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Technological developments such as microarray-based DNA, RNA and protein detection have opened new fields in genomics and proteomics. This review aims to highlight the potential value and limitation of this methodology to design and extract signature-based diagnostic markers for infectious disease.
Proteins affected by anti-mIgM stimulation during B-cell maturation were identified using 2-DE-based proteomics. We investigated the proteome profiles of stimulated and nonstimulated Ramos B-cells at eight time points during 5 d and compared the obtained proteomic data to the corresponding data from DNA-microarray studies. Anti-mIgM stimulation of the cells resulted in significant differences (> or =twofold) in the protein abundance close to 100 proteins and differences in post-translational protein modifications. Forty-eight up- or down-regulated proteins were identified by mass spectrometric methods and database searches. The identities of a further nine proteins were revealed by comparing their positions to the known proteins in other lymphocyte 2-DE databases. Several of the proteins are directly related to the functional and morphological characteristics of B-cells, such as cytoskeleton rearrangement and intracellular signalling triggered by the crosslinking of B-cell receptors. In addition to proteins known to be involved in human B-cell maturation, we identified several proteins that were not previously linked to lymphocyte differentiation. The results provide deeper insights into the process of B-cell maturation and may lead to novel therapeutic strategies for immunodeficiencies. An interactive 2-DE reference map is available at http://bioinf.uta.fi/BcellProteome.
Mice with a fat-specific insulin receptor knock-out (FIRKO) exhibit a polarization of white adipose tissue into two populations of cells, one small (diameter <50 microm) and one large (diameter >100 microm), accompanied by changes in insulin-stimulated glucose uptake, triglyceride synthesis, and lipolysis. To characterize these subclasses of adipocytes, we have used a proteomics approach in which isolated adipocytes from FIRKO and control (IR lox/lox) mice were separated by size, fractionated into cytosolic and membrane subfractions, and analyzed by sucrose gradient, SDS-PAGE, and mass spectrometry. A total of 27 alterations in protein expression at key steps in lipid and energy metabolism could be defined, which were coordinately regulated by adipocyte cell size, impaired insulin signaling, or both. Nine proteins, including vimentin, EH-domain-containing protein 2, elongation factor 2, glucose-regulated protein 78, transketolase, and succinyl-CoA transferase were primarily affected by presence or absence of insulin signaling, whereas 21 proteins, including myosin non-muscle form A, annexin 2, annexin A6, and Hsp47 were regulated in relation to adipocyte size. Of these 27 alterations in protein expression, 14 changes correlated with altered levels of mRNA, whereas the remaining 13 were the result of changes in protein translation or turnover. These data suggest an intrinsic heterogeneity in adipocytes with differences in protein expression patterns caused by transcriptional and post-transcriptional alterations related to insulin action and cellular lipid accumulation.
Aptamers are nucleic acid species that are selected in vitro for their specific binding properties. We describe methods for the production and processing of aptamer microarrays, including detailed procedures for the high-throughput, enzymatic synthesis of 5' RNA biotinylated aptamers and for arraying them onto streptavidin-coated glass slides. Also presented are methods for processing the aptamer microarrays, including blocking, washing, drying, and scanning. Examples are shown for the specific capture of fluorescently labeled target proteins either alone in binding buffer or in competition with labeled intracellular proteins from cell lysates. Consideration is given to the challenges involved in producing multiplex aptamer chips composed of aptamers taken from disparate literature sources, and to the development of standardized methods for characterizing the performance of capture reagents used in biosensors.
A credit to microarray technology is its broad application. Two experiments--the tiling microarray experiment and the protein microarray experiment--are exemplars of the versatility of the microarrays. With the technology's expanding list of uses, the corresponding bioinformatics must evolve in step. There currently exists a rich literature developing statistical techniques for analyzing traditional gene-centric DNA microarrays, so the first challenge in analyzing the advanced technologies is to identify which of the existing statistical protocols are relevant and where and when revised methods are needed. A second challenge is making these often very technical ideas accessible to the broader microarray community. The aim of this chapter is to present some of the most widely used statistical techniques for normalizing and scoring traditional microarray data and indicate their potential utility for analyzing the newer protein and tiling microarray experiments. In so doing, we will assume little or no prior training in statistics of the reader. Areas covered include background correction, intensity normalization, spatial normalization, and the testing of statistical significance.
To better understand the molecular mechanisms governing oligodendrocyte (OL) differentiation, we have used gene profiling to quantitatively analyze gene expression in synchronously differentiating OLs generated from pure oligodendrocyte precursor cells in vitro. By comparing gene expression in these OLs to OLs generated in vivo, we discovered that the program of OL differentiation can progress normally in the absence of heterologous cell-cell interactions. In addition, we found that OL differentiation was unexpectedly prolonged and occurred in at least two sequential stages, each characterized by changes in distinct complements of transcription factors and myelin proteins. By disrupting the normal dynamic expression patterns of transcription factors regulated during OL differentiation, we demonstrated that these sequential stages of gene expression can be independently controlled. We also uncovered several genes previously uncharacterized in OLs that encode transmembrane, secreted, and cytoskeletal proteins that are as highly upregulated as myelin genes during OL differentiation. Last, by comparing genomic loci associated with inherited increased risk of multiple sclerosis (MS) to genes regulated during OL differentiation, we identified several new positional candidate genes that may contribute to MS susceptibility. These findings reveal a previously unexpected complexity to OL differentiation and suggest that an intrinsic program governs successive phases of OL differentiation as these cells extend and align their processes, ensheathe, and ultimately myelinate axons.
Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.
Previous work from this laboratory has shown that amiodarone induces alveolar epithelial cell apoptosis that was abrogated by antagonists of angiotensin II. In this study, amiodarone up-regulated angiotensinogen mRNA and protein in primary cultures of rat type II pneumocytes and in the human A549 cell line. The mechanism of amiodarone-induced angiotensinogen expression was studied in A549 cells with a human angiotensinogen promoter-luciferase reporter (angiotensinogen/luciferase). Amiodarone (3 microg/ml) induced both angiotensinogen/luciferase and endogenous angiotensinogen mRNA; the latter was completely blocked by actinomycin-D. Amiodarone did not affect the half-life of endogenous angiotensinogen mRNA. Deletion analyses of angiotensinogen/luciferase identified at least two amiodarone-responsive domains in the angiotensinogen promoter between -350 to -260 bp and -203 to -46 bp. DNA/Protein array and electrophoretic mobility shift assays showed that amiodarone increases DNA binding of both activation protein-1 and STAT-5 transcription factors. Site-directed mutagenesis of three IL-6-responsive signal transducer activator of transcription (STAT) binding sites within the amiodarone-response domains had no effect on amiodarone-induced angiotensinogen/luciferase expression. In contrast, amiodarone-induced angiotensinogen/luciferase expression was abrogated by a dominant-negative fos construct and was stimulated over five times by c-fos and c-jun expressed together but not separately. Mutagenesis of the activation protein-1 binding site at -15 to -12 bp completely eliminated the response to amiodarone. These data show that activation protein-1 family transcription factors mediate amiodarone-induced angiotensinogen expression in human alveolar epithelial cells and identify an activation protein-1 site, located between the TATA (DNA sequence) box and the transcription initiation site, that is required for the response.
Recent advances in DNA and protein microarray methodology and the emerging technology of cell-based sensors have massively increased the speed and sensitivity with which we can detect viral infections. The advantages of the multi-parameter microarray technologies could be combined with the speed and sensitivity of cell-based systems to give 'cell-omic' sensors.
Technological advances in miniaturization have found a niche in biology and signal the beginning of a new revolution. Most of the attention and advances have been made with DNA chips yet a lot of progress is being made in the use of other biomolecules and cells. A variety of reviews have covered only different aspects and technologies but leading to the shared terminology of "biochips." This review provides a basic introduction and an in-depth survey of the different technologies and applications involving the use of non-DNA molecules such as proteins and cells. The review focuses on microarrays and microfluidics, but also describes some cellular systems (studies involving patterning and sensor chips) and nanotechnology. The principles of each technology including parameters involved in biochip design and operation are outlined. A discussion of the different biological and biomedical applications illustrates the significance of biochips in biotechnology.
Semisynthetic DNA-protein conjugates are synthesized by covalent coupling of thiol-modified DNA oligonucleotides and streptavidin. The resulting conjugates have a binding capacity for four equivalents of biotin and one nucleic acid of complementary sequence. The conjugates are purified to homogeneity by ultrafiltration and chromatography and characterized by photometry and gel electrophoresis. Subsequently, the conjugates are applied as molecular linkers in the DNA-directed immobilization of a biotinylated enzyme on a microplate, containing complementary capture oligonucleotides.
Chicken metallothionein (ckMT) is the paradigm for the study of metallothioneins (MTs) in the Aves class of vertebrates. Available literature data depict ckMT as a one-copy gene, encoding an MT protein highly similar to mammalian MT1. In contrast, the MT system in mammals consists of a four-member family exhibiting functional differentiation. This scenario prompted us to analyse the apparently distinct evolutionary patterns followed by MTs in birds and mammals, at both the functional and structural levels. Thus, in this work, the ckMT metal binding abilities towards Zn(II), Cd(II) and Cu(I) have been thoroughly revisited and then compared with those of the mammalian MT1 and MT4 isoforms, identified as zinc- and copper-thioneins, respectively. Interestingly, a new mechanism of MT dimerization is reported, on the basis of the coordinating capacity of the ckMT C-terminal histidine. Furthermore, an evolutionary study has been performed by means of in silico analyses of avian MT genes and proteins. The joint consideration of the functional and genomic data obtained questions the two features until now defining the avian MT system. Overall, in vivo and in vitro metal-binding results reveal that the Zn(II), Cd(II) and Cu(I) binding abilities of ckMT lay between those of mammalian MT1 and MT4, being closer to those of MT1 for the divalent metal ions but more similar to those of MT4 for Cu(I). This is consistent with a strong functional constraint operating on low-copy number genes that must cope with differentiating functional limitation. Finally, a second MT gene has been identified in silico in the chicken genome, ckMT2, exhibiting all the features to be considered an active coding region. The results presented here allow a new insight into the metal binding abilities of warm blooded vertebrate MTs and their evolutionary relationships.
This review examines the role of advances in biochip and microarray technologies in the development of personalized medicine. Biochips (eg, GeneChip, CYP450, electrochemical biochips, protein biochips, microfluidic biochips and nanotechnology-based biochips) are assuming an important role in molecular diagnostics, and their application in point-of-care diagnosis is expected to facilitate the development of personalized medicine. Gene expression profiling by microarrays should advance the progress of personalized cancer treatment based on the molecular classification of subtypes. Refinements in biochip miniaturization with the advent of nanotechnology will further contribute to molecular diagnostics and the development of personalized medicine.
Fluorescent-labeled molecules have been used extensively for a wide range of applications in biological detection and diagnosis. A new form of highly luminescent and photostable nanoparticles was generated by doping the fluorescent dye tris(2'2-bipyridyl)dichlororuthenium(II)hexahydrate (Rubpy) inside silica material. Because thousands of fluorescent dye molecules are encapsulated in the silica matrix that also serves to protect Rubpy dye from photodamaging oxidation, the Rubpy-dye-doped nanoparticles are extremely bright and photostable. We have used these nanoparticles successfully in various fluorescence labeling techniques, including fluorescent-linked immunosorbent assay, immunocytochemistry, immunohistochemistry, DNA microarray, and protein microarray. By combining the high-intensity luminescent nanoparticles with the specificity of antibody-mediated recognition, ultrasensitive target detection has been achieved. In all cases, assay results clearly demonstrated the superiority of the nanoparticles over organic fluorescent dye molecules and quantum dots in probe labeling for sensitive target detection. These results demonstrate the potential to apply these newly developed fluorescent nanoparticles in various biodetection systems.
Long-term arsenic exposure is associated with an increased risk of vascular diseases including ischemic heart disease, cerebrovascular disease, and carotid atherosclerosis. The pathogenic mechanisms of arsenic atherogenicity are not completely clear. A fundamental role for inflammation in atherosclerosis and its complications has become appreciated recently. To investigate molecular targets of inflammatory pathway possibly involved in arsenic-associated atherosclerosis, we conducted an exploratory study using cDNA microarray and enzyme-linked immunosorbent assay to identify genes with differential expression in arsenic-exposed yet apparently healthy individuals. As an initial experiment, array hybridization was performed with mRNA isolated from activated lymphocytes of 24 study subjects with low (0-4.32 microg/L), intermediate (4.64-9.00 microg/L), and high (9.60-46.5 microg/L) levels of blood arsenic, with each group comprising eight age-, sex-, and smoking frequency-matched individuals. A total of 708 transcripts of known human genes were analyzed, and 62 transcripts (8.8%) showed significant differences in the intermediate or high-arsenic groups compared with the low-level arsenic group. Among the significantly altered genes, several cytokines and growth factors involving inflammation, including interleukin-1 beta, interleukin-6, chemokine C-C motif ligand 2/monocyte chemotactic protein-1 (CCL2/MCP1), chemokine C-X-C motif ligand 1/growth-related oncogene alpha, chemokine C-X-C motif ligand 2/growth-related oncogene beta, CD14 antigen, and matrix metalloproteinase 1 (interstitial collagenase) were upregulated in persons with increased arsenic exposure. Multivariate analyses on 64 study subjects of varying arsenic exposure levels showed that the association of CCL2/MCP1 plasma protein level with blood arsenic remained significant after adjustment for other risk factors of cardiovascular diseases. The results of this gene expression study indicate that the expression of inflammatory molecules may be increased in human subjects after prolonged exposure to arsenic, which might be a contributory factor to the high risk of atherosclerosis in arseniasis-endemic areas in Taiwan. Further multidisciplinary studies, including molecular epidemiologic investigations, are needed to elucidate the role of arsenic-associated inflammation in the development of atherosclerosis and subsequent cardiovascular disease.
Individual genetic findings associated with complex diseases are unlikely to fully explain their substantial impact or provide new comprehensive insights into disease pathogenesis. These also lack the comprehensive data much needed for development of new effective drugs in majority of the disease cases in a population. In fact multilevel etiologic factors underlie almost all human diseases, including: environmental causes, epigenetic factors, DNA mutations, amplifications, and deletions, RNA expression levels, protein (translation, post translation modification, localization) and combinations thereof. Each individual might consist of different combinations of these multiple etiologic factors. Integrative evaluation of all these modifications will shed light on the whole identity of the disease and the underlying molecular mechanisms. Until now it was inconceivable to have a full grasp of such a complex etiology. Microarrays enable us to interrogate the individualized various factors (DNA, RNA and protein content) involved in disease state on genome-wide scale simultaneously and expeditiously in single cell or the tissue of interest (Figure 1). The new disciplines of microarray studies in combination hold the promise of effective, current, and comprehensive understanding of complex diseases and may be a good approach for reducing the costs and time lines associated with discovery and efficacy improvement of therapeutic drugs. In the future, through utilizing the colossal amount of microarray data findings, defining the structure, function, and dynamics of entire biological pathways and cellular networks under various physiological states, and the development of robust and efficient methods for analyzing and interpreting high dimensional data, it will be possible to connect combination of experimental results with individualized disease state. This will facilitate precise diagnosis prognosis and therapy.
A multiplexed assay based on the codetection of nucleic acids and antibodies in human serum infected by human immunodeficiency virus (HIV), hepatitis B virus (HBV) or hepatitis C virus was proposed. The combined immuno- and oligosorbent array (CombOLISA) microarray is prepared in 96-well standard microplates by spotting (1). nucleic probes specific for a virus genome, (2). viral proteins for the capture of serum antibodies, and (3). nonspecific proteins for verifying specificity. Experimental assay conditions were optimized so that both DNA hybridization and immunological reactions can be achieved simultaneously in the same well and buffer and all at the same temperature. A generic detection system based on the precipitation of an insoluble colorimetric substrate in the presence of enzyme-labeled antibodies or streptavidin was proposed. The optical density of each spot was correlated to the corresponding analyte concentration. The influence of critical parameters on CombOLISA performance such as serum concentration was studied. Calibration curves and sensitivity thresholds were established for each parameter. Serial dilutions of serum were correlated to results obtained with validated immunoassay platforms such as a microplate enzyme-linked immunosorbent assay or the VIDAS automat. Also, several HIV- and HBV-infected serum samples were tested independently by CombOLISA and VIDAS. Coefficients of variation for genomic and proteomic parameters vs spot density were below 15%.
Iron is limiting in the human host, and bacterial pathogens respond to this environment by activating genes required for bacterial virulence. Transcriptional regulation in response to iron in Gram-negative bacteria is largely mediated by the ferric uptake regulator protein Fur, which in the presence of iron binds to a specific sequence in the promoter regions of genes under its control and acts as a repressor. Here we describe DNA microarray, computational and in vitro studies to define the Fur regulon in the human pathogen Neisseria meningitidis group B (strain MC58). After iron addition to an iron-depleted bacterial culture, 153 genes were up-regulated and 80 were down-regulated. Only 50% of the iron-regulated genes were found to contain Fur-binding consensus sequences in their promoter regions. Forty-two promoter regions were amplified and 32 of these were shown to bind Fur by gel-shift analysis. Among these genes, many of which had never been described before to be Fur-regulated, 10 were up-regulated on iron addition, demonstrating that Fur can also act as a transcriptional activator. Sequence alignment of the Fur-binding regions revealed that the N. meningitidis Fur-box encompasses the highly conserved (NATWAT)3 motif. Cluster analysis was effective in predicting Fur-regulated genes even if computer prediction failed to identify Fur-box-like sequences in their promoter regions. Microarray-generated gene expression profiling appears to be a very effective approach to define new regulons and regulatory pathways in pathogenic bacteria.