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PubMed2006

Quantification of N-(deoxyguanosin-8-yl)-4-aminobiphenyl adducts in human lymphoblastoid TK6 cells dosed with N-hydroxy-4-acetylaminobiphenyl and their relationship to mutation, toxicity, and gene expression profiling.

Gene expression profiles that are anchored to phenotypic endpoints may lead to the identification of signatures that predict mutagenicity or carcinogenicity. The study presented here describes the analysis of DNA adducts in the human TK6 lymphoblastoid cell line after exposure to N-hydroxy-4-aminobiphenyl, a mutagenic metabolite of 4-aminobiphenyl. A validated nano-LC microelectrospray mass spectrometry assay is reported for the detection and quantification of N-(deoxyguanosin-8-yl)-4-aminobiphenyl (dG-C8-ABP), the principal DNA adduct of 4-aminobiphenyl. Limits of quantification, based on a signal-to-noise ratio of 10:1, are determined to correspond to approximately 27 fg of dG-C8-ABP injected on-column. The assay has been used to measure the steady-state levels of the adduct in the human TK6 lymphoblastoid cell line as a function of dose (0.5, 1.0, and 10.0 microM) and time (2, 6, and 27 h) after exposure to N-hydroxy-4-aminobiphenyl. The levels of dG-C8-ABP adducts in the cells, ranging from 18 to 500 adducts in 10(9) nucleotides, were then correlated to cell toxicity, induced mutation at the TK (thymidine kinase) and HPRT loci, and gene expression profiling through microarray analysis. Cell cultures were evaluated for toxicity by growth curve extrapolation, mutation assays were performed on the HPRT and TK loci, and gene expression profiles were generated by analyses using microarray technology. In the mutation assay analysis, as the toxicant concentration increased, there was an increase in mutation fraction, indicating a direct correlation to metabolite dosing level and mutations occurring at these two loci. Statistical analysis of the gene expression data determined that a total of 2250 genes exhibited statistically significant changes in expression after treatment with N-OH-AABP (P < 0.05). Among the genes identified, 2245 were up-regulated, whereas 5 genes that had functions in cell survival and cell growth and, hence, could be indicators of toxicity, were down-regulated relative to controls. The results demonstrate the value of anchoring gene expression patterns to phenotypic markers, such as DNA adduct levels, toxicity, and mutagenicity.

Aminobiphenyl Compounds↗

PubMed1996

Identification and cloning of neuroblastoma-specific and nerve tissue-specific genes through compiled expression profiles.

An expression profile of active genes in a human neuroblastoma cell line CHP134 was obtained by collecting 1222 partial sequences from a 3'-directed cDNA library representing a non-biased mRNA population. By comparing this expression profile with the compiled profiles of multiple tissues, several novel gene transcripts that appeared only in the profile of the neuroblastoma cell line were identified. Further analyses by Northern blotting revealed two specific cDNA clones that are expressed in most of the human neuroblastomas examined, and three that are in some of the human neuroblastoma cell lines as well as in the adult human brain. Full-size cDNAs were cloned using these five partial cDNA sequences as probes and sequenced. A database search revealed that they are all novel and unique sequences: one sharing some amino acid sequence similarities with a cytoskeletal protein, two clones likely to be transcriptional factors, a clone that has characteristic potassium channel properties, and a clone that is non-homologous to any one of the known proteins. Thus, we argue that the collection of 3'-directed cDNA sequences in combination with the compiled expression profiles of active genes in multiple tissues is a powerful tool for discovering novel genes that are specifically expressed in a given cell or tissue, in this case neuroblastomas and/or nerve tissue.

Amino Acid Sequence↗

PubMed2001

Analysis of host responses to microbial infection using gene expression profiling.

Gene expression profiling offers new opportunities for understanding host-cell responses to microbial pathogens and their products. Current strategies involve either first identifying mRNAs that differ in their expression status under different experimental conditions and later defining the identity of the respective genes (for example, differential display or serial analysis of gene expression), or alternatively assessing changes in the expression of already defined genes (for example, cDNA or oligonucleotide microarrays). Early studies indicate the power of gene expression profiling for providing new insights into groups of genes whose expression is altered during the course of host-microbe interactions, and for the discovery of cellular genes that were not previously recognized to be regulated by infection.

Gene Expression Profiling↗

PubMed2003

Gene expression profiling of differentially expressed genes in granulosa cells of bovine dominant follicles using suppression subtractive hybridization.

Development of antral follicles beyond 3 to 4 mm in cattle appears as a wave pattern that occurs two to three times during the estrous cycle. Each wave presents a cyclic recruitment of multiple follicles at the 3- to 4-mm stage, followed by the selection of a single follicle that becomes the dominant follicle (DF). The molecular determinants involved in the follicular dominance process remain poorly understood. The objective of the current study was to compare gene expression in granulosa cells (GCs) between growing dominant follicles from Day 5 of the estrous cycle and nonselected small follicles (<or=4 mm) using the suppression subtractive hybridization (SSH) approach to identify candidate genes differentially expressed in GCs of the DF. Small follicle cDNAs were subtracted from DF cDNAs (DF-SF) and used to establish a DF GC-subtracted cDNA library. A total of 42 nonredundant cDNAs were identified. Detection of previously identified genes such as CX43, CYP19, INHBA, and SERPINE2 supported the validity of our experimental model and the use of SSH as the method of analysis. For selected genes such as ApoER2, CPD, CSPG2, 14-3-3 epsilon, NR5A2/SF2, RGN/SMP30, and SERPINE2, gene expression profiles were compared by virtual Northern blot or reverse transcriptase-polymerase chain reaction, and results confirmed an increase or induction of their mRNA in GCs of dominant follicles compared with that of small follicles. We conclude that we have identified novel genes (known and unknown) that are up-regulated in bovine GCs that may affect follicular growth, dominance, or both.

Animals↗

PubMed2006

Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution.

Evolutionary rates provide important information about the pattern and mechanism of evolution. Although the rate of gene sequence evolution has been well studied, the rate of gene expression evolution is poorly understood. In particular, it is unclear whether the gene expression level and tissue specificity influence the divergence of expression profiles between orthologous genes. Here we address this question using a microarray data set comprising the expression signals of 10,607 pairs of orthologous human and mouse genes from over 60 tissues per species. We show that the level of gene expression and the degree of tissue specificity are generally conserved between the human and mouse orthologs. The rate of gene expression profile change during evolution is negatively correlated with the level of gene expression, measured by either the average or the highest level among all tissues examined. This is analogous to the observation that the rate of gene (or protein) sequence evolution is negatively correlated with the gene expression level. The impacts of the degree of tissue specificity on the evolutionary rate of gene sequence and that of expression profile, however, are opposite. Highly tissue-specific genes tend to evolve rapidly at the gene sequence level but slowly at the expression profile level. Thus, different forces and selective constraints must underlie the evolution of gene sequence and that of gene expression.

Animals↗

PubMed2006

Acupuncture regulates the aging-related changes in gene profile expression of the hippocampus in senescence-accelerated mouse (SAMP10).

To examine molecular events in hippocampus associated with aging and acupuncture effect, we employed cDNA arrays providing data of 588 genes to define transcriptional patterns. Male 8-month-old SAMP10 and its homologous SAMRl were selected and randomly divided into four groups: R1 control group (Rc), P10 control group (Pc), P10 acupuncture group (Pa) and P10 non-acupoint group (Pn). The points consisted Shanzhong (CV17), Zhongwan (CV12), Qihai (CV6), Zusanli (ST36) and Xuehai (SP10). In Pa, we found that points stimuli could completely or partly reverse some genes expression profiles in hippocampus with aging. Simultaneously, some genes not related with brain aging were affected by acupuncture as well. Meanwhile, non-acupoint had some effect on aging-unrelated genes expression and little or negative effect on aging-related genes. We verified array results with RT-PCR and Northern blotting for three genes which are related to oxidative damage closely, including Hsp84, Hsp86 and YB-1. In conclusion, acupuncture could be a potential intervention to retard molecular events with aging in mammals.

Acupuncture Therapy↗

PubMed2006

Molecular diagnosis of chronic liver disease and hepatocellular carcinoma: the potential of gene expression profiling.

Gene expression profile analysis through DNA microarrays and other high-throughput technologies permit simultaneous investigation of all genes within a biologic sample, providing a snapshot of the transcriptional state of healthy or diseased tissue. Although most of the current applications are still geared toward research (study of disease mechanisms/signaling pathways involved, identification of novel oncogenes/tumor suppressor genes), clinical diagnostic applications of this approach are beginning to enter more routine molecular usage. There are clear examples where a group of genes, or "signature," can provide clinically useful information (e.g., cancer prognosis and response to treatment). Importantly, the identification of genes that are up-regulated during tumorigenesis is heralding a new era of targeted molecular therapies in oncology. In addition, the high capacity of the technologies available allow for the identification of new biomarkers for early diagnosis. In the future, gene expression profiling ("disease fingerprinting") is likely to complement liver biopsy in the molecular differential diagnosis of chronic liver diseases and hepatocellular carcinoma (HCC). There has already been some success in the identification of subtypes of HCC based on derived sets of signature gene clusters. Data recently reported have been able to provide the first molecular classification of HCC, although more comprehensive studies are required to confirm these results and translate them into the clinical practice. In fact, variations in gene expression in normal and diseased livers, as well technical factors, are obstacles to the routine use of microarray-based methods in the liver clinic. Continued progress is anticipated in the practical application of gene array methods to refine diagnosis and therapy of HCC.

Carcinoma, Hepatocellular↗

PubMed2002

Molecular diagnosis of colorectal tumors by expression profiles of 50 genes expressed differentially in adenomas and carcinomas.

Most colon cancers are thought to develop through the 'adenoma-to-carcinoma sequence' model. To elucidate the mechanisms underlying this pathway, we analysed gene-expression profiles of 20 colorectal tumors (nine adenomas and 11 differentiated adenocarcinomas) by means of a cDNA microarray representing 23,040 genes coupled with laser-capture microdissection. A two-dimensional hierarchical clustering analysis of expression profiles of the 20 tumors correctly separated the carcinoma group from the adenoma group. Furthermore we identified 51 genes whose expression was commonly up-regulated, 376 that were commonly down-regulated in both types of tumors as opposed to normal colonic epithelium and 50 whose expression levels were significantly different between adenomas and carcinomas. On the basis of expression profiles of the 50 discriminating genes, we established a scoring system to separate adenomas from carcinomas. Application of this scoring system for evaluating five additional colorectal tumors correctly predicted their histological features. The genome-wide information reported here should contribute to a more profound understanding of colorectal tumorigenesis, particularly of adenoma-carcinoma progression, and provide indicators for developing novel strategies to diagnose, treat, and ultimately prevent colorectal carcinomas.

Adenocarcinoma↗

PubMed2005

A quality-controlled microarray method for gene expression profiling.

Gene expression profiling on microarrays is widely used to measure the expression of large numbers of genes in a single experiment. Because of the high cost of this method, feasible numbers of replicates are limited, thus impairing the power of statistical analysis. As a step toward reducing technically induced variation, we developed a procedure of sample preparation and analysis that minimizes the number of sample manipulation steps, introduces quality control before array hybridization, and allows recovery of the prepared mRNA for independent validation of results. Sample preparation is based on mRNA separation using oligo(dT) magnetic beads, which are subsequently used for first-strand cDNA synthesis on the beads. cDNA covalently bound to the magnetic beads is used as template for second-strand cDNA synthesis, leaving the intact mRNA in solution for further analysis. The quality of the synthesized cDNA can be assessed by quantitative polymerase chain reaction using 3'- and 5'-specific primer pairs for housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase. Second-strand cDNA is chemically labeled with fluorescent dyes to avoid dye bias in enzymatic labeling reactions. After hybridization of two differently labeled samples to microarray slides, arrays are scanned and images analyzed automatically with high reproducibility. Quantile-normalized data from five biological replica display a coefficient of variation 45% for 90% of profiled genes, allowing detection of twofold changes with false positive and false negative rates of 10% each. We demonstrate successful application of the procedure for expression profiling in plant leaf tissue. However, the method could be easily adapted for samples from animal including human or from microbial origin.

DNA, Complementary↗

PubMed2006

Gene expression profiles of the fibroblasts from breast tumors and normal tissue compared with the tumor expression profiles.

OBJECTIVE: The study was designed to examine whether the gene expression profiles of fibroblast cell lines, established from the tumor and the normal tissue from the same breast, exhibit any similarities with the profiles of the original tissues. METHODS: Fibroblast cell lines were established from invasive ductal carcinoma (IDC) and ductal carcinoma in situ (DCIS) of the breast and the adjacent normal tissues. Isolated total RNA from the cell lines and tissues were used to prepare labeled cDNA which was hybridized to Becton Dickinson Atlas microarrays for obtaining profiles of expressed genes. The profiles of tumors and cell lines were compared. This study was carried out at King Faisal specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia, during 2004 and 2005. RESULTS: Alterations of expression of most of the genes in the tissues were not detectable in the cell lines. The expression of a lower number of genes was altered in DCIS compared with that in IDC tumors. CONCLUSION: Although the fibroblasts discharge important functions, their gene expression profiles do not represent the breast tissue to the extent that any prognostic decisions could be made.

Adult↗

PubMed2004

Identifying superficial, muscle-invasive, and metastasizing transitional cell carcinoma of the bladder: use of cDNA array analysis of gene expression profiles.

PURPOSE: Expression profiling by DNA microarray technology permits the identification of genes underlying clinical heterogeneity of bladder cancer and which might contribute to disease progression, thereby improving assessment of treatment and prediction of patient outcome. EXPERIMENTAL DESIGN: Invasive (20) and superficial (22) human bladder tumors from 34 patients with known outcome regarding disease recurrence and progression were analyzed by filter-based cDNA arrays (Atlas Human Cancer 1.2; BD Biosciences Clontech) containing 1185 genes. For 9 genes, array data were confirmed using real-time reverse transcription-PCR. Additionally, Atlas array data were validated using Affymetrix GeneChip oligonucleotide arrays with 22,283 human gene fragments and expressed sequence tags sequences in a subset of three superficial and six invasive bladder tumors. RESULTS: A two-way clustering algorithm using different subsets of gene expression data, including a subset of 41 genes validated by the oligonucleotide array (Affymetrix), classified tumor samples according to clinical outcome as superficial, invasive, or metastasizing. Furthermore, (a) a clonal origin of superficial tumors, (b) highly similar gene expression patterns in different areas of invasive tumors, and (c) an invasive-like pattern was observed in bladder mucosas derived from patients with locally advanced disease. Several gene clusters that characterized invasive or superficial tumors were identified. In superficial bladder tumors, increased mRNA levels of genes encoding transcription factors, molecules involved in protein synthesis and metabolism, and some proteins involved into cell cycle progression and differentiation were observed, whereas transcripts for immune, extracellular matrix, adhesion, peritumoral stroma and muscle tissue components, proliferation, and cell cycle controllers were up-regulated in invasive tumors. CONCLUSIONS: Gene expression profiling of human bladder cancers provides insight into the biology of bladder cancer progression and identifies patients with distinct clinical phenotypes.

Algorithms↗

PubMed2003

Serial analysis of gene expression in circulating gamma delta T cell subsets defines distinct immunoregulatory phenotypes and unexpected gene expression profiles.

Gene expression profiles were compared in circulating bovine GD3.5+ (CD8-) and GD3.5- (predominantly CD8+) gammadelta T cells using serial analysis of gene expression (SAGE). Approximately 20,000 SAGE tags were generated from each library. A comparison of the two libraries demonstrated 297 and 173 tags representing genes with 5-fold differential expression in GD3.5+ and GD3.5- gammadelta T cells, respectively. Consistent with their localization into sites of inflammation, GD3.5+ gammadelta T cells appeared transcriptionally and translationally more active than GD3.5- gammadelta cells. GD3.5- gammadelta T cells demonstrated higher expression of the cell proliferation inhibitor BAP 37, which was associated with their less activated gene expression phenotype. The immune regulatory and apoptosis-inducing molecule, galectin-1, was identified as a highly abundant molecule and was higher in GD3.5+gammadelta T cells. Surface molecules attributed to myeloid cells, such as CD14, CD68, and scavenger receptor-1, were identified in both populations. Furthermore, expression of B lymphocyte-induced maturation protein, a master regulator of B cell and myeloid cell differentiation, was identified by SAGE analysis and was confirmed at the RNA level to be selectively expressed in gammadelta T cells vs alphabeta T cells. These results provide new insights into the inherent differences between circulating gammadelta T cell subsets.

Animals↗

PubMed2006

Multiple dysregulated pathways in nasopharyngeal carcinoma revealed by gene expression profiling.

Gene expression profiling was conducted using primary human nasopharyngeal carcinoma (NPC) biopsy samples to improve the understanding of the molecular pathways defining NPC and to identify novel potential therapeutic targets. RNA samples were extracted from 36 patients suspected to have NPC and hybridized onto the Affymetrix U133A chip. NPC was diagnosed in 19 patients, 11 had lymphoid hyperplasia (LH), and 6 were "normal" biopsies. Clinical stages for these NPC patients ranged from I-IV, including one M1. All NPC patients (except the M1) were treated with curative intent, which included radiotherapy alone (4 patients), or combined with chemotherapy (14 patients). Unsupervised clustering demonstrated a distinct NPC expression pattern, compared to normal biopsies. Subsequent Significance Analysis of Microarrays (SAM) derived from 14 NPC and 6 normal samples discovered 1,089 differentially regulated genes. Pathway analyses revealed novel insights into the mechanisms leading to NPC, whereby upregulation of NFkappaB2 and survivin play central roles in increasing resistance to apoptosis, and changes in integrin and WNT/beta-catenin signaling leading to uncontrolled proliferation. The role of survivin in resisting apoptosis in NPC was confirmed by RNA interference. Our data provide novel insights into the development and progression of NPC, and suggest survivin as a novel therapeutic target for NPC.

Apoptosis↗

PubMed2006

Tumor-specific gene expression patterns with gene expression profiles.

Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues. First, a variation of the Relief algorithm, "RFE_Relief algorithm" was proposed to learn the relations between genes and tissue types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.

Algorithms↗

PubMed2003

MLL-rearranged leukemias: insights from gene expression profiling.

Gene expression analysis of human leukemias has provided insight into disease classification and mechanisms of oncogenesis. Its success is particularly evident for acute leukemias with rearrangement of the mixed lineage leukemia (MLL) gene on chromosome 11q23. Unlike most other recurrent translocations, MLL rearrangements are found in leukemias classified as acute myelogenous leukemia (AML) or acute lymphoblastic leukemia (ALL). In addition, MLL-rearranged leukemias often express both myeloid- and lymphoid-associated genes. These unusual characteristics have generated much interest in the cell of origin and the mechanism of transformation by MLL rearrangements. Here we review insights gained from characterization of MLL-rearranged human leukemias by genome-wide expression profiling and compare these to data from model systems.

Cell Lineage↗

PubMed2000

General method for HPLC purification and sequencing of selected dsDNA gene fragments from complex PCRs generated during gene expression profiling.

Gene expression profiling using an AFLP-based technique generates a large number of gene fragments that require identification by sequencing. The DNA fragments vary in length from about 50-500 bp. Ion-pair reversed-phase HPLC can be used to purify selected double-stranded DNA fragments that represent differentially expressed genes. The gene fragments are sequenced directly after vacuum drying of the collected HPLC fractions.

Animals↗

PubMed2004

Gene expression profile following stable expression of the cellular prion protein.

1. The cellular prion protein (PrPC) is expressed widely in neural and nonneural tissues at the highest level in neurons in the central nervous system (CNS). 2. Recent studies indicated that transgenic mice with the cytoplasmic accumulation of PrPC exhibited extensive neurodegeneration in the cerebellum, although the underlying mechanism remains unknown. To identify the genes whose expression is controlled by over-expression of PrPC in human cells, we have established a stable PrPC-expressing HEK293 cell line designated P1 by the site-specific recombination technique. 3. Microarray analysis identified 33 genes expressed differentially between P1 and the parent PrPC-non-expressing cell line among 12,814 genes examined. They included 18 genes involved in neuronal and glial functions, 5 related to production of extracellular matrix proteins, and 2 located in the complement cascade. 4. Northern blot analysis verified marked upregulation in P1 of the brain-specific protein phosphatase 2A beta subunit (PPP2R2B), a causative gene of spinocerebellar ataxia 12, and the cerebellar degeneration-related autoantigen (CDR34) gene associated with development of paraneoplastic cerebellar degeneration. 5. These results indicate that accumulation of PrPC in the cell caused aberrant regulation of a battery of the genes important for specific neuronal function. This represents a possible mechanism underlying PrPC-mediated selective neurodegeneration.

Cell Line↗

PubMed2001

Gene expression profiling in human fetal liver and identification of tissue- and developmental-stage-specific genes through compiled expression profiles and efficient cloning of full-length cDNAs.

Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functional characteristics, HFL22w was studied by generating expressed sequence tags (ESTs) and by analyzing the compiled expression profiles of liver at different developmental stages. A total of 13,077 ESTs were sequenced from a 3'-directed cDNA library of HFL22w, and classified as follows: 5819 (44.5%) matched to known genes; 5460 (41.8%) exhibited no significant homology to known genes; and the remaining 1798 (13.7%) were genomic sequences of unknown function, mitochondrial genomic sequences, or repetitive sequences. Integration of ESTs of known human genes generated a profile including 1660 genes that could be divided into 15 gene categories according to their functions. Genes related to general housekeeping, ESTs associated with hematopoiesis, and liver-specific genes were highly expressed. Genes for signal transduction and those associated with diseases, abnormalities, or transcription regulation were also noticeably active. By comparing the expression profiles, we identified six gene groups that were associated with different developmental stages of human fetal liver, tumorigenesis, different physiological functions of Itoh cells against the other types of hepatic cells, and fetal hematopoiesis. The gene expression profile therefore reflected the unique functional characteristics of HFL22w remarkably. Meanwhile, 110 full-length cDNAs of novel genes were cloned and sequenced. These novel genes might contribute to our understanding of the unique functional characteristics of the human fetal liver at 22 wk.

Cloning, Molecular↗