Combinatorial Chemistry & High
Throughput Screening, Vol. 7, No. 3, 2004
Contents
Molecular Diversity on a
Chip
Guest Editor: Edson Lima
Clinical
Impact of Gene Expression Profiling on Oncology Diagnosis, Prognosis, and
Treatment Pp.183-206
DNA
Microarrays as a Tool in Toxicogenomics Pp.207-211
F.
de Longueville, V. Bertholet and J. Remacle
Strategies
for Immobilization of Biomolecules in a Microarray Pp.213-221
Dawn
S.Y. Yeo, Resmi C. Panicker, Lay-Pheng Tan and Shao Q. Yao
Protein
Microarrays and Multiplexed Sandwich Immunoassays:What Beats the Beads? Pp.223-229
Markus
F. Templin, Dieter Stoll, Jutta Bachmann and Thomas O. Joos
Making
Sense of Molecular Signatures in The Immune System Pp.231-238
Nicholas
J. Davies, Mahlet G.T. Tadesse, Marina Vannucci, Hugh Kikuchi, VictorTrevino,
Donatella Sarti, Ilaria Dragoni, Andrea Contestabile, Edward Zanders and
Francesco Falciani
Anti-Endotoxin
Agents. 1. Development of a Fluorescent Probe Displacement Method Optimized for
the Rapid Identification of Lipopolysaccharide-Binding Agents Pp.239-249
Stewart
J. Wood, Kelly A. Miller and Sunil A. David
Combinatorial
Synthesis of Biheterocyclic Benzimidazoles by Microwave Irradiation Pp.251-255
Wen-Bing
Yeh, Mei-Jung Lin and Chung-Ming Sun
Abstracts
[Back to top] Clinical
Impact of Gene Expression Profiling on Oncology Diagnosis, Prognosis, and
Treatment
Annette
S. Kim
Genomics has enabled the examination of the totality of disease at the transcriptome level. Dependent upon a myriad of genetic aberrations for its pathogenesis, cancer has been the focus of gene expression profiling studies that have highlighted the potential clinical applications of this technology. This type of molecular profiling has the potential to enhance the ability of pathologists and oncologists to correctly classify tumors, not just into existing subgroups which may or may not have clear prognostic implications, but into new groups which carry predictable correlations with outcomes. Ultimately, these outcome predictions can be tied to specific treatment regimens, allowing clinicians to predict at the time of diagnosis to which therapy a given patient may best respond. Although this ultimate goal of personalized therapy remains in the future, the numerous studies to date have clearly demonstrated the overall feasibility of this approach. This review will showcase a few of these studies in several key tumor types with the goal of demonstrating which type of studies have been conducted and what types of results are currently possible.
[Back to top] DNA Microarrays as a Tool in
Toxicogenomics
F.
de Longueville, V. Bertholet and J. Remacle
Toxicogenomics is an emerging technology that defines the use of novel genomic techniques to investigate the adverse effects of xenobiotic on gene expression. Toxicogenomics is based on the fact that most of relevant toxicological effects of a compound affect directly or indirectly the gene expression. The most common methods to profile gene expression at the transcript level are Northern Blotting and the real-time PCR. While commonly used and well accepted, these techniques are now superseded by new technologies allowing the analysis of the expression for multiple genes simultaneously. DNA microarrays are now developed for simultaneous gene analysis but inherent to such multiple assays, their quantitative aspect and their relevance for toxicogenomics have been questioned. We will review here recent studies on their use for toxicogenomics and examine the possible future of such technology in complementation with the other toxicology methods.
[Back to top] Strategies
for Immobilization of Biomolecules in a Microarray
Dawn
S.Y. Yeo, Resmi C. Panicker, Lay-Pheng Tan and Shao Q. Yao
Recent advances in the generation of peptide and protein microarrays are reviewed, with special focuses on different strategies available for site-specific immobilization of proteins and peptides.
[Back to top] Protein Microarrays and Multiplexed Sandwich Immunoassays:What Beats the
Beads?
Markus F. Templin, Dieter Stoll, Jutta Bachmann and Thomas O. Joos
Protein microarray technology allows the simultaneous determination of a large variety of parameters from a minute amount of sample within a single experiment. Assay systems based on this technology are currently applied for the identification, quantitation and functional analysis of proteins. Protein microarray technology is of major interest for proteomic research in basic and applied biology as well as for diagnostic applications. Miniaturized and parallelized assay systems have reached adequate sensitivity and hence have the potential to replace singleplex analysis systems. However, robustness and automation needs to be demonstrated before this technology will finally prove suitable for high-throughput applications. Miniaturized and parallelized sandwich immunoassays are the most advanced assays formats among the different protein microarray applications. Multiplexed sandwich immunoassays can be used for the identification of biomarkers and the validation of potential target molecules. In this review an overview will be given on the current stage of protein microarray technology with a special focus on miniaturized multiplexed sandwich immunoassays.
[Back to top] Making Sense of Molecular Signatures in The Immune System
Nicholas J. Davies, Mahlet G.T. Tadesse, Marina Vannucci, Hugh Kikuchi, VictorTrevino, Donatella Sarti, Ilaria Dragoni, Andrea Contestabile, Edward Zanders and Francesco Falciani
The development of Functional Genomics technologies has opened new avenues to investigate the complexity of the immune system. Microarray technology has been particularly successful because of its relatively low cost and high genome coverage.
Consequently to our ability to monitor the expression of a significant proportion of an organism genome, our understanding of the molecular dynamics behind cell differentiation and cell response has greatly improved. Molecular signatures associated to immune cells have provided important tools to investigate the molecular basis of diseases and have been often associated to diagnostic and prognostic markers. The availability of such large collection of data has stimulated the application of complex machine learning techniques in the attempt to link molecular signatures and cell physiology. Here we review the most recent developments in the analysis of molecular signatures in the immune system.
[Back to top] Anti-Endotoxin Agents. 1. Development of a Fluorescent Probe
Displacement Method Optimized for the Rapid Identification of
Lipopolysaccharide-Binding Agents
Stewart J. Wood, Kelly A. Miller and Sunil A. David
Lipopolysaccharides (LPS),
otherwise termed ‘endotoxins’, are outer-membrane constituents of Gram-negative
bacteria. Lipopolysaccharides play a key role in the pathogenesis of ‘Septic
Shock’, a major cause of mortality in the critically ill patient. Therapeutic
options aimed at limiting downstream systemic inflammatory processes by
targeting lipopolysaccharide do not exist at the present time. We have defined
the pharmacophore necessary for small molecules to specifically bind and
neutralize LPS, and have shown using animal models of sepsis that the
sequestration of circulatory LPS by small molecules is a therapeutically viable
strategy. Assays reported previously in the literature do not lend themselves
well to the rapid screening of large numbers of structurally diverse compounds.
In this report, we describe a highly sensitive and robust fluorescent
displacement assay using BODIPY TR cadaverine (BC), which binds specifically to
the toxic center of LPS, lipid A, and is competitively displaced by compounds
displaying an affinity for lipid A. The assay clearly discriminates subtle
differences in the binding of polymyxin B, and its nonapeptide derivative, with
LPS. The spectral properties of the BODIPY fluorophore are ideally suited for
screening diverse structural classes of compounds, including those with
conjugated aromatic groups, or with chromophores in the 260-500 nm range. The
fluorescent probe: LPS complex is stable under physiologically relevant salt
concentrations, resulting in the rapid rejection of spurious binders
interacting via non-specific electrostatic interactions, and, therefore,
in greatly improved dispersion of ED50 values.
[Back to top] Combinatorial Synthesis of Biheterocyclic Benzimidazoles by
Microwave Irradiation
Wen-Bing Yeh, Mei-Jung Lin and Chung-Ming Sun
Liquid phasel synthesis of biheterocyclic benzimidazoles by controlled microwave irradiation was investigated. Polymer immobilized o-phenylenediamines was synthesized under microwave irradiation. The resulting PEG bound diamines was N-acylated with 4-fluoro-3-nitrobenzoic acid selectively in primary aromatic amino moiety. Nucleophilic aromatic substitution of amide was performed with various amines then cyclized to form the first benzimidazole scaffold in acidic condition. Successive reduction, cyclization with isothiocyanates yielded 5-(benzimidazol-2-yl)benzimidazoles. The desired products were released from the polymer support to afford the tri-substituted bis-benzimidazoles in good yields and purity.