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PubMedDate not supplied

Ribosomal protein P2: a potential molecular target for antisense therapy of human malignancies.

BACKGROUND: Ribosomal protein P2 is an important component of protein translation machinery. We hypothesized that antisense-mediated depletion may disrupt the proteome of cancer cells. This study includes experiments to ascertain whether this could be a useful approach for cancer therapies. MATERIALS AND METHODS: MIA PaCa-2 and BxPC-3 cells were transfected with P2-antisense oligonucleotide or controls. Growth was assayed using MTT. Protein P2 was measured using Western blotting. Proteomes were compared using two-dimensional electrophoresis and changes were characterized by mass spectrometry. A macroarray was used to identify cancers which may be vulnerable. RESULTS: Antisense-P2 reduced P2 levels by 63% (p < 0.05) and inhibited BxPC-3 growth to 65% of control (p < 0.05). Seventeen (5.4%) proteins changed on two-dimensional electrophoresis including Rho C, translationally-controlled tumor protein, vinculin, LDH, ribosomal protein L23a, F-actin capping protein and eIF-3. Breast cancer underexpressed P2 compared to normal tissue (p < 0.001). CONCLUSION: Antisense-P2 technology has potential to slow growth of cancer cells. This effect is mediated through multiple proteomic changes.

Base Sequence↗
PubMed2004

[Comparison of changes in left ventricular gene expression profiles from different cardiac hypertrophy models in rats].

To get insights into the principles of gene expression changes during cardiac hypertrophy, three rat cardiac hypertrophy models were prepared, i.e., suprarenal abdominal aortic stenosis (SRS), arterial-vein fistula (AVF) and continuous jugular vein infusion of norepinephrine (NEi). The cardiac function and structure were analyzed by echocardiograph as well as histological examination. Total RNA of left ventricles was extracted and gene expression profiles were analyzed by cDNA microarray. SRS and NEi induced concentric cardiac hypertrophy and AVF induced eccentric hypertrophy in rats, among which NEi caused obvious cardiac fibrosis. The changes of gene expression profiles were compared comprehensively across different pathologic cardiac hypertrophy models. While gene expression profiles of different cardiac hypertrophy models compared with pairs, parts of the genes involved were found overlapped, and mostly the gene expression changed in the same direction between two models, but some of them changed in the opposite directions. Expression levels of 19 genes were found changed across all cardiac hypertrophy models, and genes relatively regulated in a specific model was also found when comparison of all the three models was carried out. Novel clues for further study might derive from the results mentioned above, and some genes might be the marker genes of cardiac hypertrophy or the targets of therapy.

Animals↗
PubMed2004

Implementation of DNA chips obtained by microprojection for diagnostic and personalized medicine.

It is expected that rapidly emergent new fields of application for DNA chips will be Diagnostic and Personalized Medicine. These new applications will require a limited number of probes, generally from 100 to 1000. So, after a brief review of the existing techniques to manufacture DNA chips, which are efficient for R&D applications and which often require a higher number of probes, we shall first report some advances in the silanization of the substrates and the grafting of probes to improve the robustness and the reliability of the devices. Then we shall discuss two manufacturing processes working at the scale of a nanoliter of reactant: ex situ and in situ fabrication by microprojection. We shall see how these processes are complementary and may be used to design and produce chips, at a large scale, for these new applications.

Equipment Design↗
PubMed2004

Polyomavirus middle T-induced mammary intraepithelial neoplasia outgrowths: single origin, divergent evolution, and multiple outcomes.

The development of models to investigate the pathobiology of premalignant breast lesions is a critical prerequisite for development of breast cancer prevention and early intervention strategies. Using tissue transplantation techniques, we modified the widely used polyomavirus middle T (PyV-mT) transgenic mouse model of breast cancer to study the premalignant stages of tumorigenesis. Premalignant atypical lesions were isolated from PyV-mT transgenic mice and used to generate two sets of three mammary intraepithelial neoplasia (MIN) outgrowth lines. Investigation of these six unique lines, each of which fulfills the criteria for MIN, has provided new information regarding the biology of PyV-mT-induced neoplasia. Although expression of the PyV-mT transgene was the primary initiating event for all lines, they exhibited different tumor latencies, metastatic potentials, and morphologies. Six distinguishable morphologic patterns of differentiation were identified within the premalignant outgrowths that are likely to represent several tumorigenic pathways. Further, several tumor phenotypes developed from each line and the tumors developing from the six lines had different metastatic potentials. These observations are consistent with the hypothesis that distinct pathways of PyV-mT-initiated neoplastic progression lead to different outcomes with respect to latency and metastasis. The MIN outgrowth lines share several characteristics with precursors of human breast cancer including the observation that gene expression profiles of tumors are more similar to those of the MIN outgrowth line outgrowth from which they developed than to other tumors. These lines provide an opportunity to study the full range of events occurring secondary to PyV-mT expression in the mammary gland.

Animals↗
PubMed2004

[Progress and prospects of HLA genotyping technology].

Over a long period of time, studies on HLA structure and function have been the research hotspots. for it is very important to understand the essential of life science and disease mechanism. With the rapid development of molecular biology, HLA typing makes great progress. It has changed from traditional serological typing to DNA-based typing. More and more HLA genotyping methods have been developed and applied. In this essay, the author reviewed and appraised all kinds of HLA genotyping techniques and introduced two new techniques.

DNA Primers↗
PubMed2004

[Interferon-inducible genes lymphocyte antigen 6 complex E and tetratricopeptide repeats 1 are correlated with clinical features of patients with systemic lupus erythematosus].

OBJECTIVE: To investigate the expression levels of lymphocyte antigen 6 complex, locus E (LY6E) and interferon-induced protein with tetratricopeptide repeats 1 (IFIT1) genes in the peripheral blood mononuclear cells (PBMCs) of patients with systemic lupus erythematosus (SLE), and to evaluate the relations between these gene expression levels and disease activity. METHODS: The clinical data of 144 SLE patients, 27 non-SLE patients with rheumatic diseases, and 59 normal controls were collected. The SLE patients were further divided into 2 subgroups: active SLE group (n = 87) and non-active SLE group (n = 57) according to SLEDAI scores. Specimens of peripheral blood were drawn; total RNA was extracted and transcribed into cDNA. Sybr green dye based real-time quantitative PCR method was used to compare the expression levels (indicated as-DeltaDeltaCT value) of LY6E and IFIT1 in patients with SLE and those in the controls. RESULTS: (1) The-DeltaDeltaCT value of LY6E expression level of the SLE patients was 5.4760 +/- 1.9806, significantly higher than those of the non-SLE patients (3.4323 +/- 1.7456) and normal controls (4.5198 +/- 1.6359, both P = 0.001). (2) The-DeltaDeltaCT value of LY6E and IFIT1 mRNA expression of the active SLE patients were 6.1960 +/- 1.7729 and 6.4997 +/- 2.6297 respectively, significantly higher than those observed in the inactive SLE patients (4.3770 +/- 1.7764 and 4.1327 +/- 2.6044 respectively, both P = 0.000). The-DeltaDeltaCT values of LY6E and IFIT1 mRNA of the SLE patients were correlated with the SLEDAI scores, and with the numbers of matched criteria used in the diagnosis of SLE (P < 0.001). CONCLUSION: As IFN-induced genes, elevated expression of LY6E mRNA is specific to diagnosis of SLE. The real time expression levels of LY6E and IFIT1 genes are associated with SLE disease activity. To inhibit the expression of LY6E and IFIT1 may become a novel therapeutic approach for SLE.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Disruption of WT1 gene expression and exon 5 splicing following cytotoxic drug treatment: antisense down-regulation of exon 5 alters target gene expression and inhibits cell survival.

Deregulated expression of the Wilms' tumor gene (WT1) has been implicated in the maintenance of a malignant phenotype in leukemias and a wide range of solid tumors through interference with normal signaling in differentiation and apoptotic pathways. Expression of high levels of WT1 is associated with poor prognosis in leukemias and breast cancer. Using real-time (Taqman) reverse transcription-PCR and RNase protection assay, we have shown up-regulation of WT1 expression following cytotoxic treatment of cells exhibiting drug resistance, a phenomenon not seen in sensitive cells. WT1 is subject to alternative splicing involving exon 5 and three amino acids (KTS) at the end of exon 9, producing four major isoforms. Exon 5 splicing was disrupted in all cell lines studied following a cytotoxic insult probably due to increased exon 5 skipping. Disruption of exon 5 splicing may be a proapoptotic signal because specific targeting of WT1 exon 5-containing transcripts using a nuclease-resistant antisense oligonucleotide (ASO) killed HL60 leukemia cells, which were resistant to an ASO targeting all four alternatively spliced transcripts simultaneously. K562 cells were sensitive to both target-specific ASOs. Gene expression profiling following treatment with WT1 exon 5-targeted antisense showed up-regulation of the known WT1 target gene, thrombospondin 1, in HL60 cells, which correlated with cell death. In addition, novel potential WT1 target genes were identified in each cell line. These studies highlight a new layer of complexity in the regulation and function of the WT1 gene product and suggest that antisense directed to WT1 exon 5 might have therapeutic potential.

Alternative Splicing↗
PubMed2004

[Oligonucleotide microarray preparation using enhanced poly-L-lysine glass slides].

OBJECTIVE: To modify conventional poly-L-lysine coating for oligonucleotide microarray preparation so as to enhance the sensitivity of the microarray. METHOD: The proposed chemical approaches included silanizing the slides with 3-glycid-oxypropyltrimethoxysilane (GOPS) after cleaning, followed by slide coating with polymers (poly-L-lysine) that was covalently bound to the modified glass. Subsequent attachment of the oligonucleotide to the modified slide surface was achieved after 1,4-phenylene diisothiocyanate (PDITC) activation of the surface. Various experiments were carried out, such as the immobilization efficiency and hybridization assays to test the modified slides, which were then used tentatively in the preparation of microarrays for SARS coronavirus detection. RESULTS: The improved surface had high immobilization efficiency, good uniformity and satisfactory hybridization efficiency, better than those slides with conventional poly-L-lysine coating. In addition, such modified slides rendered the microarrays more resistant to consecutive probing/stripping cycles. CONCLUSION: The modified slide surface is satisfactory to immobilize unmodified oligonucleotide by covalent binding, which enhances not only the sensitivity of the prepared oligonucleotide microarray but also the binding of the oligonucleotide to the slide surface.

DNA, Viral↗
PubMedDate not supplied

[Development of microchips for the detection of mutations of HIV-1 variability to protease inhibitors and the usage results].

An original biochip was constructed for the detection of 34 mutations of HIV-1 resistance to protease. A technology was worked out, which is based on the hybridization of a fluorescence-labeled amplified fragment of the pol gene of the HIV-1 provirus DNA with a set of specific oligonucleotides immobilized in 3-D hydrogel pads of the biological microchip. The biochip was used to analyze 115 samples of the subtype-1 provirus HIV-1 DNA isolated from untreated IDUs and their sexual partners in 15 regions of former USSR countries. Substitution of Val/IIe in position 77 of protease (V771) is known as secondary mutation of resistance to Nelfinavir detected in 55 (47.8%) of 115 HIV-1 variations. Its first appearance was registered in a patient with HIV in April 1997 in Tver, where its carrying variant caused an HIV outbreak. It is demonstrated that the V771-substitution variant, that dominates in Moscow, caused outbreaks in Irkutsk and Yekaterinburg and spread into separate districts of Perm and Perm Region. At the same time, no V771 HIV-1 was detected in any of the HIV studied cases diagnosed before 1998 in Moldova, Ukraine and Rostov Region.

Amino Acid Substitution↗
PubMed2005

Cyclin D3 immunoreactivity is an independent predictor of survival in laryngeal squamous cell carcinoma.

PURPOSE: To analyze the prevalence and clinical relevance of cyclin D3 abnormalities in laryngeal squamous cell carcinoma (LSCC). EXPERIMENTAL DESIGN: Cyclin D3 immunoreactivity was evaluated in 223 formalin-fixed and paraffin-embedded samples of LSCC patients with a mean follow-up of 62.8 +/- 43.2 months. The occurrence of cyclin D3 extra signals was analyzed by fluorescence in situ hybridization in 47 randomly selected cases collected in a tissue microarray. Cyclin D1 immunoreactivity had been previously investigated in 133 cases. RESULTS: Cyclin D3 immunoreactivity and gene extra signals were found in 39.5% and 42.6% of the cases, respectively, and the concordance between immunohistochemical and fluorescence in situ hybridization results was 70.2% (P = 0.0085). Cyclin D3 immunoreactivity was significantly associated with a high risk of death. Multivariate analysis showed that high tumor grade, exophytic/ulcerating tumor type, low performance status, and cyclin D3 immunoreactivity were the only independent predictors of poor overall survival. In the 133 cases analyzed for both cyclin D1 and cyclin D3, patients with cyclin D1+/cyclin D3+ tumors experienced the worst prognosis, patients with cyclin D1-/cyclin D3- exhibited the most prolonged survival, and with cyclin D1-/cyclin D3+ or cyclin D1+/cyclin D3- tumors an intermediate course was associated. CONCLUSIONS: Our data suggest that cyclin D3 immunoreactivity, possibly due to the occurrence of gene extra copies, may represent an adjunct in LSCC patients' prognostication and contribute to identify D-type cyclins as potential targets of newly developed therapies.

Adult↗
PubMed2004

Molecular impacts of antisense complementary to the liver fatty acid binding protein (FABP) mRNA in DU 145 prostate cancer cells in vitro.

Previous studies in our laboratory have showed that liver (L)-FABP and intestine-FABP were upregulated in prostate cancer cells whereas Adipose-FABP and epidermal-FABP were down regulated in cancer cells when compared to normal cells in tissue cultures and biopsy samples (Das et al, 2001). We have also shown that blocking the expression of L-FABP resulted in remarkable effects on apoptosis and cell proliferation of prostate cancer cell lines. Another study showed that induction of A-FABP inhibited proliferation DU 145 prostate cancer cells (DeSantis et. al., Journal of Experimental Therapeutics and Oncology, 4:91-100, 2004) and caused a downregulation of the L-FABP transcript levels. This suggests that there is a correlation in the expression between of A-FABP and L-FABP in prostate cancer cells and that high expression of A-FABP is associated with a downregulation of L-FABP and vice versa. This study examines the mechanism by which L-FABP antisense regulates proliferation and apoptosis in prostate cancer cell lines. We used human cDNA array blots and custom DNA microarrays to explore differentially expressed genes in DU 145 prostate cancer cells treated with L-FABP antisense oligonucleotide. Genes that were differentially expressed were confirmed using quantitative RT-PCR. Genes correlating with proliferation were downregulated and antiproliferative genes were upregulated in response to antisense to L-FABP. This suggests a possible use of these antisense ODNs as therapeutic agents for prostate cancer in future.

Antigens, Differentiation↗
PubMed2002

Rapid large-scale oligonucleotide selection for microarrays.

We present the first algorithm that selects oligonucleotide probes (e.g. 25-mers) for microarray experiments on a large scale. For example, oligos for human genes can be found within 50 hours. This becomes possible by using the longest common substring as a specificity measure for candidate oligos. We present an algorithm based on a suffix array with additional information that is efficient both in terms of memory usage and running time to rank all candidate oligos according to their specificity. We also introduce the concept of master sequences to describe the sequences from which oligos are to be selected. Constraints such as oligo length, melting temperature, and self-complementarity are incorporated in the master sequence at a preprocessing stage and thus kept separate from the main selection problem. As a result, custom oligos can now be designed for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.

Algorithms↗
PubMed2005

Trends in the quality of data from 5168 oligonucleotide microarrays from a single facility.

Improvements in the quality of gene expression data were investigated based on a database consisting of 5168 oligonucleotide microarrays collected over 3 years. The database includes diverse treatments of human and mouse samples collected from multiple laboratories. The array designs and algorithms used to capture the data have also changed over the 3 years of data collection. All hybridizations and labeling were conducted in the Hartwell Center for Bioinformatics and Biotechnology at St. Jude's Children's Research Hospital. Quality metrics for each human and mouse array were collected and analyzed. Statistical tests, such as ANOVA and linear regression, were applied to test for the effects of array design, algorithm, and time. The quality metrics tested were average background, actin 3'/5' ratio, Bio B signal, percent present, and scale factor. ANOVA results indicate that both recent algorithms and chip designs significantly correlate with improvements in Bio B, scale factor, percent present, and average background. Significant quality improvements correlated with new chip designs, algorithms, and their interaction. In addition, within one chip type analyzed by the same algorithm significant improving trends were still observed. Scale factor, percent present, and average background significantly improved over time for U133A arrays analyzed by the Affymetrix MicroArray Suite 5.0 algorithm according to linear regression. Proportionally fewer outlier arrays (those with less than 25% present calls) were seen over time. Also, high throughput periods did not increase the proportion of outliers, indicating that laboratory monitoring of quality is successfully preventing failures.

Actins↗
PubMed2005

Differential gene expression assessed by cDNA microarray analysis in breast cancer tissue under tamoxifen treatment.

Our purpose was to identify tamoxifen (TAM) responsive genes after 30 days of TAM treatment in tumor tissues obtained from women with breast cancer using microarray expression analysis. In our study, we identified 12 candidates to be considered as tamoxifen-modulated genes. Among them, we selected two candidates the TEGT BI-1 (testis enhanced gene transcript Bax Inhibitor-1) and the CD63 gene in order to further confirm their differential expression under tamoxifen effects. We observed that both were down-regulated in tumor tissues of patients during TAM treatment. TEGT is able to inhibit the expression of Bax, which is known to promote apoptosis. On the other hand, CD63 encodes a cell membrane protein and it seems to be involved in mechanisms of platelet activation, cell adhesion and cell motility. We therefore hypothesize that TAM would be able to modulate tumor growth by down-regulating genes involved in mechanisms such as cell cycle control, tumor invasion and metastasis.

Breast Neoplasms↗
PubMed2003

Computing highly specific and mismatch tolerant oligomers efficiently.

The sequencing of the genomes of a variety of species and the growing databases containing expressed sequence tags (ESTs) and complementary DNAs (cDNAs) facilitate the design of highly specific oligomers for use as genomic markers, PCR primers, or DNA oligo microarrays. The first step in evaluating the specificity of short oligomers of about twenty units in length is to determine the frequencies at which the oligomers occur. However, for oligomers longer than about fifty units this is not efficient, as they usually have a frequency of only 1. A more suitable procedure is to consider the mismatch tolerance of an oligomer, that is, the minimum number of mismatches that allows a given oligomer to match a sub-sequence other than the target sequence anywhere in the genome or the EST database. However, calculating the exact value of mismatch tolerance is computationally costly and impractical. Therefore, we studied the problem of checking whether an oligomer meets the constraint that its mismatch tolerance is no less than a given threshold. Here, we present an efficient dynamic programming algorithm solution that utilizes suffix and height arrays. We demonstrated the effectiveness of this algorithm by efficiently computing a dense list of oligo-markers applicable to the human genome. Experimental results show that the algorithm runs faster than well-known Abrahamson's algorithm by orders of magnitude and is able to enumerate 63% to approximately 79% of qualified oligomers.

Algorithms↗
PubMed2006

[HLA-DQA1 genotyping by using oligonucleotide microarrays].

In order to fabricate the HLA-DQA1 genotyping chip and develop an integrated, parallel technical platform to type HLA system, a pair of primers and a set of probes were designed according to the sequences of HLA-DQA1 exon 2, where the polymorphism is concentrated. The oligonucleotide chip was made with the methods developed in our laboratory. The target DNA was asymmetrically amplified with the labeled sense primer. The signals were scanned and analyzed after the hybridization between microarray and PCR product. The allele types of the samples were identified. The result was verified by the standard DNA and DNA sequencing. The results showed that the genotyping was successfully carried out in 50 standard DNA samples and 50 clinical samples. Among them, results of the 50 standard DNA samples matched their templates. In the other 50 samples, results of the randomly selected 10 matched their sequencing results except that two of them got the incompletely result. In reproducible tests, the signal reappear rate was 95%. It is concluded that HLA-DQA1 genotyping by using our array system is simple and convenient with satisfied accuracy and reproducibility.

Genotype↗
PubMed2006

[With genechip technique to investigate HLA-DQB1 gene polymorphisms in south and north regions of China].

OBJECTIVE: To research and compare HLA-DQB1 gene frequency(GF) and polymorphism distribution between south and north population of Chinese in China. METHODS: Combining PCR-sequence specific primers(SSP) and sequence specific oligonucleotide probe(SSOP) techniques and DNA Microarray Kit for HLA-DQB1 Low Res Genotyping from Shenzhen Yi-Shengtang Biological LTD. Co. was used to type HLA-DQB1 gene polymorphisms of 700 individuals living in south China and 320 individuals in north China. RESULTS: We inspected 10 alleles of HLA-DQB1 and got a series of comprehensive and accurate statistic data. CONCLUSION: It is tested that HLA-DQB1*02, 05, 0601, 0602, 0603 gene frequencies are different obviously(P<0.05) between south and north Chinese. And those data will be useful to kinds of research associated with disease relevant and anthropology research.

Alleles↗
PubMed2006

Global assessment of cross-hybridization for oligonucleotide arrays.

Cross-hybridization is the tendency for chains of nucleic acids to bind to other chains of nucleic acids that have similar but not identical sequences. This has the potential to make the interpretation of microarray experiments difficult since intensity at a spot on the array does not simply depend on the quantity of target in the sample. We propose a method for evaluating the extent of cross-hybridization in oligonucleotide arrays for data arising from a typical microarray experiment. We show that the level of cross-hybridization can be quite substantial. We argue that this makes the interpretation of the difference calls provided by MAS 5.0 difficult.

CD28 Antigens↗