Glial inflammation and neurodegeneration induced by candoxin, a novel neurotoxin from Bungarus candidus venom: global gene expression analysis using microarray

Cobra Three-Finger Toxins Interact with RNA and DNA: Nucleic Acids as Their Putative Biological Targets

Three-finger toxins (TFTs), including neurotoxins and cytotoxins, form one of the largest families of snake venom proteins and interact with various biological targets. Neurotoxins target proteinaceous receptors while cytotoxins interact mainly with the lipids of cell membranes and to a lesser extent with carbohydrates. However, no data about the interaction of TFTs with nucleic acids can be found. To detect this interaction, we applied spectrophotometry, ion-paired HPLC and electrophoretic mobility shift assay (EMSA). Using spectrophotometry, we found that TFTs from cobra venom increased the optical density of an RNA solution in a time-dependent manner indicating toxin interaction with RNA. A decrease in the net negative charge of the RNA molecule upon interaction with neurotoxin II from cobra venom was revealed by ion-pair HPLC. EMSA showed decreased electrophoretic mobility of both RNA and DNA upon addition of different TFTs including the non-conventional cobra toxin WTX and water-soluble recombinant human three-finger protein lynx1. We suggest that the interaction with nucleic acids may be a common property of TFTs, and some biological effects of TFTs, for example, cytotoxin-induced apoptosis in cancer cell lines, may be mediated by interaction with nucleic acids.

Toxinology provides multidirectional and multidimensional opportunities: A personal perspective

In nature, toxins have evolved as weapons to capture and subdue the prey or to counter predators or competitors. When they are inadvertently injected into humans, they cause symptoms ranging from mild discomfort to debilitation and death. Toxinology is the science of studying venoms and toxins that are produced by a wide variety of organisms. In the past, the structure, function and mechanisms of most abundant and/or most toxic components were characterized to understand and to develop strategies to neutralize their toxicity. With recent technical advances, we are able to evaluate and determine the toxin profiles using transcriptomes of venom glands and proteomes of tiny amounts of venom. Enormous amounts of data from these studies have opened tremendous opportunities in many directions of basic and applied research. The lower costs for profiling venoms will further fuel the expansion of toxin database, which in turn will provide greater exciting and bright opportunities in toxin research.

Altered gene expression profile in a rat model of gentamicin-induced ototoxicity and nephrotoxicity, and the potential role of upregulated Ifi44 expression

As demonstrated by Alport syndrome, the co-occurrence of auditory and urinary system malformations, and gentamicin-induced ototoxicity and nephrotoxicity, the ears and kidneys potentially share certain molecular pathways. In the present study, microarray chips were used to analyze the changes in the gene expression profile using a rat model of gentamicin-induced ototoxicity and nephrotoxicity, using rat liver tissue as a control. A number of genes were identified to exhibit similar expression changes in the rat ears and kidney tissues, among which microtubule-associated protein 44 (Ifi44), was selected for further analysis to validate its expression changes and confirm potential involvement in the inflammation process in the disease model. Ifi44 is a member of the type I interferon-inducible gene family. Reverse transcription-quantitative polymerase chain reaction, western blotting and immunohistochemistry were performed; the results demonstrated that more inflammatory cells were present in cochlear and renal parenchyma in gentamycin-induced rats, and Ifi44 expression was increased in these two organs compared with control rats. Taken together, with its role in lupus nephritis and expression in the inner ear, the results suggested that Ifi44 is potentially involved in the inflammation associated with gentamicin-induced ototoxicity and nephrotoxicity. The approach of the current study has also provided a strategy for delineating common pathways shared by organs involved in specific diseases.

Screening and functional analysis of glioma‑related genes induced by candoxin

This study aimed to identify time‑specific and common differential genes (CDGs) expressed in glioma cells following exposure to candoxin at three different time‑points. Gene expression data from candoxin‑treated human glioma (Hs 683) cells were downloaded from the Gene Expression Omnibus database (accession number, GSE1682), from a 12‑time‑point set of samples. Differentially expressed genes were screened between control and candoxin‑treated samples at different time‑points, and three time‑specific gene sets and CDGs were identified. All genes were subject to pathway enrichment analysis to gain further insight into gene function. CDGs were clustered based upon their original expression between 0 and 48 h, and, from this subset, feature genes were selected. Small molecules associated with candoxin were identified by comparing the expression pattern of the most valid candidate genes with that of differential genes exposed to small molecules in the Connectivity Map. From the 12‑, 24‑ and 48‑h time‑points, 746, 265 and 539 differentially expressed genes were identified, respectively. A total of 129 genes were differentially expressed and significantly enriched in focal adhesion and gap junction pathways. From these, 11 feature genes and one marker gene (EPS8L1) were identified. Four small molecules that were most relevant to candoxin action were identified. In conclusion, it is hypothesized that candoxin stimulation can cause glial inflammation through mutations in cell adhesion activity. The EPS8L1 gene may be a valid marker for glioma diagnosis, and the four small molecules identified may be relevant for future drug design.

A molecular imaging primer: modalities, imaging agents, and applications

Molecular imaging is revolutionizing the way we study the inner workings of the human body, diagnose diseases, approach drug design, and assess therapies. The field as a whole is making possible the visualization of complex biochemical processes involved in normal physiology and disease states, in real time, in living cells, tissues, and intact subjects. In this review, we focus specifically on molecular imaging of intact living subjects. We provide a basic primer for those who are new to molecular imaging, and a resource for those involved in the field. We begin by describing classical molecular imaging techniques together with their key strengths and limitations, after which we introduce some of the latest emerging imaging modalities. We provide an overview of the main classes of molecular imaging agents (i.e., small molecules, peptides, aptamers, engineered proteins, and nanoparticles) and cite examples of how molecular imaging is being applied in oncology, neuroscience, cardiology, gene therapy, cell tracking, and theranostics (therapy combined with diagnostics). A step-by-step guide to answering biological and/or clinical questions using the tools of molecular imaging is also provided. We conclude by discussing the grand challenges of the field, its future directions, and enormous potential for further impacting how we approach research and medicine.

Deciphering the structure and function of FcεRI/mast cell axis in the regulation of allergy and anaphylaxis: a functional genomics paradigm

Allergy and anaphylaxis are inflammatory disorders caused by immune reactions mainly induced by immunoglobulin-E that signal through the high-affinity FcεRI receptor to release the inflammatory mediators from innate immune cells. The FcεRI/mast cell axis is potently involved in triggering various intracellular signaling molecules to induce calcium release from the internal stores, induction of transcription factors such as NF-kB, secretion of various cytokines as well as lipid mediators, and degranulation, resulting in the induction of allergy and anaphylaxis. In this review, we discuss various cellular and molecular mechanisms triggered through FcεRI/mast cell axis in allergy and anaphylaxis with a special emphasis on the functional genomics paradigm.

Transcriptome and Coexpression Network Analysis of the Human Glioma Cell Line Hs683 Exposed to Candoxin

OBJECTIVE: Gliomas are the most common primary tumours of the central nervous system. Snake venom, such as candoxin (CDX) isolated from Bungarus candidus, inhibits glioma cell proliferation. This study explored the gene regulation profile of CDX-treated human glioma Hs683 cells. METHODS: Using microarray technology and bioinformatics analyses the underlying molecular mechanism of action of CDX was evaluated by constructing gene regulation and protein—protein interaction coexpression networks. RESULTS: CDX treatment induced a large number of related genes at the transcriptional level. The MYC gene (v-myc myelocytomatosis viral oncogene homologue [avian]) had a key role in the response of Hs683 cells to CDX treatment. Activation of MYC upregulated NDRG1 (N-myc downstream regulated 1), WNT10B (wingless-type mouse mammary tumour virus integration site family, member 10B), CASP9 (caspase 9, apoptosis-related cysteine peptidase) and CDKN2A (cyclin-dependent kinase inhibitor 2A), and downregulated ID3 (inhibitor of DNA binding 3, dominant negative helix—loop—helix protein) and SLC1A4 (solute carrier family 1 [glutamate/neutral amino acid transporter], member 4). In addition, a subnetwork was constructed among SPP1 (secreted phosphoprotein 1), SDC1 (syndecan 1) and CD44 based on protein—protein interactions, and these genes were predicted to be involved in glioma cell invasion. CONCLUSION: These findings might provide novel therapeutic targets for glioma chemotherapy.

BTECH: a platform to integrate genomic, transcriptomic and epigenomic alterations in brain tumors

The identification of molecular signatures predictive of clinical behavior and outcome in brain tumors has been the focus of many studies in the recent years. Despite the wealth of data that are available in the public domain on alterations in the genome, epigenome and transcriptome of brain tumors, the underlying molecular mechanisms leading to tumor initiation and progression remain largely unknown. Unfortunately, most of these data are scattered in multiple databases and supplementary materials of publications, thus making their retrieval, evaluation, comparison and visualization a rather arduous task. Here we report the development and implementation of an open access database (BTECH), a community resource for the deposition of a wide range of molecular data derived from brain tumor studies. This comprehensive database integrates multiple datasets, including transcript profiles, epigenomic CpG methylation data, DNA copy number alterations and structural chromosomal rearrangements, tumor-associated gene lists, SNPs, genomic features concerning Alu repeats and general genomic annotations. A genome browser has also been developed that allows for the simultaneous visualization of the different datasets and the various annotated features. Besides enabling an integrative view of diverse datasets through the genome browser, we also provide links to the original references for users to have a more accurate understanding of each specific dataset. This integrated platform will facilitate uncovering interactions among genetic and epigenetic factors associated with brain tumor development. BTECH is freely available at http://cmbteg.childrensmemorial.org/.

Decoding the differential biomarkers of Rheumatoid arthritis and Osteoarthritis: A functional genomics paradigm to design disease specific therapeutics

Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease of unidentified aetiology, chiefly affecting the synovial membranes of joints, cartilage, bone, bursa and tendon sheath. Osteoarthritis (OA) is a degenerative disorder and encompass different sets of pathogenic pathways than RA; however, it shows a medley of clinical manifestations or symptoms resembling RA. Hence, we intend to identify more disease specific biomarkers through the meta-analysis of microarray datasets that can be crucial in the differential diagnosis, disease specific treatment as well as management of both RA and OA in a typical clinical setting.

Structure, function and evolution of three-finger toxins: mini proteins with multiple targets

Snake venoms are complex mixtures of pharmacologically active peptides and proteins. These protein toxins belong to a small number of superfamilies of proteins. Three-finger toxins belong to a superfamily of non-enzymatic proteins found in all families of snakes. They have a common structure of three beta-stranded loops extending from a central core containing all four conserved disulphide bonds. Despite the common scaffold, they bind to different receptors/acceptors and exhibit a wide variety of biological effects. Thus, the structure-function relationships of this group of toxins are complicated and challenging. Studies have shown that the functional sites in these 'sibling' toxins are located on various segments of the molecular surface. Targeting to a wide variety of receptors and ion channels and hence distinct functions in this group of mini proteins is achieved through a combination of accelerated rate of exchange of segments as well as point mutations in exons. In this review, we describe the structural and functional diversity, structure-function relationships and evolution of this group of snake venom toxins.

Suppressive effect of secretory phospholipase A2 inhibitory peptide on interleukin-1beta-induced matrix metalloproteinase production in rheumatoid synovial fibroblasts, and its antiarthritic activity in hTNFtg mice

INTRODUCTION

Secretory phospholipase A2 (sPLA2) and matrix metalloproteinase (MMP) inhibitors are potent modulators of inflammation with therapeutic potential, but have limited efficacy in rheumatoid arthritis (RA). The objective of this study was to understand the inhibitory mechanism of phospholipase inhibitor from python (PIP)-18 peptide in cultured synovial fibroblasts (SF), and to evaluate its therapeutic potential in a human tumor necrosis factor (hTNF)-driven transgenic mouse (Tg197) model of arthritis.

METHODS

Gene and protein expression of sPLA2-IIA, MMP-1, MMP-2, MMP-3, MMP-9, tissue inhibitor of metalloproteinase (TIMP)-1, and TIMP-2 were analyzed by real time PCR and ELISA respectively, in interleukin (IL)-1beta stimulated rheumatoid arthritis (RA) and osteoarthritis (OA) synovial fibroblasts cells treated with or without inhibitors of sPLA2 (PIP-18, LY315920) or MMPs (MMP Inhibitor II). Phosphorylation status of mitogen-activated protein kinase (MAPK) proteins was examined by cell-based ELISA. The effect of PIP-18 was compared with that of celecoxib, methotrexate, infliximab and antiflamin-2 in Tg197 mice after ip administration (thrice weekly for 5 weeks) at two doses (10, 30 mg/kg), and histologic analysis of ankle joints. Serum sPLA2 and cytokines (tumor necrosis factor (TNF)alpha, IL-6) were measured by Escherichia coli (E coli) assay and ELISA, respectively.

RESULTS

PIP-18 inhibited sPLA2-IIA production and enzymatic activity, and suppressed production of MMPs in IL-1beta-induced RA and OA SF cells. Treatment with PIP-18 blocked IL-1beta-induced p38 MAPK phosphorylation and resulted in attenuation of sPLA2-IIA and MMP mRNA transcription in RA SF cells. The disease modifying effect of PIP-18 was evidenced by significant abrogation of synovitis, cartilage degradation and bone erosion in hTNF Tg197 mice.

CONCLUSIONS

Our results demonstrate the benefit that can be gained from using sPLA2 inhibitory peptide for RA treatment, and validate PIP-18 as a potential therapeutic in a clinically relevant animal model of human arthritis.

Apoptosis-related genes change their expression with age and hearing loss in the mouse cochlea

To understand possible causative roles of apoptosis gene regulation in age-related hearing loss (presbycusis), apoptotic gene expression patterns in the CBA mouse cochlea of four different age and hearing loss groups were compared, using GeneChip and real-time (qPCR) microarrays. GeneChip transcriptional expression patterns of 318 apoptosis-related genes were analyzed. Thirty eight probes (35 genes) showed significant differences in expression. The significant gene families include Caspases, B-cell leukemia/lymphoma2 family, P53, Calpains, Mitogen activated protein kinase family, Jun oncogene, Nuclear factor of kappa light chain gene enhancer in B-cells inhibitor-related and tumor necrosis factor-related genes. The GeneChip results of 31 genes were validated using the new TaqMan Low Density Array (TLDA). Eight genes showed highly correlated results with the GeneChip data. These genes are: activating transcription factor3, B-cell leukemia/lymphoma2, Bcl2-like1, caspase4 apoptosis-related cysteine protease 4, Calpain2, dual specificity phosphatase9, tumor necrosis factor receptor superfamily member12a, and Tumor necrosis factor superfamily member13b, suggesting they may play critical roles in inner ear aging.

Viper metalloproteinase (Agkistrodon halys pallas) with antimicrobial activity against multi-drug resistant human pathogens

Metalloproteinases are abundant enzymes in crotalidae and viperidae snake venoms. Snake venom metalloproteinases (SVMPs) comprise a family of zinc-dependent enzymes, which display many different biological activities. A 23.1 kDa protein was isolated from Agkistrodon halys (pallas, Chinese viper) snake venom. The toxin is a single chain polypeptide with a molecular weight of 23146.61 and an N-terminal sequence (MIQVLLVTICLAVFPYQGSSIILES) relatively similar to that of other metalloprotein-like proteases isolated from the snake venoms of the Viperidae family. The antibacterial effect of Agkistrodon halys metalloproteinase (AHM) on Burkholderia pseudomallei (strains TES and KHW), Escherichia coli, Enterobacter aerogenes, Proteus vulgaris, Proteus mirabilis, Pseudomonas aeruginosa (Gram-negative bacteria) and Staphylococcus aureus (Gram-positive bacterium) was studied at a concentration 120 microM. Interestingly, we found that the metalloproteinase exhibited antibacterial properties and was more active against S. aureus, P. vulgaris, P. mirabilis and multi-drug resistant B. pseudomallei (strain KHW) bacteria. AHM variants with high bacteriostatic activity (MIC 1.875-60 microM) also tended to be less cytotoxic against U-937 human monocytic cells up to 1 mM concentrations. These results suggest that this metalloprotein exerts its antimicrobial effect by altering membrane packing and inhibiting mechanosensitive targets.

Cytokinin represses phosphate-starvation response through increasing of intracellular phosphate level

The involvement of cytokinins (CTKs) in the repression of phosphate (Pi)-starvation signalling has been widely documented. However, the full physiological and molecular relevance of this role remains unclear. To gain further insights into the regulation system of CTK repression of Pi-starvation signalling, a global analysis of gene expression events in rice seedlings under Pi starvation, and the exogenous CTK treatment under Pi-sufficient (+P) and Pi-deficient (-P) conditions, was conducted using oligonucleotide array analysis. Physiological and biochemical adaptation was observed after 10 d Pi starvation in rice seedlings. A global reduction of the Pi-starvation signalling was detected after 3 d treatment of exogenous CTK. Expression profiling data indicate that, together with a significant increase of intracellular Pi content, many expression changes responsive to Pi starvation were reversed by exogenous CTK treatment while CTK-responsive genes behaved normally under -P condition. These results suggest that the interplay of CTK signal and Pi-starvation response can be partially explained by the rise of Pi concentration after exogenous CTK treatment. Microarray data also revealed that a small number of genes have different CTK response patterns under different Pi levels, suggesting a subtle interaction between CTK and Pi-starvation signalling pathway.

In vitro antimicrobial activity of natural toxins and animal venoms tested against Burkholderia pseudomallei

Background

Burkholderia pseudomallei are the causative agent of melioidosis. Increasing resistance of the disease to antibiotics is a severe problem in treatment regime and has led to intensification of the search for new drugs. Antimicrobial peptides are the most ubiquitous in nature as part of the innate immune system and host defense mechanism.

Methods

Here, we investigated a group of venoms (snakes, scorpions and honey bee venoms) for antimicrobial properties against two strains of Gram-negative bacteria Burkholderia pseudomallei by using disc-diffusion assay for in vitro susceptibility testing. The antibacterial activities of the venoms were compared with that of the isolated L-amino acid oxidase (LAAO) and phospholipase A₂ (PLA₂s) enzymes. MICs were determined using broth dilution method. Bacterial growth was assessed by measurement of optical density at the lowest dilutions (MIC 0.25 mg/ml). The cell viability was measured using tetrazolium salts (XTT) based cytotoxic assay.

Results

The studied venoms showed high antimicrobial activity. The venoms of C. adamanteus, Daboia russelli russelli, A. halys, P. australis, B. candidus and P. guttata were equally as effective as Chloramphenicol and Ceftazidime (30 μg/disc). Among those tested, phospholipase A₂ enzymes (crotoxin B and daboiatoxin) showed the most potent antibacterial activity against Gram-negative (TES) bacteria. Naturally occurring venom peptides and phospholipase A₂ proved to possess highly potent antimicrobial activity against Burkholderia pseudomallei. The XTT-assay results showed that the cell survival decreased with increasing concentrations (0.05–10 mg/mL) of Crotalus adamanteus venom, with no effect on the cell viability evident at 0.5 mg/mL.

Conclusion

This antibacterial profile of snake venoms reported herein will be useful in the search for potential antibacterial agents against drug resistant microorganisms like B. pseudomallei.