Discrimination of Alternative Spliced Isoforms by Real-Time PCR Using Locked Nucleic Acid (LNA) Substituted Primer

Determination of quantitative expression levels of alternatively spliced isoforms provides an important approach to the understanding of the functional significance of each isoform. Real-time PCR using exon junction overlapping primers has been shown to allow specific detection of each isoform. However, this design often suffers from severe cross amplification of sequences with high homology at the exon junctions. We used human GFRα2b as a model to evaluate the specificity of primers substituted with locked nucleic acids (LNAs). We demonstrate here that single LNA substitutions at different positions of 3’ terminus could improve the discrimination of the primers against GFRα2a template, a highly homologous isoform. While LNA substitutions of GFRα2b primer at the residues possessing different sequences as GFRα2a has limited improvement in specificity, two consecutive LNA substitutions preceding the different sequences has dramatically improved the discrimination by greater than 100,000-fold compared to the non-substituted primer. Thus, LNA when substituted at certain residues can allow the discrimination of highly homologous sequences.Singapore-MIT Alliance (SMA

Study of GDNF-Family Receptor Alpha 2 And Inhibitory Activity of GDNF-Family Receptor Alpha 2b (GFRα2b) Isoform

The glial cell-line derived neurotrophic factor (GDNF) and neurturin (NTN) belong to a structurally related family of neurotrophic factors. NTN exerts its effect through a multi-component receptor system consisting of the GDNF family receptor alpha 2 (GFRα2), proto-oncogene RET and/or NCAM. GFRα2 is spliced into at least three isoforms, GFRα2a, GFRα2b and GFRα2c. The present study investigated the expression and functional differences of GFRα2 isoforms. These receptor isoforms are differentially expressed in specific human brain regions. Using Neuro2A model, GDNF and NTN promote neurite outgrowth via GFRα2a and GFRα2c, but not GFRα2b. These GFRα2 isoforms regulate different early response genes when stimulated with GDNF and NTN. Interestingly, using co-expression models, GFRα2b inhibits ligand induced neurites outgrowth of GFRα2a and GFRα2c, and also the related receptor, GFRα1a. More intriguingly, ligands activated GFRα2b was also able to attenuate neurite extension induced by an unrelated stimulation using retinoic acid. MAPK activation induced by GDNF was not attenuated by GFRα2b in a co-expression model, while the early response genes expression profile (up-regulation of FosB) was similar to that induced by GFRα2b alone. This study suggest that GFRα2b is not merely a dominant negative isoform, but signals through a yet to be determined mechanism to antagonize and inhibit neuritogenesis. Together, these data suggest a new paradigm for the regulation of growth factor signaling and neurite outgrowth via an inhibitory splice variant of the receptor.Singapore-MIT Alliance (SMA

Site-directed mutagenesis of structural hot spots for enhanced solubility of deoxyxylulose phosphate pathway enzymes

Increasing the metabolic flux through a biochemical pathway is highly desirable for metabolic engineering. One strategy is to enhance the solubility of overexpressed pace-making enzymes. Accurate theoretical prediction of target mutation sites is instrumental to reduce the experimental efforts and speed up the optimization process. In this study, the rate-limiting steps along the non-mevalonate (DXP) pathway, namely E. coli Dxs and IspG, were used as the model enzymes to learn and develop a set of bioinformatics tools that would enable rational optimization of enzyme solubility. TANGO prediction was first used to identify the aggregation-prone regions (APRs), and then SIFT analysis was carried out to eliminate the non-tolerable amino acids in the APRs. Preliminary results have shown that 5 out of 8 tested mutations have resulted in an increase in Dxs solubility. Similarly, 7 out of 12 IspG mutants have displayed enhanced solubility. Importantly, the in vivo activities of the more soluble mutants were improved. Taken together, the solubility of both Dxs and IspG were enhanced by ~2-fold, by targeted single amino acid mutation. The study demonstrated rapid improvement of enzyme solubility by combinations of computational tools. The information gained would be useful for rational engineering of over-expressed pathway enzymes and improve pathway efficiencies

Single Stranded DNA Induced Assembly of Gold Nanoparticles

The binding affinity of single stranded DNA (ssDNA) for gold nanoparticle surface is studied in this work. The data indicate that the strength of interaction between ssDNA and Au particle surface is closely related to the particle size, with smaller particles (5 nm) producing the most pronounced effects. From these experimental findings, a single stranded DNA (ssDNA) based method to assimilate 13 and 5 nm gold nanoparticles was developed, and verified by transmission electron microscopy (TEM).Singapore-MIT Alliance (SMA

Multivariate Perturbation of a Growth Factor-Cytokine Signalling Network Reveals Complex Systemic Responses in Glioblastoma Cells

Glioblastoma cells can evade TRAIL-induced apoptosis through various strategies involving the growth factor-activated MEK–MAPK/ERK and PI3K–Akt/PKB pro-survival signalling cascades. Although these signalling cascades have been studied extensively, our understanding of how they interact and participate in modulating apoptosis as part of a dynamic cell-wide network of signalling proteins is limited by traditional univariate experimental paradigms. Here, we study three human glioblastoma cell lines with differential response to TRAIL-induced apoptosis: LN229 (resistant), T98G, and A172 (both susceptible). We show that differential TRAIL susceptibility in these cell lines is unrelated to expression levels of agonist (DR4 and DR5) or antagonist (DcR1, DcR2, and OPG) receptors for TRAIL and thus TRAIL-induced apoptosis in these cell lines is modulated at the intracellular signalling level. Serum, comprising multiple factors that regulate cellular activity, enhances TRAIL resistance in T98G but not LN229 and A172 cell lines. This protective effect against TRAIL-induced apoptosis is recapitulated by the prototypical survival factor PDGF in T98G cells. Univariate inhibition of cell survival signalling cascades with MEK inhibitor U0126 and PI3K inhibitor LY294002 sensitized T98G cells to TRAIL but did not abrogate PDGF-mediated protection. However, further perturbation with inhibitors in a combinatorial and multivariate manner reveal synergistic effects and complex systemic responses which may be a basis for uncovering novel insights into the regulation of TRAIL-induced apoptosis.Singapore-MIT Alliance (SMA

Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells

<p>Abstract</p> <p>Background</p> <p>Gene regulation at transcript level can provide a good indication of the complex signaling mechanisms underlying physiological and pathological processes. Transcriptomic methods such as microarray and quantitative real-time PCR require stable reference genes for accurate normalization of gene expression. Some but not all studies have shown that housekeeping genes (HGKs), β-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which are routinely used for normalization, may vary significantly depending on the cell/tissue type and experimental conditions. It is currently unclear if these genes are stably expressed in cells undergoing drastic morphological changes during neuronal differentiation. Recent meta-analysis of microarray datasets showed that some but not all of the ribosomal protein genes are stably expressed. To test the hypothesis that some ribosomal protein genes can serve as reference genes for neuronal differentiation, a genome-wide analysis was performed and putative reference genes were identified based on stability of expressions. The stabilities of these potential reference genes were then analyzed by reverse transcription quantitative real-time PCR in six differentiation conditions.</p> <p>Results</p> <p>Twenty stably expressed genes, including thirteen ribosomal protein genes, were selected from microarray analysis of the gene expression profiles of GDNF and NGF induced differentiation of PC12 cells. The expression levels of these candidate genes as well as ACTB and GAPDH were further analyzed by reverse transcription quantitative real-time PCR in PC12 cells differentiated with a variety of stimuli including NGF, GDNF, Forskolin, KCl and ROCK inhibitor, Y27632. The performances of these candidate genes as stable reference genes were evaluated with two independent statistical approaches, geNorm and NormFinder.</p> <p>Conclusions</p> <p>The ribosomal protein genes, RPL19 and RPL29, were identified as suitable reference genes during neuronal differentiation of PC12 cells, regardless of the type of differentiation conditions. The combination of these two novel reference genes, but not the commonly used HKG, GAPDH, allows robust and accurate normalization of differentially expressed genes during PC12 differentiation.</p

Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production

Artemisinin is a potent antimalarial drug; however, it suffers from unstable and insufficient supply from plant source. Here, we established a novel multivariate-modular approach based on experimental design for systematic pathway optimization that succeeded in improving the production of amorphadiene (AD), the precursor of artemisinin, in Escherichia coli. It was initially found that the AD production was limited by the imbalance of glyceraldehyde 3-phosphate (GAP) and pyruvate (PYR), the two precursors of the 1-deoxy-d-xylulose-5-phosphate (DXP) pathway. Furthermore, it was identified that GAP and PYR could be balanced by replacing the phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) with the ATP-dependent galactose permease and glucose kinase system (GGS) and this resulted in fivefold increase in AD titer (11 to 60 mg/L). Subsequently, the experimental design-aided systematic pathway optimization (EDASPO) method was applied to systematically optimize the transcriptional expressions of eight critical genes in the glucose uptake and the DXP and AD synthesis pathways. These genes were classified into four modules and simultaneously controlled by T7 promoter or its variants. A regression model was generated using the four-module experimental data and predicted the optimal expression ratios among these modules, resulting in another threefold increase in AD titer (60 to 201 mg/L). This EDASPO method may be useful for the optimization of other pathways and products beyond the scope of this study.Singapore-MIT Alliance for Research and Technology (SMART

Profiling of ligand-receptor induced signalling- a novel protein chip technique

Cellular signalling pathways are the master controls of the biology of the cell, which includes cell communication, growth, death, and differentiation. The activities of these signalling proteins directly influence gene function by regulation of the signalling pathways that mediate cellular responses. Recent advanced techniques have given rise to a number of emerging tools for the analysis of cellular signalling that profile the proteome or the protein complement of the genome. However, these tools for signal profiling still face significant challenges such as sensitivity, specificity and be a high throughput method before they are widely adopted. Sensitivity issues are paramount in detecting signalling proteins that are normally in low amounts. Conventional protein chip technology promises to be a powerful tool for large scale high-throughput proteome profiling but there are still significant drawbacks. Here we report the development and application of a novel multiplexed and high-throughput platform for the quantitative profiling of activated intracellular sig nalling proteins subsequent to ligand-receptor induced signalling. This spatially addressable biochip platform will allow comprehensive mapping of interconnected signal pathways, through identification of key functional signalling proteins (ânodes’) in each pathway and quantifying their state of activity.Singapore-MIT Alliance (SMA

Correlating Gene Transfection Efficiency and the Physical Properties of Various Cationic Poly(methacrylate) Systems

Transfection efficiencies of several polymeric gene carriers were compared and correlated quantitatively to the amounts of cellular accumulation of plasmid DNA and to the expression of mRNA by quantitative real time PCR. Three cationic methacrylate polymer systems with similar chemical structure were used in this study, namely: poly(dimethylamino)ethyl methacrylate (PDMA) homopolymer, PEO-b-PDMA copolymer and PEO-b-poly(diethylamino)ethyl methacrylate (PEO-b-PDEA) copolymer. Despite their similar chemical structures, their transfection efficiencies were significantly different. PEO-b-PDEA copolymer was significantly less efficient as gene carrier compared to both PDMA and PEO-b-PDMA systems. Results from quantitative real-time polymerase chain reaction (real-time PCR), cytotoxicity and Zeta potential measurements showed correlations between the physical properties of the polymers and the efficiencies of cellular uptake of the transgene and transfections. In the case of PEO-b-PDEA system, cytotoxicity was due primarily to the excess polymers that did not participate in the DNA binding. In addition, the inability of the polymer/DNA complexes to interact with cell effectively was identified as the main barrier for high efficiency of transfection. This study demonstrated that the use of quantitative real-time PCR in combination with other physical characterization techniques can provide greater insights into the transfection barrier at different cellular levels.Singapore-MIT Alliance (SMA

SCAPA (Spacially Addressable Protein Array) – a Novel Protein Array for the Differential Profiling of Ligand-receptor Induced Signalling

While protein microarray technology has been successful in demonstrating its usefulness for large scale high-throughput proteome profiling, performance of antibody/antigen microarrays has been only moderately productive. Immobilization of either the capture antibodies or the protein samples on solid supports has severe drawbacks. Denaturation of the immobilized proteins as well as inconsistent orientation of antibodies/ligands on the arrays can lead to erroneous results. This has prompted a number of studies to address these challenges by immobilizing proteins on biocompatible surfaces, which has met with limited success. Our strategy relates to a multiplexed, sensitive and high-throughput method for the screening quantification of intracellular signalling proteins from a complex mixture of proteins. Each signalling protein to be monitored has its capture moiety linked to a specific oligo âtag’. The array involves the oligonucleotide hybridization-directed localization and identification of different signalling proteins simultaneously, in a rapid and easy manner. Antibodies have been used as the capture moieties for specific identification of each signaling protein. The method involves covalently partnering each antibody/protein molecule with a unique DNA or DNA derivatives oligonucleotide tag that directs the antibody to a unique site on the microarray due to specific hybridization with a complementary tag-probe on the array. Particular surface modifications and optimal conditions allowed high signal to noise ratio which is essential to the success of this approach.Singapore-MIT Alliance (SMA