elevated in challenged relative to control animals. The effects of synthetic peptides corresponding to functional region helices 2 and 3 of each gene product were tested on both model membranes and bio-membranes. Circular dichroism spectroscopy indicated that these peptides adopted a more helical secondary structure upon binding to an anionic model membrane and liposome leakage assays suggested that these peptides disrupt membranes. Bacterial killing assays further confirmed the antimicrobial effects of these peptides on BRD-associated bacteria, including both Pasteurella multocida and Mannhemia haemolytica and an ultrastructural examination of NK-lysin-treated P. multocida cells by transmission electron microscopy revealed the lysis of target membranes. These studies demonstrate that the expanded bovine NK-lysin gene family is potentially important in host defense against pathogens involved in bovine respiratory disease. [ABSTRACT FROM AUTHOR]

Jasmonates (JAs) act as conserved elicitors of plant secondary metabolism. JAs perception triggers extensive transcriptional reprogramming leading to activation of the entire metabolic pathways. The family of basic helix-loop-helix (bHLH) transcription factors (TFs) has essential roles in JA signaling; however, little is known about their roles in regulation of secondary metabolites in Isatis indigotica . In this study, we identified 78 putative IibHLH sequences using the annotation of I. indigotica transcriptome. The identified proteins were characterized based on phylogenetic and conserved motif analyses. Using RNA sequencing, 16 IibHLHs showed significant positive response to MeJA (methyl jasmonate) at 1 h, indicating their roles as early signaling events of JA-mediated transcriptional reprogramming. Ten IibHLHs presented co-expression pattern with biosynthetic pathway genes, suggesting their regulating role in secondary metabolite synthesis. These gene expression profiling data indicate that bHLHs can be used as candidate genes in molecular breeding programs to improve metabolite production in I. indigotica . [ABSTRACT FROM AUTHOR]

Background: Numerous studies have recorded the function of long noncoding RNAs (lncRNAs) in cancer development, including lung adenocarcinoma (LUAD). Previous studies have reported the crucial role of lncRNA PTPRG antisense RNA 1 (PTPRG-AS1) in various cancers. However, the role of PTPRG-AS1 in LUAD remains unknown. Materials and Methods: Real-time quantitative polymerase chain reaction (RT-qPCR) was applied for detecting PTPRG-AS1 expression in LUAD cell lines. Functional assays and in vivo experiments explored cell proliferation, whereas flow cytometry analysis was used to detect cell cycle. In addition, fluorescent in situ hybridization (FISH) and subcellular fractionation assay measured the localization of PTPRG-AS1 in LUAD cells. RNA pulldown, luciferase reporter, and RNA immunoprecipitation (RIP) assays were used to investigate the interaction of PTPRG-AS1/miR-124-3p/cyclin D1 (CCND1) axis. Results: PTPRG-AS1 expression was notably high in LUAD cell lines. PTPRG-AS1 knockdown suppressed cell proliferation and cycle as well as the level of CCND1. Moreover, miR-124-3p was the mutual target of PTPRG-AS1 and CCND1. In addition, PTPRG-AS1 sponged miR-124-3p to upregulate CCND1 in LUAD cells. Moreover, miR-124-3p depletion reversed the suppression of PTPRG-AS1 silence on LUAD cell behaviors, but then CCND1 knockdown countervailed the promoting influence of downregulated miR-124-3p. Conclusions: PTPRG-AS1 propels cell proliferation and cell cycle of LUAD by targeting miR-124-3p/CCND1 axis. [ABSTRACT FROM AUTHOR]

Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in adipogenesis and myogenic differentiation, but their impact on porcine muscle traits is not well understood. We compared their expressional profiles in the longissimus dorsi muscle of Chinese Huainan pigs (HN, the fat type) and Western commercial Duroc × (Landrace × Yorkshire) (DLY, the thin type) pigs, and 854 mRNAs, 233 lncRNAs, and 66 circRNAs (p < 0.05 and | log2FoldChange | >1) were found to be differentially expressed. The differentially expressed mRNA and circRNA parental genes were enriched in the Wnt signaling pathway (adipogenesis), the transition between fast and slow fibers (myogenic differentiation), and alanine, aspartate and glutamate metabolism (pork flavor). The potential lncRNAs/circRNAs-miRNAs-mRNAs regulatory networks shared MYOD1, PPARD, miR-423-5p and miR-874, which were associated with skeletal muscle muscular proliferation, differentiation/regeneration and adipogenesis. Taken together, these differentially expressed non-coding RNAs may be involved in the molecular basis of muscle traits, acting as the competing endogenous RNA (ceRNA) for miRNAs. [ABSTRACT FROM AUTHOR]