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Increasing evidence suggests that circular RNA (circRNA) plays an important role in tumorigenesis by regulating gene expression at the transcriptional and post-transcriptional levels. Alternative splicing events permit multiple transcript isoforms of circRNA to be produced; however, changes in the expression of circRNA full-length transcripts in cervical cancer remain unclear. Here, we systematically explored the dysregulation circRNA full-length transcripts and constructed an improved circRNA-miRNA-mRNA regulatory network to provide potential biomarkers and possible treatment targets in cervical cancer. We identified 9359 circular full-length transcripts from RNase R-treated RNA-seq data in cervical cancer, of which 353 circular full-length transcripts were significantly differentially expressed (DE) between the tumor and normal group. A total of 881 DE mRNA transcript isoforms were also identified from total RNA-seq data in cervical cancer, of which 421 (47.8%) transcript isoforms were up-regulated, and 460 (52.2%) transcript isoforms were down-regulated in tumor samples. Two circRNA-miRNA-mRNA competitively regulated networks, including 33 circRNA transcripts, 2 miRNAs, and 189 mRNA transcripts were constructed. Three genes (COPE, RAB3B, and TFPI) in the network were significantly associated with overall survival (P < 0.05), which indicated that these genes could act as prognostic biomarkers for patients with cervical cancer. Our study revealed genome-wide differential expression of full-length circRNA transcripts and constructed a more accurate circRNA-miRNA-mRNA network at the full-length transcript expression level in cervical cancer. CircRNA may thus be involved in the development of cervical cancer by regulating the expression of COPE, RAB3B, and TFPI. However, the specific regulatory mechanism in cervical cancer requires further study.

Objective To study the expression of tumor necrosis factor receptor-associated protein 1 (TRAP1) in gastric cancer tissue and its correlation with malignant biology. Methods Gastric cancer tissue and adjacent normal tissue were collected, and mRNA content and protein content of TRAP1 were detected; gastric cancer cell lines SGC7901, BGC823, AGS and MGC803 were cultured, and mRNA contents and protein contents of TRAP1, CyclinB1, CyclinD1, CyclinE, MMP-2 and VEGF were detected. Results mRNA and protein expression levels of TRAP1 in gastric cancer tissue were significantly higher than those in adjacent normal tissue, and mRNA and protein expression levels of TRAP1 in gastric cancer tissue with muscularis and serosa infiltration, lymph node metastasis, distant organ metastasis and TNM Ⅲ/Ⅳ stage were significantly higher than those in gastric cancer tissue with mucosa and submucosa infiltration, non-lymph node metastasis, non-distant organ metastasis and TNM Ⅰ/Ⅱ stage. mRNA and protein expression levels of TRAP1, CyclinB1, CyclinD1, CyclinE, MMP-2 and VEGF in MGC803 were the highest, and mRNA and protein expression levels of TRAP1, CyclinB1, CyclinD1, CyclinE, MMP-2 and VEGF in SGC7901 were the lowest. mRNA and protein expression levels of TRAP1 in gastric cancer cell lines were positively correlated with mRNA and protein expression of CyclinB1, CyclinD1, CyclinE, MMP-2 and VEGF. Conclusions The expression of TRAP1 significantly increases in gastric cancer tissue; TRAP1 may regulate the malignant biology of cells by increasing the expression of CyclinB1, CyclinD1, CyclinE, MMP-2 and VEGF, thereby resulting in the occurrence and development of gastric cancer.

The incidence of melanoma, the most aggressive and life-threatening form of skin cancer, has significantly risen over recent decades. Therefore, it is essential to identify the mechanisms that underlie melanoma tumorigenesis and metastasis and to explore novel and effective melanoma treatment strategies. Accumulating evidence s uggests that aberrantly expressed long noncoding RNAs (lncRNAs) have vital functions in multiple cancers. However, lncRNA functions in melanoma tumorigenesis and metastasis remain unclear. In this study, we investigated lncRNA and messenger RNA (mRNA) expression profiles in primary melanomas, metastatic melanomas and normal skin samples from the Gene Expression Omnibus database. We used GSE15605 as the training set (n = 74) and GSE7553 as the validation set (n = 58). In three comparisons (primary melanoma versus normal skin, metastatic melanoma versus normal skin, and metastatic melanoma versus primary melanoma), 178, 295 and 48 lncRNAs and 847, 1758, and 295 mRNAs were aberrantly expressed, respectively. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses to examine the differentially expressed mRNAs, and potential core lncRNAs were predicted by lncRNA-mRNA co-expression networks. Based on our results, 15 lncRNAs and 144 mRNAs were significantly associated with melanoma tumorigenesis and metastasis. A subsequent analysis suggested a critical role for a five-lncRNA signature during melanoma tumorigenesis and metastasis. Low expression of U47924.27 was significantly associated with decreased survival of patients with melanoma. To the best of our knowledge, this study is the first to explore the expression patterns of lncRNAs and mRNAs during melanoma tumorigenesis and metastasis by re-annotating microarray data from the Gene Expression Omnibus (GEO) microarray dataset. These findings reveal potential roles for lncRNAs during melanoma tumorigenesis and metastasis and provide a rich candidate reservoir for future studies.

There are two main mechanisms of miRNA-mediated gene silencing: either mRNA degradation or translational repression. However, the precise mechanism of target mRNAs regulated by miRNA remains unclear. As a complementary approach to experiment, a computational method was proposed to recognize the mechanism of miRNA-mediated gene silencing in human. We have analyzed extensive features correlated with miRNA-mediated silencing mechanism of mRNA. It is found that, the duplex structure, the number of binding sites and the structural accessibility of target site region are effective factors in determining whether a target mRNA is cleaved or only translationally inhibited. An SVM-based classifier was constructed to predict the regulation mode of miRNA based on these informative features. The results indicated that the approach proposed is effective in distinguishing whether a target mRNA is cleaved or translationally inhibited in human. Furthermore, the web server microDoR (http://reprod.njmu.edu.cn/microdor) has been developed and is freely available for users.

Trafficking of mRNA molecules from the nucleus to distal processes in neural cells is mediated by heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 trans-acting factors. Although hnRNP A2/B1 is alternatively spliced to generate four isoforms, most functional studies have not distinguished between these isoforms. Here, we show, using isoform-specific antibodies and isoform-specific green fluorescent protein (GFP)-fusion expression constructs, that A2b is the predominant cytoplasmic isoform in neural cells, suggesting that it may play a key role in mRNA trafficking. The differential subcellular distribution patterns of the individual isoforms are determined by the presence or absence of alternative exons that also affect their dynamic behavior in different cellular compartments, as measured by fluorescence correlation spectroscopy. Expression of A2b is also differentially regulated with age, species and cellular development. Furthermore, coinjection of isoform-specific antibodies and labeled RNA into live oligodendrocytes shows that the assembly of RNA granules is impaired by blockade of A2b function. These findings suggest that neural cells modulate mRNA trafficking by regulating alternative splicing of hnRNP A2/B1 and controlling expression levels of A2b, which may be the predominant mediator of cytoplasmic-trafficking functions. These findings highlight the importance of considering isoform-specific functions for alternatively spliced proteins.

Background: The cytokine signals that regulate myofibroblast differentiation and the resulting reorganization of matrix are incompletely understood. We studied the response of fibroblasts to mediators known to affect matrix reorganization, TGF-β and TNF-α in a collagen matrix. Further, we sought to determine if any cell phenotype changes resulted in quantifiable alterations in the mechanical performance of the matrix. Methods: Normal human dermal fibroblasts were cultured in collagen type I lattices for 1 and 5 days in DMEM with .5% FBS and TGF-β(1 ng/ml), TNF-α(10 ng/ml), or combinations TGF-β(1 ng/ml) + TNF-α(1,5, and 10 ng/ml). Western blot and immunohistochemistry were used to determine α-SMA expression. Quantitative real-time PCR was used to measure α-SMA mRNA. An indentation mechanical method was used to measure Young’s modulus which represents matrix stiffness. Results: TGF-β increases α-SMA, while TNF-α alone has no effect on basal α-SMA expression. When TGF-β + TNF-α were both added, the expression of α-SMA returned to basal levels. Immunohistochemistry showed α-SMA is incorporated into prominent stress fibers only in the TGF-β group. Real-time PCR showed that TNF-α did not affect α-SMA mRNA, while TGF-β increased α-SMA mRNA 19-fold. Combination treatment reduced mRNA level by 16-fold, to 2.7-fold compared to control. Indentation testing showed that, in all treatment groups, lattices after 5 days in culture were stiffer. TNF-α appeared to reduce the stiffness of the lattices on both day 1 and 5 compared to control. Conclusion: TNF-α decreases TGF-β induction of α-SMA expression at the transcriptional level and decreases lattice stiffness. The cellular responses to cytokines are reflected in both biochemical and mechanical behaviors. Understanding both will be necessary to understand how tissues remodel into functional tissue and scar.

Some members of the Solanaceae have a self-incompatibility mechanism preventing self-fertilization. Stylar ribonucleases (S-RNases) are responsible for growth inhibition of self-pollen tubes. A prevalent model postulates that the S-RNases act as intracellular cytotoxins that degrade ribosomal RNA, and possibly also messenger RNA, in the incompatible pollen tubes. Since ribosomes and polysomes are easily noticed with the electron microscope, it should be possible to confirm disintegration of these structures. However, our inspection by electron microscopy revealed the presence of ribosomes and polysomes in pollen tubes formed after self-pollination of the self-sterile species Brugmansia (Datura) suaveolens and Nicotiana alata. There was no decrease over time in the number of bound ribosomes per unit of rough endoplasmic reticulum (RER) membrane. The results indicate that the inhibition of tube growth is not due to a general degradation of ribosomal and messenger RNA. Therefore, the substrate for S-RNases presumably is very specific.

Chronic cold stress (4 degrees C) produced a sustained increase in mean arterial pressure in both normotensive and borderline hypertensive rats (BHR). The high blood pressure in BHRs was significantly reversed by a neuropeptide Y (NPY) Y1 receptor antagonist suggesting that NPY is involved in mediating stress-induced hypertension. Corresponding increases in adrenal NPY messenger RNA and NPY immunoreactivity were found during the stress; furthermore, chronic cold stress also potentiated the pressor response of rats to a subsequent acute stress test in which NPY has been shown to play a role. These results suggest that chronic cold stress-induced hypertension is mediated by elevated NPY release and vascular tone as a result of increased NPY gene expression and storage.

To further our understanding of the structure and function of phosphodiesterases of the newly identified family of high affinity cAMP-specific phosphodiesterases (PDE7), we identified and characterized the isozyme expressed in human skeletal muscle and the protein product of the previously isolated isozyme HCP1 (designated HSPDE7A1). We report the isolation of a cDNA encoding the full-length skeletal muscle isoform of human PDE7A (HSPDE7A2). The DNA sequence of this skeletal muscle cDNA indicates thatPDE7A2 is a novel 5′ splice variant of PDE7Aencoding an isoform with a novel, hydrophobic N terminus. The 456-amino acid PDE7A2 protein is detected on Western blots as a band with an apparent mobility of 50 kDa. PDE7A2 is a high affinity cAMP-specific PDE (K m = 0.1 μm), which is localized to particulate cellular fractions. The PDE7A1 (HCP1) isozyme is detected on Western blots as a band with an apparent mobility of 57 kDa, demonstrating that the previously isolated HCP1cDNA encodes the full-length PDE7A1 protein. The even distribution of PDE7A mRNA among fetal tissues and the relative abundance of its two mRNAs strongly suggest that the expression ofPDE7A is regulated throughout development.

Previously, we have shown that E5a can induce ex pression of the c-jun gene in human papillomavirus (HPV)-11 E5a transformed NIH 3T3 cells and human epidermal keratinocytes. In this study, we investigated the relationship between expression of the E5a gene and c-jun in pathologically confirmed condylomata specimens using mRNA hybridization in situ. The c-jun RNA concentration was significantly higher in condylomata specimens with E5a mRNA expression than in specimens without E5a mRNA expression, or in normal cervical specimens. The cells with c-jun expression were located predominantly in the basal and parabasal cell layers. These layers were also the primary location of E5a-expressing cells. This is the first demonstration of a strong correlation (74%) between expression of the E5a and c-jun genes in condylomata specimens. This correlation might reflect regulation by HPV-11 E5a of c-jun gene expression in condyloma.

Inhibitor of differentiation (Id)-1 and nuclear factor-kappa B (NF-κB) have been detected in many malignant tumors, and their presence has been correlated with the metastatic potential of these tumors. This study was undertaken to investigate the prognostic significance of the expression of Id-1 and the p65 subunit of NF-κB (NF-κB/p65) and the proteins' roles in the invasion process of nasopharyngeal carcinoma (NPC) cells. The messenger RNA (mRNA) and protein levels of Id-1 and NF-κB/p65 in normal nasopharyngeal epithelial cells and NPC cell lines were examined using reverse transcription-PCR and western blot analysis, whereas the mRNA and protein levels of Id-1 and NF-κB/p65 in clinical NPC specimens were determined by reverse transcription-PCR and immunohistochemistry. Short hairpin RNA (shRNA) was used to silence Id-1 and NF-κB/p65 to allow for the examination of matrix metalloproteinase (MMP)-9 expression and migratory capacity changes in CNE-2 cells. Multivariate Cox analysis revealed that elevated Id-1 expression was a significant independent predictor of the 5 year overall survival rate (hazards ratio = 16.720, P = 0.005). Furthermore, elevated expression of both Id-1 and NF-κB/p65 was associated with poor clinical survival (P = 0.049). Targeting Id-1 and NF-κB/p65 mRNA with shRNA in CNE-2 cells inhibited MMP-9 expression and decreased the migratory capacity of CNE-2 cells. In conclusion, Id-1 expression is a novel independent prognostic marker molecule that helps identify NPC patients with a poor prognosis. Additionally, combined analysis of Id-1 and NF-κB/p65 can be useful for identifying patients at risk for unfavorable clinical outcomes. Id-1 or/and NF-κB/p65 enhanced tumor cell migration, which is associated with the secretion of MMP-9.

OBJECTIVE To investigate the influence of najanalgesin on glutamate-glial transporter 1(GLT-1) in spinal cord of rats after L5 spinal nerve ligation and transection (SNL), and explore the spinal analgesic mechanism of najanalgesin. METHOD One hundred male SD rats were randomly divided into 6 groups: sham(A), SNL(B), SNL + najanalgesin(C), SNL + saline (D), SNL + najanalgesin + liposome (E), SNL + najanalgesin + liposome + GLT-1 As-ODNs(F) and treated with intrathecal injections of 10 p.L saline (A and D), 40 ng X kg(-1) najanalgesin (C, E and F), qd, respectively. Besides intrathecal administration of najanalgesin the rats were intrathecally injected with 10 microL of GLT-1 antisense oligodeoxynucleotides (As-ODNs) (F) and 10 micdroL of liposome(E) once daily on day 3. The L4-L6 segments of the spinal cord were isolated in 1, 4 and 7 d(A,B,C and D), 7 d(E and F) after surgery. The mRNA and protein of GLT-1 were determined. RESULT The SNL model has successfully been set up. Compared to sham group, the expression of GLT-1 mRNA and protein level in group B and D both increased firstly and decreased later, the expression of GLT-1 in group C was significantly increased and kept stable, which were also higher when compared to group D in day 7th. Compared to SNL + najanalgesin group, after intrathecal injection of GLT-1 As-ODNs the GLT-1, expression of GLT-1 in F group significantly decreased. While intrathecal administration of liposome had no significant effect on the spinal GLT-1 expression. CONCLUSION Najanalgesin could increase the mRNA and protein expression of GLT-1 in spinal cord, which may be one of its spinal mechanisms of analgesia.