Over-expression of LRIG1 suppresses biological function of pituitary adenoma via attenuation of PI3K/AKT and Ras/Raf/ERK pathways in vivo and in vitro

Pituitary adenomas (PAs) are well known as a common intracranial benign tumor, and a portion of PAs are refractory to current therapeutic methods. ErbB receptors family signaling pathway regulates the expression of PAs activation associated gene. Inhibition of epidermal growth factor receptor (EGFR) can inhibit proliferation of PAs. Leucine-rich repeats and immunoglobulin-like domains protein 1 ( LRIG1), a negative mediated gene of ErbB receptors family, plays a role in many tumors. However, there are seldom researches about the functional role of LRIG1 in PAs. The aim of this study is to explore the potential effect of LRIG1 and its regulating mechanism in PAs. First, we investigated the role of LRIG1 in cell migration, invasion of PAs with transfected LRIG1 or control. Then, we explored its impact on cell proliferation and apoptosis of PAs in vivo. To study the regulating mechanism of LRIG1, we examined the expression of molecular factor of PI3K/AKT and Ras/Raf/ERK pathway using Western blotting in vitro and RT-PCR in vitro and in vivo. It was found that LRIG1 over-expression inhibited cell migration, invasion and proliferation, and promoted apoptosis of PAs in vivo and in vitro. Furthermore, LRIG1 suppressed the expression of signaling of PI3K/AKT and Ras/Raf/ERK pathways in PAs. LRIG1, as a negative mediated gene of tumor, can inhibit biological function of PAs via inhibiting PI3K/AKT and Ras/Raf/ERK pathways, and it might be a new target for gene therapy of PAs.

Structure, functional regulation and signaling properties of Rap2B

The Ras family small guanosine 5'-triphosphate (GTP)-binding protein Rap2B is is a member of the Ras oncogene family and a novel target of p53 that regulates the p53-mediated pro-survival function of cells. The Rap2B protein shares ~90% homology with Rap2A, and its sequence is 70% identical to other members of the Rap family such as RaplA and RaplB. As a result, Rap2B has been theorized to have similar signaling effectors to the GTPase-binding protein Rap, which mediates various biological functions, including the regulation of sterile 20/mitogen-activated proteins. Since its identification in the early 1990s, Rap2B has elicited a considerable interest. Numerous studies indicate that Rap2B exerts specific biological functions, including binding and stimulating phospholipase C-ε and interferon-γ. In addition, downregulation of Rap2B affects the growth of melanoma cells. The present review summarizes the possible effectors and biological functions of Rap2B. Increasing evidence clearly supports the association between Rap2B function and tumor development. Therefore, it is conceivable that anticancer drugs targeting Rap2B may be generated as novel therapies against cancer.

Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins

Using a new bioinformatic method to analyze ribosome profiling data, we show that 40% of lncRNAs and pseudogene RNAs expressed in human cells are translated. In addition, ~35% of mRNA coding genes are translated upstream of the primary protein-coding region (uORFs) and 4% are translated downstream (dORFs). Translated lncRNAs preferentially localize in the cytoplasm, whereas untranslated lncRNAs preferentially localize in the nucleus. The translation efficiency of cytoplasmic lncRNAs is nearly comparable to that of mRNAs, suggesting that cytoplasmic lncRNAs are engaged by the ribosome and translated. While most peptides generated from lncRNAs may be highly unstable byproducts without function, ~9% of the peptides are conserved in ORFs in mouse transcripts, as are 74% of pseudogene peptides, 24% of uORF peptides and 32% of dORF peptides. Analyses of synonymous and nonsynonymous substitution rates of these conserved peptides show that some are under stabilizing selection, suggesting potential functional importance.

DOI:http://dx.doi.org/10.7554/eLife.08890.001

Our genes encode the instructions needed to make proteins. When a gene is switched on, it’s DNA is used as a template to make molecules of messenger ribonucleic acid (RNA). These RNAs are then “translated” into proteins by large cell machines called ribosomes. Within the messenger RNA, a long region called an “open reading frame” is the section that encodes the protein.

The human genome also contains a vast amount of DNA that is not part of any gene. Cells can produce molecules of RNA from this DNA (so-called “non-coding RNAs”), but these RNAs are not thought to code for proteins because they lack long open reading frames. Non-coding RNAs can also be made from sections of DNA called “pseudogenes”, which have lost their ability to code for proteins over the course of evolution. Furthermore, messenger RNAs also contain short open reading frames in the “untranslated” regions that flank the protein-coding region.

The extent to which cells translate non-coding RNAs to produce small proteins (or peptides) is not known. “Ribosome profiling” is a powerful method to determine which RNAs are translated, but it is not always possible to distinguish between the RNAs that are genuinely translated and those that just happen to be bound to ribosomes. Ji et al. overcome these limitations by developing a new computational method to analyse data from ribosome profiling.

The experiments show that thousands of non-coding RNAs in the human genome are, in fact, translated. This is many more than anticipated and represents approximately 40% of the lncRNAs and pseudogene RNAs, and 35% of untranslated regions in messenger RNAs. Ji et al. also found that a small group of all the lncRNA peptides in the human genome appear to have changed little over the course of evolution, which strongly suggests that they have specific roles in cells. The next challenge is to find out what roles the peptides encoded by these lncRNAs play in cells.

DOI:http://dx.doi.org/10.7554/eLife.08890.002

New scaling relation for information transfer in biological networks

We quantify characteristics of the informational architecture of two representative biological networks: the Boolean network model for the cell-cycle regulatory network of the fission yeast Schizosaccharomyces pombe (Davidich et al. 2008 PLoS ONE 3, e1672 (doi:10.1371/journal.pone.0001672)) and that of the budding yeast Saccharomyces cerevisiae (Li et al. 2004 Proc. Natl Acad. Sci. USA 101, 4781-4786 (doi:10.1073/pnas.0305937101)). We compare our results for these biological networks with the same analysis performed on ensembles of two different types of random networks: Erdös-Rényi and scale-free. We show that both biological networks share features in common that are not shared by either random network ensemble. In particular, the biological networks in our study process more information than the random networks on average. Both biological networks also exhibit a scaling relation in information transferred between nodes that distinguishes them from random, where the biological networks stand out as distinct even when compared with random networks that share important topological properties, such as degree distribution, with the biological network. We show that the most biologically distinct regime of this scaling relation is associated with a subset of control nodes that regulate the dynamics and function of each respective biological network. Information processing in biological networks is therefore interpreted as an emergent property of topology (causal structure) and dynamics (function). Our results demonstrate quantitatively how the informational architecture of biologically evolved networks can distinguish them from other classes of network architecture that do not share the same informational properties.

Biological Investigations of (+)-Danicalipin A Enabled Through Synthesis

A total synthesis of the chlorosulfolipid (+)-danicalipin A has been accomplished in 12 steps and 4.4% overall yield. The efficient and scalable synthesis enabled in-depth investigations of the lipid's biological properties, in particular cytotoxicity towards various mammalian cell lines. Furthermore, the ability of (+)-danicalipin A to increase the uptake of fluorophores into bacteria and mammalian cells was demonstrated, indicating it may enhance membrane permeability. By comparing (+)-danicalipin A with racemic 1,14-docosane disulfate, and the diol precursor of (+)-danicalipin A, we have shown that both chlorine and sulfate functionalities are necessary for biological activity.

ChSeq: A database of chameleon sequences

Chameleon sequences (ChSeqs) refer to sequence strings of identical amino acids that can adopt different conformations in protein structures. Researchers have detected and studied ChSeqs to understand the interplay between local and global interactions in protein structure formation. The different secondary structures adopted by one ChSeq challenge sequence-based secondary structure predictors. With increasing numbers of available Protein Data Bank structures, we here identify a large set of ChSeqs ranging from 6 to 10 residues in length. The homologous ChSeqs discovered highlight the structural plasticity involved in biological function. When compared with previous studies, the set of unrelated ChSeqs found represents an about 20-fold increase in the number of detected sequences, as well as an increase in the longest ChSeq length from 8 to 10 residues. We applied secondary structure predictors on our ChSeqs and found that methods based on a sequence profile outperformed methods based on a single sequence. For the unrelated ChSeqs, the evolutionary information provided by the sequence profile typically allows successful prediction of the prevailing secondary structure adopted in each protein family. Our dataset will facilitate future studies of ChSeqs, as well as interpretations of the interplay between local and nonlocal interactions. A user-friendly web interface for this ChSeq database is available at prodata.swmed.edu/chseq.

Gene expression profiling by mRNA array reveals different pattern in Chinese glioblastoma patients between Uygur and Han populations

OBJECTIVE

To identify differentially expressed genes in Chinese glioblastoma patients of Uygur and Han populations, and investigate their potential clinical value for pathogenesis determination and progress prediction.

METHODS

Gene expression profiling was obtained from three patients of each Uygur and Han nationalities, respectively, by mRNA expression array. Data were processed by the GenomeStudio software and language R of the Lumi package, followed by GO (Gene Ontology) term and KEGG pathway annotation analysis by the Web Gestalt software.

RESULTS

The comparative analysis of genome-scale gene expression in glioblastomas revealed 1,475 differentially expressed genes, with 669 and 807 genes up-regulated and down-regulated, respectively. These included the STRC gene, which has two transcripts, one up-regulated and one down-regulated. GO term analysis suggested that 1,175 out of 1,475 key genes were involved in small GTPase mediated signal transduction, Ras protein signal transduction, bioprocess of neuronal response regulation, and central nervous system myelination. The KEGG pathway enrichment analysis showed that the differentially expressed genes were covered by 28 signaling pathways associated with tumorigenesis, including metabolic pathways, tumor suppressor pathways, MAP kinase signaling pathways, TGF-β signaling pathway, neurotrophin signaling pathways, and mTOR signaling pathway.

CONCLUSION

The comparative study of gene expression profiling in glioblastomas between Uygur and Han nationalities revealed differentially expressed genes, whose functions and expression localization were analyzed by GO term analysis and KEGG pathway enrichment analysis. Different pathogenesis mechanisms were proposed for glioblastomas in Chinese patients of Uygur and Han nationalities from a molecular biology perspective.

The role of miR-29b in cancer: regulation, function, and signaling

MicroRNAs (miRNAs) are endogenous small non-coding RNAs with the capacity to regulate gene expression post-transcriptionally. The miRNA-29 family consists of miR-29a, miR-29b, and miR-29c, among which miR-29b is the most highly expressed and is found at two genomic loci. Recently, numerous studies have demonstrated that aberrant expression of miR-29b is common in the majority of human cancers. miR-29b is known to critically affect cancer progression by functioning as a tumor suppressor. However, it may also act as an oncogene under certain conditions. In this review, we illustrate the role of miR-29b in cancer regulation, function, and signaling. This is the first review highlighting the role of miR-29b in cancer. Our review aims to summarize the effects of miR-29b on cancer activity and its interactions with target genes and signaling pathways, as well as to provide therapeutic implications for overcoming cancer chemoresistance.

CKS2 in human cancers: Clinical roles and current perspectives (Review)

Cyclin-dependent kinase subunit 2 (CKS2) is indicated in the processes of cell cycle and cell proliferation. Through these processes, CKS2 is identified as a cancer gene, but its role has not been well reviewed. The aim of the present study was to summarize the clinicopathological significance and the molecular mechanisms of CKS2 in human cancers. Its expression was upregulated in the majority of the types of cancer studied. CKS2 was shown to have a function in cancers of the digestive tract, genital tract, thyroid, nerve and certain other types of cancer. CKS2 can promote progression of certain cancers via positive control of proliferation, invasion and migration. Downregulation of CKS2 induces cancer cell apoptosis. CKS2 can change a multitude of cellular mechanisms in cancer pathogenesis by regulating the gene translation of numerous validated targets, such as p53, CDK1, cyclin A, cyclin B1, caspase-3 and Bax. In addition, the molecular mechanism that causes aberrant expression of CKS2 was epigenetic modification of miR-26a and the Y-box-binding protein 1 (YB-1) gene. In conclusion, CKS2 is commonly elevated in cancer, most likely due to its ability to promote cancer cell growth, invasion and migration through regulating certain significant genes. Understanding the mechanisms by which CKS2 is involved with cancer pathogenesis will be useful in the development of tumor therapy for patients with cancer.

Serine proteases of parasitic helminths

Serine proteases form one of the most important families of enzymes and perform significant functions in a broad range of biological processes, such as intra- and extracellular protein metabolism, digestion, blood coagulation, regulation of development, and fertilization. A number of serine proteases have been identified in parasitic helminths that have putative roles in parasite development and nutrition, host tissues and cell invasion, anticoagulation, and immune evasion. In this review, we described the serine proteases that have been identified in parasitic helminths, including nematodes (Trichinella spiralis, T. pseudospiralis, Trichuris muris, Anisakis simplex, Ascaris suum, Onchocerca volvulus, O. lienalis, Brugia malayi, Ancylostoma caninum, and Steinernema carpocapsae), cestodes (Spirometra mansoni, Echinococcus granulosus, and Schistocephalus solidus), and trematodes (Fasciola hepatica, F. gigantica, and Schistosoma mansoni). Moreover, the possible biological functions of these serine proteases in the endogenous biological phenomena of these parasites and in the host-parasite interaction were also discussed.

E3 ubiquitin ligase Cbl-b in innate and adaptive immunity

Casitas B-lineage lymphoma proto-oncogene-b (Cbl-b), a RING finger E3 ubiquitin-protein ligase, has been demonstrated to play a crucial role in establishing the threshold for T-cell activation and controlling peripheral T-cell tolerance via multiple mechanisms. Accumulating evidence suggests that Cbl-b also regulates innate immune responses and plays an important role in host defense to pathogens. Understanding the signaling pathways regulated by Cbl-b in innate and adaptive immune cells is therefore essential for efficient manipulation of Cbl-b in emerging immunotherapies for human disorders such as autoimmune diseases, allergic inflammation, infections, and cancer. In this article, we review the latest developments in the molecular structural basis of Cbl-b function, the regulation of Cbl-b expression, the signaling mechanisms of Cbl-b in immune cells, as well as the biological function of Cbl-b in physiological and pathological immune responses in animal models and human diseases.

[Effect of the peri-implantitis on the biological function of osteoblasts obtained from the mandibles]

OBJECTIVE

To study the effect of peri-implantitis inflammatory microenvironment on the biological function of jaw bone osteoblasts.

METHODS

Primary mandible osteoblasts from peri-implantitis and normal tissue were isolated and cultured. Third-generation purified osteoblasts were identified and detected. The proliferative activity of osteoblasts was evaluated through MTT assay. Osteocalcin (OCN), Runx2, and collagen I (Col I) mRNA levels were examined by real-time quantitative polymerase chain reaction. OCN protein levels were determined by Western blot.

RESULTS

: After 4 d of culture, the proliferative activity of osteoblasts from peri-implantitis became lower than that of normal tissue ( P <0.05). After 7 d of culture, OCN, Runx2, and Col I mRNA expression decreased ( P <0.05). The OCN protein levels also decreased ( P <0.05).

CONCLUSION

Peri-implantitis inflammatory microenvironment can decrease the proliferation and differentiation activity of mandible osteoblasts.

Bioactivity and potential health benefits of licorice

Licorice is an herbal plant named for its unique sweet flavor. It is widely used in the food and tobacco industries as a sweetener. Licorice is also used in traditional Chinese medicine (TCM) and complementary medicine. Because the use of licorice has long been a part of TCM, the details of its therapeutic applications have been thoroughly established. In modern science, licorice is of interest because of its broad range of applications. Extracts of and compounds isolated from licorice have been well studied and biologically characterized. In this review, we discuss the nutraceutical and functional activities of licorice as well as those of the extracts of and the isolated compounds from licorice, including agents with anti-inflammatory activity, cell-protective abilities, and chemopreventive effects. The side effects of licorice are also enumerated. A comparison of the activities of licorice described by modern science and TCM is also presented, revealing the correspondence of certain characteristics.

Osteopontin splice variants differentially exert clinicopathological features and biological functions in gastric cancer

Purpose: Gastric cancer (GC) remains a leading cause of death worldwide, and an elevated expression of osteopontin (OPN) may correlate with its poor survival. Alternative splicing of OPN can result in three isoforms, OPN-a, OPN-b and OPN-c. The aim of our current study is to examine the expression pattern and biological functions of OPN splice variants in GC.

Methods: Firstly, we evaluated the expression of OPN splice variants in 7 gastric cell lines, 101 pairs of GC tissues and their adjacent non-tumor tissues by Quantative real-time PCR (QT-PCR). Gain-of-function experiments were subsequently performed to determine their diverse roles in malignant behaviors of GC. Besides, their differential effects on the regulation of crucial downstream molecules were further explored in the anti-apoptotic and pro-metastatic process.

Results: We found that OPN-b is the dominant kind of OPN isoform in GC cell lines. Although the expression levels of three variants were all elevated in GC tissues, increased OPN-b or OPN-c expression could correlate with clinicopathological features. Functional analyses further showed that OPN-b most strongly promoted GC cell survival possibly by regulation of Bcl-2 family proteins and CD44v expressions. Moreover, OPN-c most effectively stimulated GC metastatic activity by increasing secretion of MMP-2, uPa, and IL-8.

Conclusions: Our results suggest that OPN splice variants differentially exert clinicopathological features and biological functions in GC. Therefore, focusing on specific OPN isoform could be a novel direction for developing diagnostic and therapeutic approaches in GC.

Peripheral blood microRNAs: A novel tool for diagnosing disease?

Peripheral blood microRNAs (miRNAs) are endogenous, noncoding small RNAs present in blood. Because of their size, abundance, tissue specificity, and relative stability in peripheral circulation, they offer great promise of becoming a novel noninvasive biomarker. However, the mechanism by which they are secreted, their biological function, and the reason for the existence of extracellular miRNAs are largely unclear. This article describes advances in the study of the mechanism of origin and biological function of extracellular miRNAs along with approaches adopted by research and questions that remain. This work also discusses the potential for peripheral blood miRNAs to serve as a diagnostic tool.

The macro domain protein family: structure, functions, and their potential therapeutic implications

Macro domains are ancient, highly evolutionarily conserved domains that are widely distributed throughout all kingdoms of life. The 'macro fold' is roughly 25kDa in size and is composed of a mixed α-β fold with similarity to the P loop-containing nucleotide triphosphate hydrolases. They function as binding modules for metabolites of NAD(+), including poly(ADP-ribose) (PAR), which is synthesized by PAR polymerases (PARPs). Although there is a high degree of sequence similarity within this family, particularly for residues that might be involved in catalysis or substrates binding, it is likely that the sequence variation that does exist among macro domains is responsible for the specificity of function of individual proteins. Recent findings have indicated that macro domain proteins are functionally promiscuous and are implicated in the regulation of diverse biological functions, such as DNA repair, chromatin remodeling and transcriptional regulation. Significant advances in the field of macro domain have occurred in the past few years, including biological insights and the discovery of novel signaling pathways. To provide a framework for understanding these recent findings, this review will provide a comprehensive overview of the known and proposed biochemical, cellular and physiological roles of the macro domain family. Recent data that indicate a critical role of macro domain regulation for the proper progression of cellular differentiation programs will be discussed. In addition, the effect of dysregulated expression of macro domain proteins will be considered in the processes of tumorigenesis and bacterial pathogenesis. Finally, a series of observations will be highlighted that should be addressed in future efforts to develop macro domains as effective therapeutic targets.

β-Glucosidases

β-Glucosidases (3.2.1.21) are found in all domains of living organisms, where they play essential roles in the removal of nonreducing terminal glucosyl residues from saccharides and glycosides. β-Glucosidases function in glycolipid and exogenous glycoside metabolism in animals, defense, cell wall lignification, cell wall β-glucan turnover, phytohormone activation, and release of aromatic compounds in plants, and biomass conversion in microorganisms. These functions lead to many agricultural and industrial applications. β-Glucosidases have been classified into glycoside hydrolase (GH) families GH1, GH3, GH5, GH9, and GH30, based on their amino acid sequences, while other β-glucosidases remain to be classified. The GH1, GH5, and GH30 β-glucosidases fall in GH Clan A, which consists of proteins with (β/α)(8)-barrel structures. In contrast, the active site of GH3 enzymes comprises two domains, while GH9 enzymes have (α/α)(6) barrel structures. The mechanism by which GH1 enzymes recognize and hydrolyze substrates with different specificities remains an area of intense study.

The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis

The focus of this paper is the hotdog-fold thioesterase THEM2 from human (hTHEM2; Swiss-Prot entry Q9NPJ3 ). In an earlier communication (Cheng, Z., Song, F., Shan, X., Wei, Z., Wang, Y., Dunaway-Mariano, D., and Gong, W. (2006) Crystal structure of human thioesterase superfamily member 2, Biochem. Biophys. Res. Commun. 349, 172-177) we reported the apo crystal structure of hTHEM2. Herein, we report the results of an extensive hTHEM2 substrate screen, the structure determination of hTHEM2 complexed with the inert substrate analogue undecan-2-one-CoA (in which OC-CH(2)-S substitutes for OC-S) and the kinetic analysis of active site mutants. The work described in this paper represents the first reported structure-function based analysis of a human hotdog-fold thioesterase. The catalytic mechanism proposed involves the Asp65/Ser83 assisted attack of a water molecule at the Gly57/Asn50 polarized thioester CO and the Asn50 assisted departure of the thiolate leaving group. Thioesterase activity was observed with acyl-CoAs but not with the human acyl-ACP or with an acyl-Cys peptide. The medium-to-long-chain fatty acyl-CoAs displayed the smallest K(m) values. The substrate specificity profile was analyzed within the context of the liganded enzyme to define the structural determinants of substrate recognition. Based on the results of this structure-function analysis we hypothesize that the physiological role of hTHEM2 involves catalysis of the hydrolysis of cytosolic medium-to-long-chain acyl-CoA thioesters.

A fast response mechanism for insulin storage in crystals may involve kink generation by association of 2D clusters

Crystals that are likely rhombohedral of Zn-insulin hexamers form in the islets of Langerhans in the pancreases of many mammals. The suggested functions of crystal formation is to protect the insulin from proteases and increase the degree of conversion of soluble proinsulin. To accomplish these ends, crystal growth should be fast and adaptable to rate fluctuations in the conversion reaction. Zn-insulin crystals grow layer by layer. Each layer spreads by the attachment of molecules to kinks located at the layers' edges, also called steps. The kinks are thought to be generated either by thermal fluctuations, as postulated by Gibbs, or by 1D nucleation of new crystalline rows. The kink density determines the rate at which steps advance, and these two kink-generation mechanisms lead to weak near-linear responses of the growth rate to concentration variations. We demonstrate for the crystallization of Zn-insulin a mechanism of kink generation whereby 2D clusters of several insulin molecules preformed on the terraces between steps associate to the steps. This mechanism results in several-fold-higher kink density, a faster rate of crystallization, and a high sensitivity of the kinetics to small increases of the solute concentration. If the found mechanism operates during insulin crystallization in vivo, it could be a part of the biological regulation of insulin production and function. For other crystallizing materials in biological and nonbiological systems, this mechanism provides an understanding of the often seen nonlinear acceleration of the kinetics.

Structural and physiological properties of mengovirus: avirulent, hemagglutination-defective mutants express altered alpha (1 D) proteins and are adsorption-defective

Structural and physiological properties of two mutants of mengovirus, 205 and 280, were compared to those of wild-type virus to understand the molecular basis of changes exhibited in their biological function. Two dimensional gel electrophoresis of wild-type and mutant structural proteins revealed alterations in the isoelectric character of the alpha (1 D) protein of both mutant 205 and 280. These data suggest that alterations in the alpha (1 D) protein may be responsible for the phenotypic changes by the mutants. A delay in detectable virus-specified protein synthesis was exhibited in mutant-infected cells in comparison to wild-type. The amount of RNA synthesized in mutant- and revertant-infected cells was less than that synthesized in wild-type infected cells. Changes in virus-specified macromolecular synthesis in mutant and revertant-infected cells reflected a decrease in the ability of the viruses to attach to cells.