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PubMed2005

The use of peptide nucleic acids for in situ identification of human chromosomes.

The peptide nucleic acids (PNAs) constitute a remarkable new class of synthetic nucleic acid analogues, based on their peptide-like backbone. This structure gives to PNAs the capacity to hybridize with high affinity and specificity to complementary RNA and DNA sequences and a great resistance to nucleases and proteinases. Originally conceived as ligands for the study of double-stranded DNA, the unique physicochemical properties of PNAs have led to the development of a large variety of research and diagnostic assays, including antigene and antisense therapy, genome mapping, and mutation detection. Over the past few years, PNAs have been shown to be powerful tools in cytogenetics for the rapid in situ identification of human chromosomes and the detection of aneuploidies. Recent studies have reported the successful use of chromosome-specific PNA probes on human lymphocytes, amniocytes, and spermatozoa, as well as on isolated oocytes and blastomeres. Multicolor PNA protocols have been described for the identification of several human chromosomes, indicating that PNAs could become a powerful complement to FISH for in situ chromosomal investigation.

Chromosomes, Human↗
PubMed2004

Identification of G-protein-coupled receptor mRNA expression by Northern blotting and in situ hybridization.

G-protein-coupled receptor mRNAs are expressed at low levels and therefore present a challenge for the study of their sites and levels of expression. In situ hybridization (ISH) and Northern blotting are powerful methods for the localization of mRNAs and the study of regulation of mRNA expression. ISH combines the power of precise cellular localization with the ability to perform semiquantitative analysis of the mRNA level, whereas Northern blotting has the ability to identify genetic splice variants, or to study multiple RNA molecules sequentially in the same tissue samples. These protocols give step-by-step instructions for the performance of these techniques, and the analysis of the data that can be obtained using them.

Animals↗
PubMed2005

Gene expression profiling of primary tumor cell populations using laser capture microdissection, RNA transcript amplification, and GeneChip microarrays.

Gene expression profiling from microdissected cell populations is a powerful approach to explore molecular processes involved in development and solid tumor biology. In this chapter, we detail robust and validated methods for tissue preparation and isolation of high-quality RNA from microdissected cell populations. A protocol is also provided for linear transcript amplification using as little as 10 ng of total RNA to produce labeled cRNA targets for hybridization to GeneChip high-density oligonucleotide microarrays. Particular emphasis is placed on troubleshooting each technical step in the protocol and measures of quality assurance for both RNA isolation and resulting microarray data.

Animals↗
PubMed2005

Cellular delivery of peptide nucleic acid by cell-penetrating peptides.

Peptide nucleic acid (PNA) is a promising tool in biomedical research. PNA oligomers can be synthesized according to peptide synthesis protocols, but they hybridize to complementary RNA and DNA strands like oligonucleotides. The main hindrance to the use of PNA oligomers has been their poor uptake by cells. Fortunately, this limitation can be overcome by the application of peptide vectors. Different strategies are used to conjugate peptide vectors and PNA oligomers. In this chapter we discuss different types of delivery vectors (receptor ligands and cell-penetrating peptides) and strategies for the design and synthesis of PNA-vector conjugates. A protocol for the delivery of antisense PNA oligomer-cell-penetrating peptide conjugates is also described.

Cells↗
PubMed2006

In situ hybridization using cRNA probes: isotopic and nonisotopic detection methods.

In this chapter we describe the use of cRNA (riboprobes) in the detection of gene expression in tissue sections. Riboprobes offer good sensitivity and allow the detection of low-level mRNA expression. In some cases, the use of radiolabeling is justified because this method is still sensitive. However, recent advances in nonisotopic detection methods mean that in some cases digoxigenin (DIG) or biotin labeling also may be sufficiently sensitive to detect mRNA expression in tissues of interest. The use of alkaline phosphatase conjugated anti-DIG antibodies improves the sensitivity of DIG detection over peroxidase systems, and the use of amplification systems based on biotinyl tyramide has improved the sensitivity of biotin labelled probe detection. Finally, it can be shown that low-level mRNA expression is easier to detect in frozen sections than in paraffin-embedded material, with a consequent loss in quality of morphology.

Animals↗
PubMed2005

Gene expression levels in small specimens from patients detected using oligonucleotide arrays.

Large-scale gene expression profiling using microarray technology is often limited by the amount of tissue or cells available. A number of RNA amplification protocols have been published to overcome this problem. However, additional amplification steps can result in both a 3' bias and poor reproducibility for low abundance transcripts. We performed microarray experiments using HG-U133A GeneChip arrays to ascertain whether less than the recommended amount of RNA can be used, thus avoiding additional amplification steps. In a titration experiment, 2-10 microg of total RNA from a single cryopreserved patient specimen was used to prepare biotinylated cRNA, and the recommended standard amount of 15 microg of each preparation was used for hybridization. Statistical analysis using box plots, correlation coefficients, MvA plots, and concordance percentages revealed almost identical levels of gene expression, independent of the amount of RNA used for target preparation. Most importantly, there was no statistically significant difference when the concordance percentages for low abundance genes were compared, demonstrating that as little as 2 microg of total RNA is sufficient to perform GeneChip analysis.

Child↗
PubMed2001

Clinical trials of a new class of therapeutic agents: antisense oligonucleotides.

Antisense oligodeoxynucleotides (ODNs) are short stretches of DNA complementary to a target mRNA. The ODNs selectively hybridise to their complementary RNA by Watson-Crick base pairing rules. In theory, the use of antisense ODNs provides a method to specifically inhibit the intracellular expression of any disorder whose genetic aetiology is well known. For this reason, researchers thought that if antisense drugs proved to be so specific there would be no side effects. However, toxicity-related problems arose in initial animal studies of antisense drugs in the early 1990s and since then companies have been using these compounds cautiously. In order to be useful therapeutically, an ODN must (a) exhibit reasonable stability in the physiological environment, (b) be taken up and retained in adequate quantities by the target cells, (c) specifically bind target mRNA with high affinity, (d) have an acceptable therapeutic ratio, free of unwanted toxic and non-specific side effects and (e) be easily synthesised in sufficient quantities to allow clinical use. Most of these criteria have already been met by ODNs recently used in this way. This review describes certain therapeutic applications of antisense techniques currently under investigation in oncology, haematopathology and inflammatory diseases.

Journal Article↗
PubMedDate not supplied

Epithelial-mesenchymal transition in colonies of rhesus monkey embryonic stem cells: a model for processes involved in gastrulation.

Rhesus monkey embryonic stem (rhES) cells were grown on mouse embryonic fibroblast (MEF) feeder layers for up to 10 days to form multilayered colonies. Within this period, stem cell colonies differentiated transiently into complex structures with a disc-like morphology. These complex colonies were characterized by morphology, immunohistochemistry, and marker mRNA expression to identify processes of epithelialization as well as epithelial-mesenchymal transition (EMT) and pattern formation. Typically, differentiated colonies were comprised of an upper and a lower ES cell layer, the former growing on top of the layer of MEF cells whereas the lower ES cell layer spread out underneath the MEF cells. Interestingly, in the central part of the colonies, a roundish pit developed. Here the feeder layer disappeared, and upper layer cells seemed to ingress and migrate through the pit downward to form the lower layer while undergoing a transition from the epithelial to the mesenchymal phenotype, which was indicated by the loss of the marker proteins E-cadherin and ZO-1 in the lower layer. In support of this, we found a concomitant 10-fold upregulation of the gene Snail2, which is a key regulator of the EMT process. Conversion of epiblast to mesoderm was also indicated by the regulated expression of the mesoderm marker Brachyury. An EMT is a characteristic process of vertebrate gastrulation. Thus, these rhES cell colonies may be an interesting model for studies on some basic processes involved in early primate embryogenesis and may open new ways to study the regulation of EMT in vitro.

Actins↗
PubMed2003

Transcriptional profiling of neuronal differentiation by human embryonal carcinoma stem cells in vitro.

Pluripotent stem cell lines can be induced to differentiate into a range of somatic cell types in response to various stimuli. Such cell-based systems provide powerful tools for the investigation of molecules that modulate cellular development. For instance, the formation of the nervous system is a highly regulated process, controlled by molecular pathways that determine the expression of specific proteins involved in cell differentiation. To begin to decipher this mechanism in humans, we used oligonucleotide microarrays to profile the complex patterns of gene expression during the differentiation of neurons from pluripotent human stem cells. Samples of mRNA were isolated from cultured NTERA2 human embryonal carcinoma stem cells and their retinoic-acid-induced derivatives and were prepared for hybridization on custom microarrays designed to detect the expression of genes primarily associated with the neural lineage. In response to retinoic acid, human NTERA2 cells coordinately regulate the expression of large numbers of neural transcripts simultaneously. Transcriptional profiles of many individual genes aligned closely with expression patterns previously recorded by developing neural cells in vitro and in vivo, demonstrating that cultured human pluripotent stem cells appear to form neurons in a conserved manner. These experiments have produced many new expression data concerning neuronal differentiation from human stem cells in vitro. Of particular interest was the regulated expression of Pax6 and Nkx6.1 mRNA and the absence of Pax7 transcription, indicating that neurons derived from NTERA2 pluripotent stem cells are characteristic of neuroectodermal cells of the ventral phenotype.

Blotting, Northern↗
PubMed1996

Localization of sites of enhanced expression of endothelin-1 in the kidney of DOCA-salt hypertensive rats.

Although the role of endothelin-1, a potent vasoconstrictor peptide, in hypertension remains unclear, there is evidence of its involvement in deoxycorticosterone acetate (DOCA)-salt hypertensive rats, in which enhanced vascular production of endothelin-1 has been documented. The study presented here examined endothelin-1 gene expression in the kidney in DOCA-salt hypertensive rats by in situ hybridization histochemistry. A high specific activity 35S-labeled complementary RNA probe was used. Significant increases in abundance of endothelin-1 mRNA transcripts were found in the endothelium of renal vessels, and in capillary endothelial and mesangial cells of glomeruli of the remaining kidney of DOCA-salt hypertensive rats, in comparison with unilaterally nephrectomized control rats. Enhanced expression of the endothelin-1 gene in the kidney of DOCA-salt hypertensive rats may participate in abnormalities of renal function in this model of hypertension, and thus contribute to the development and maintenance of elevated blood pressure.

Animals↗
PubMed1995

Tissue response to particulate polymethylmethacrylate in mice with various immune deficiencies.

We examined the tissue response to subcutaneous injections of particulate polymethylmethacrylate powder in fully immunocompetent C3Hf/Sed mice as well as three strains of mice with different levels of lymphocyte dysfunction. Five weeks after the injection, we found clearly demarcated granulomas. Histological and immunohistochemical studies showed that these granulomas were similar among all strains, with either paucity or absence of lymphoid cells. In situ hybridization with use of complementary RNA probes indicated that macrophages were synthesizing interleukin-1 beta messenger RNA (mRNA), a marker of macrophage activation, and a cytokine implicated in pathological bone resorption. We concluded that, in mice, there is a lymphocyte-independent pathway of macrophage activation in response to particulate polymethylmethacrylate. This suggests that the foreign-body response to particulate orthopaedic biomaterials is macrophage-initiated and maintained and that lymphocytes are not essential to this response, although they may modulate it.

Analysis of Variance↗
PubMed2006

Comparison of in vitro and in vivo reference genes for internal standardization of real-time PCR data.

Real-time PCR is a powerful technique for gene expression studies, which have become increasingly important in a large number of clinical and scientific fields. The significance of the obtained results strongly depends on the normalization of the data to compensate for differences between the samples. The most widely used approach is to use endogenous reference genes (housekeeping genes) as internal standards. This approach is controversially discussed in the literature because none of the reference genes is stably expressed throughout all biological samples. Therefore, candidate reference genes have to be validated for each experimental condition. In our studies, we introduced and evaluated an in vitro synthesized reference cRNA for internal standardization of relative messenger RNA (mRNA) expression patterns. This reference, consisting of the in vitro transcribed coding sequence of aequorin, a jellyfish protein, was incorporated in the extracted RNA. The experimental significance of this approach was representatively tested for the expression of the neurotrophin-3 mRNA in distinct regions of mouse brains. A comparison to three stably expressed reference genes [beta-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and hypoxanthine phosphoribosyl-transferase 1 (HPRT1)] gave evidence that the spiking of template RNA with in vitro transcribed cRNA is a valuable tool for internal standardization of real-time PCR experiments.

Actins↗
PubMed2000

Laser capture microdissection-generated target sample for high-density oligonucleotide array hybridization.

Current advances in biomolecular technology allow precise genetic fingerprinting of specific cells responsible for the pathogenesis of human diseases. This study demonstrates the feasibility of generating target samples from laser capture microdissection (LCM) tissues suitable for hybridization of high-density oligonucleotide arrays for gene expression profiling. RNA was successfully isolated by LCM from three paired specimens of oral cancer and linearly amplified using T7 RNA polymerase. Evaluation of the cDNA revealed that five of five cellular maintenance transcripts are detected. Biotinylated cRNA was generated and hybridized to the human Test 1 GeneChip probe arrays, which demonstrated that the RNA is of sufficient quality and integrity to warrant further analysis. Subsequent hybridization of the samples to the HuGenFL GeneChip probe arrays revealed that 26.5%-33.0% of the approximately 7000 represented genes are expressed in each of the six samples. These results demonstrate that LCM-generated tissues can generate sufficient quality cRNA for high-density oligonucleotide microarray analysis, an important step in determining comprehensive gene expression profiling using this high-throughput technology.

Biotinylation↗
PubMed1997

Sensitive nonradioactive dot blot/ribonuclease protection assay for quantitative determination of mRNA.

We have developed a simple and sensitive method for the rapid quantitation of mRNA from cell cultures and small tissue samples. The method combines the high sensitivity and specificity of the ribonuclease protection assay with simple handling and rapid execution of dot blotting. The use of digoxygenin-labeled cRNA probes eliminates all problems associated with radioisotopes commonly used in the ribonuclease protection assay. The RNA preparation is dotted directly onto nylon membranes, and after hybridization the filters are treated with ribonuclease A, which removes the nonhybridized single-stranded RNA. The mRNA-hybrid is then visualized by the chemiluminescence technique using labeled anti-digoxigenin antibody, and the signal intensity is quantitated. Comparison with the Northern blotting ribonuclease protection assay revealed that this dot blot technique is almost ten times more sensitive and that its signals are linear over a wide range of RNA concentrations (0.01-10 micrograms/microL/dot). This method seems particularly valuable for simultaneous processing of large numbers of samples containing a wide range of RNA concentrations.

Animals↗