Expression profiling: DNA arrays in many guises

DNA arrays have become the preferred method for large-scale expression measurement. Such data are needed in view of the large amounts of sequence data available: expression levels in a number of different tissues or situations provide a first step toward functional characterisation of new entities revealed by DNA sequencing. Although the basic principle of measurement is in all cases based on hybridisation of a mixed probe derived from tissue RNA to large sets of DNA fragments representing many genes, a number of different forms of implementation of this principle are at hand. They are briefly described and compared, emphasizing the important issue of sensitivity and sample requirements and the accessibility of the methods to academic scientists. When these factors are taken into account, it appears that, contrary to a largely prevalent impression, the “best” approach is not necessarily always provided by the widely advertised glass microarrays or oligonucleotide chips. BioEssays 21:781–790, 1999. © 1999 John Wiley & Sons, Inc.     

Gene expression profiling of breast carcinomas using nylon DNA arrays

Clinically very heterogeneous, breast cancer prognosis and treatment response are difficult to predict with the current prognostic histoclinical parameters. Mammary oncogenesis remains poorly understood. DNA array technology allows the simultaneous analysis of the mRNA expression levels of thousands of genes in biological samples. Applied to breast tumours, expression profiles will boost our knowledge of oncogenesis, will offer new potential therapeutic targets and new prognostic and predictive markers. Today, the most accessible approach for academic research teams is that of Nylon DNA arrays with radioactive detection, which in addition allows profiling of small clinical samples.     

Quantitative protein profiling using antibody arrays

Traditional approaches to microarrays rely on direct binding assays where the extent of hybridisation and the signal detected are a measure of the analyte concentration in the experimental sample. This approach, directly imported from the nucleic acid field, may fail if applied to antibody-antigen interactions due to the shortage of characterised antibodies, the significant heterogeneity of antibody affinities, their dependence on the extent of protein modification during labelling and the inherent antibody cross-reactivity. These problems can potentially limit the multiplexing capabilities of protein affinity assays and in many cases rule out quantitative protein profiling using antibody microarrays. A number of approaches aimed at achieving quantitative protein profiling in a multiplex format have been reported recently. Of those reported, the three most promising routes include signal amplification, multicolour detection and competitive displacement approaches to multiplex affinity assays. One in particular, competitive displacement, also overcomes the problems associated with quantitation of affinity interactions and provides the most generic approach to highly parallel affinity assays, including antibody arrays.     

Profiling microRNA expression using sensitive cDNA probes and filter arrays

MicroRNAs (miRNAs) are small noncoding RNAs (approximately 22 nucleotides) that have recently emerged as important regulators of gene expression in both plants and animals. With few exceptions, however, the target genes and the expression levels of most miRNAs are unknown. Here we show that direct random-primed cDNA synthesis on either chemically synthesized small RNAs (21-22 nucleotides) or gel-purified mature miRNAs from human cells can produce specific and sensitive full-length cDNA probes. Using oligonucleotide filter arrays, we demonstrate that the internally labeled cDNA probes are sensitive for detecting differential miRNA expression between untreated and O-tetradecanoylphorbol-13-acetate (TPA)-treated HL60 cells. The present study should facilitate a high-throughput analysis of miRNA expression between samples.     

Highly sensitive and specific microRNA expression profiling using BeadArray technology

We have developed a highly sensitive, specific and reproducible method for microRNA (miRNA) expression profiling, using the BeadArray™ technology. This method incorporates an enzyme-assisted specificity step, a solid-phase primer extension to distinguish between members of miRNA families. In addition, a universal PCR is used to amplify all targets prior to array hybridization. Currently, assay probes are designed to simultaneously analyse 735 well-annotated human miRNAs. Using this method, highly reproducible miRNA expression profiles were generated with 100–200 ng total RNA input. Furthermore, very similar expression profiles were obtained with total RNA and enriched small RNA species (R² ≥ 0.97). The method has a 3.5–4 log (10⁵–10⁹ molecules) dynamic range and is able to detect 1.2- to 1.3-fold-differences between samples. Expression profiles generated by this method are highly comparable to those obtained with RT–PCR (R² = 0.85–0.90) and direct sequencing (R = 0.87–0.89). This method, in conjunction with the 96-sample array matrix should prove useful for high-throughput expression profiling of miRNAs in large numbers of tissue samples.     

Strategies for profiling microRNA expression

MicroRNAs (miRNAs) are a class of small RNAs ( approximately 22-nt) that play an important role in the control of different cell processes by negative regulation of protein-coding genes. In the last several years, a number of miRNA profiling strategies have been used to document the miRNA expression changes during physiological and pathological processes. Aberrant expression of miRNAs has been linked to developmental defects, cancer, neurological disorders, and heart diseases. Over 540 human miRNAs have been validated to date; however, computer models suggest there may be thousands more. As bench work continue to verify in silico predictions, miRNA profiling will remain a prominent tool for identification of differential expression miRNAs in normal cellular courses and human disorders. This review focuses on current strategies for miRNA expression profiling and discusses their sensitivity and specificity, as well as advantage and disadvantage.     

Construction of optimal quality control for oligo arrays

MOTIVATION: Oligo arrays are important experimental tools for the high throughput measurement of gene expression levels. During production of oligo arrays, it is important to identify any faulty manufacturing step. RESULTS: We describe a practical algorithm for the construction of optimal quality control designs that identify any faulty manufacturing step. The algorithm uses hillclimbing, a search technique from combinatorial optimization. We also present the results of using this algorithm on all practical quality control design sizes. AVAILABILITY: On request from the authors.     

Signal pathway profiling of prostate cancer using reverse phase protein arrays

Reverse phase protein arrays represent a new proteomics microarray technology with which to study the fluctuating state of the proteome in minute quantities of cells. The activation status of cell signaling pathways controls cellular fate and deregulation of these pathways underpins carcinogenesis. Changes in pathway activation that occur between early stage prostatic epithelial lesions, prostatic stroma and the extracellular matrix can be analyzed by obtaining pure populations of cell types by laser capture microdissection (LCM) and analyzing the relative states of several key phosphorylation points within the cellular circuitry. We have applied reverse phase protein array technology to analyze the status of key points in cell signaling involved in pro-survival, mitogenic, apoptotic and growth regulation pathways in the progression from normal prostate epithelium to invasive prostate cancer. Using multiplexed reverse phase protein arrays coupled with LCM, the states of signaling changes during disease progression from prostate cancer study sets were analyzed. Focused analysis of phospho-specific endpoints revealed changes in cellular signaling events through disease progression and between patients. We have used a new protein array technology to study specific molecular pathways believed to be important in cell survival and progression from normal epithelium to invasive carcinoma directly from human tissue specimens. With the advent of molecular targeted therapeutics, the identification, characterization and monitoring of the signaling events within actual human biopsies will be critical for patient-tailored therapy.     

Antigen arrays for antibody profiling

Antigen array technologies enable large-scale profiling of the specificity of antibody responses against autoantigens, tumor antigens and microbial antigens. Antibody profiling will provide insights into pathogenesis, and will enable development of novel tests for diagnosis and guiding therapy in the clinic. Recent advances in the field include development of antigen array-based approaches to examine immune responses against antigens encoded in genetic libraries, post-translationally modified proteins, and other biomolecules such as lipids. A promising application is the use of antibody profiling to guide development and selection of antigen-specific therapies to treat autoimmune disease. This review discusses these advances and the challenges ahead for development and refinement of antibody profiling technologies for use in the research laboratory and the clinic.     

Expression profiling of the estrogen responsive genes in response to phytoestrogens using a customized DNA microarray

Here, we examined phytoestrogens, isoflavones (genistein, daidzein, glycitein, biochanin A and ipriflavone), flavones (chrysin, luteolin and apigenin), flavonols (kaempferol and quercetin), and a coumestan, a flavanone and a chalcone (coumestrol, naringenin and phloretin, respectively) by means of a DNA microarray assay. A total of 172 estrogen responsive genes were monitored with a customized DNA microarray and their expression profiles for the above phytoestrogens were compared with that for 17beta-estradiol (E2) using correlation coefficients, or R values, after a correlation analysis by linear regression. While R values indicate the similarity of the response by the genes, we also examined the genes by cluster analysis and by their specificity to phytoestrogens (specific to genistein, daidzein or glycitein) or gene functions. Several genes were selected from p53-related genes (CDKN1A, TP53I11 and CDC14), Akt2-related genes (PRKCD, BRCA1, TRIB3 and APPL), mitogen-activated protein kinase-related genes (RSK and SH3BP5), Ras superfamily genes (RAP1GA1, RHOC and ARHGDIA) and AP-1 family and related genes (RIP140, FOS, ATF3, JUN and FRA2). We further examined the extracts from two local crops of soy beans (Kuro-daizu or Mochi-daizu) by comparing the gene expression profiles with those of E2 or phytoestrogens as a first step in utilizing the expression profiles for various applications.     

Purification of oligo dG-tailed Okayama-Berg linker DNA fragments by oligo dC-cellulose chromatography

A simple procedure for preparation of oligo dG-tailed DNA fragments is presented. The fragments are first purified by ultracentrifugation through sucrose gradients at low salt concentration. Appropriate gradient fractions are then adjusted to 1 M NaCl and immediately applied to a column of oligo dC-cellulose equilibrated in buffered 1 M NaCl at 4 degrees C. Fragments are eluted with water at room temperature. Passage through the column achieves, in one step, the concentration and purification of oligo dG-tailed DNA fragments free from sucrose.     

microRNA profiling in Epstein-Barr virus-associated B-cell lymphoma

The Epstein–Barr virus (EBV) is an oncogenic human Herpes virus found in ∼15% of diffuse large B-cell lymphoma (DLBCL). EBV encodes miRNAs and induces changes in the cellular miRNA profile of infected cells. MiRNAs are small, non-coding RNAs of ∼19–26 nt which suppress protein synthesis by inducing translational arrest or mRNA degradation. Here, we report a comprehensive miRNA-profiling study and show that hsa-miR-424, -223, -199a-3p, -199a-5p, -27b, -378, -26b, -23a, -23b were upregulated and hsa-miR-155, -20b, -221, -151-3p, -222, -29b/c, -106a were downregulated more than 2-fold due to EBV-infection of DLBCL. All known EBV miRNAs with the exception of the BHRF1 cluster as well as EBV-miR-BART15 and -20 were present. A computational analysis indicated potential targets such as c-MYB, LATS2, c-SKI and SIAH1. We show that c-MYB is targeted by miR-155 and miR-424, that the tumor suppressor SIAH1 is targeted by miR-424, and that c-SKI is potentially regulated by miR-155. Downregulation of SIAH1 protein in DLBCL was demonstrated by immunohistochemistry. The inhibition of SIAH1 is in line with the notion that EBV impedes various pro-apoptotic pathways during tumorigenesis. The down-modulation of the oncogenic c-MYB protein, although counter-intuitive, might be explained by its tight regulation in developmental processes.     

DNA profiling

Although some concerns still remain in standard DNA profiling technology over the assumptions from population genetics used to calculate expected match frequencies, forensic scientists are preparing for the introduction of the next generation of DNA profiling techniques based on the polymerase chain reaction. These new techniques offer the prospect of dramatically increasing the speed and sensitivity of DNA profiling and have already been applied in some casework studies.     

Selecting signature oligonucleotides to identify organisms using DNA arrays

MOTIVATION: DNA arrays are a very useful tool to quickly identify biological agents present in some given sample, e.g. to identify viruses causing disease, for quality control in the food industry, or to determine bacteria contaminating drinking water. The selection of specific oligos to attach to the array surface is a relevant problem in the experiment design process. Given a set S of genomic sequences (the target sequences), the task is to find at least one oligonucleotide, called probe, for each sequence in S. This probe will be attached to the array surface, and must be chosen in a way that it will not hybridize to any other sequence but the intended target. Furthermore, all probes on the array must hybridize to their intended targets under the same reaction conditions, most importantly at the temperature T at which the experiment is conducted. RESULTS: We present an efficient algorithm for the probe design problem. Melting temperatures are calculated for all possible probe-target interactions using an extended nearest-neighbor model, allowing for both non-Watson-Crick base-pairing and unpaired bases within a duplex. To compute temperatures efficiently, a combination of suffix trees and dynamic programming based alignment algorithms is introduced. Additional filtering steps during preprocessing increase the speed of the computation. The practicability of the algorithms is demonstrated by two case studies: The identification of HIV-1 subtypes, and of 28S rDNA sequences from >or=400 organisms.