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PubMed2002

Comparison of gene expression profiles between hepatitis B virus- and hepatitis C virus-infected hepatocellular carcinoma by oligonucleotide microarray data on the basis of a supervised learning method.

Gene expression profiles of hepatocellular carcinomas (HCCs) associated with hepatitis B virus (HBV) and hepatitis C virus (HCV) were analyzed and compared. Oligonucleotide microarrays containing >6000 genes and subsequent gene selection by a supervised learning method yielded 83 genes for which expression differed between the two types of HCCs. Expression levels of 31 of these 83 genes were increased in HBV-associated HCCs, and expression levels of the remaining 52 genes were increased in HCV-associated HCCs. The 31 genes up-regulated in HBV-associated HCC included imprinted genes (H19 and IGF2) and genes relating to signal transduction, transcription, and metastasis. The 52 genes up-regulated in HCV-associated HCC included a number of genes responsible for detoxification and immune response. These results suggest that HBV and HCV cause hepatocarcinogenesis by different mechanisms and provide novel tools for diagnosis and treatment of HBV- and HCV-associated HCCs.

Aged↗

PubMed2002

Gene expression profiling of HeLa cells in G1 or G2 phases.

The cell division cycle is regulated through both transcriptional and post-transcriptional mechanisms. The altered expression of a number of genes at the mRNA level is known to be essential for progression through the cell cycle, however, a comprehensive gene expression profile of human cells remains to be completed. Here we sought to monitor the differential gene expression of genes after the transition of G2 cells into G1 prior to the restriction point. GeneChip containing microarrays of oligonucleotides corresponding to over 12 000 human genes were employed to profile differential gene expression in G1 and G2. After three independent experiments the resultant data was filtered and a set of genes was compiled based on at least threefold-altered expression, no background noise in determining expression and observation in all experiments. Our analysis identified 154 genes that were elevated in G2 phase of cells as compared to early G1 phase including 15 novel genes. This number included mRNAs whose upregulation is known to occur in G2 phase. Surprisingly only 19 genes were upregulated in G1 phase, among these six genes were novel. Some of these genes are candidates for transition through early G1. This gene inventory for G1 and G2 phases of cell cycle will provide the basis for understanding of cell cycle delay as a result of DNA damage.

Blotting, Northern↗

PubMed2001

Expression profiles and intergenic structure of head-to-head oriented Brca1 and Nbr1 genes.

Mouse and human Brca1/BRCA1 and Nbr1/NBR2 genes lie head-to-head, being transcribed from the opposite strands. The normal function of Brca1 is associated with DNA damage-related responses and the maintenance of genome integrity. Mutations of this gene are major risk factors for developing breast and ovarian cancers. The function of Nbr1 is unknown. Here we analyzed expression profiles of Brca1 and a newly identified, evolutionary conserved isoform of Nbr1(1a) transcript. In adult testis, the Nbr1(1a) mRNA showed an 18-fold higher steady-state level than the ubiquitous Nbr1(1b) form and its expression was confined mainly to spermatids. The expression profile of Brca1 paralleled that of Nbr1(1b). The Nbr1(1a) mRNA was not significantly expressed in normal somatic tissues, but was found on a list of cDNA clones from a human myeloblast cell line. The newly defined intergenic region (289 bp) between Nbr1 and Brca1 in the mouse and rat corresponds well to that of human BRCA1-NBR2 region.

Animals↗

PubMed2004

Expression profiling of mammalian male meiosis and gametogenesis identifies novel candidate genes for roles in the regulation of fertility.

We report a comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis, and gametogenesis by using high-density oligonucleotide microarrays and highly enriched cell populations. Among 11,955 rat loci investigated, 1268 were identified as differentially transcribed in germ cells at subsequent developmental stages compared with total testis, somatic Sertoli cells as well as brain and skeletal muscle controls. The loci were organized into four expression clusters that correspond to somatic, mitotic, meiotic, and postmeiotic cell types. This work provides information about expression patterns of approximately 200 genes known to be important during male germ cell development. Approximately 40 of those are included in a group of 121 transcripts for which we report germ cell expression and lack of transcription in three somatic control cell types. Moreover, we demonstrate the testicular expression and transcriptional induction in mitotic, meiotic, and/or postmeiotic germ cells of 293 as yet uncharacterized transcripts, some of which are likely to encode factors involved in spermatogenesis and fertility. This group also contains potential germ cell-specific targets for innovative contraceptives. A graphical display of the data is conveniently accessible through the GermOnline database at http://www.germonline.org.

Animals↗

PubMed2004

Gene expression profiles in HEK-293 cells with low or high store-operated calcium entry: can regulatory as well as regulated genes be identified?

Gene expression profiles were generated using cDNA microarray technology for clones of human embryonic kidney (HEK)-293 cells selected to have either high or low levels of store-operated Ca2+ entry (SOCE). For five high clones, three low clones, and control HEK-293 cells, duplicate Affymetrix U133A human gene arrays were run after extraction of total RNA from cells growing in the presence of serum. Of the approximately 22,000 genes represented on the microarray, 58 genes had readings at least twofold higher, while 32 genes had readings at least twofold lower, in all five high SOCE clones compared with control HEK-293 cells. In the low SOCE clones, 92 genes had readings at least twofold higher, while 58 genes had readings at least twofold lower, than in HEK-293 cells. Microarray results were confirmed for 18 selected genes by real-time RT-PCR analysis; for six of those genes, predicted changes in the low SOCE clone were confirmed by an alternative method, monitoring mRNA levels in HEK-293 with SOCE decreased by expression of small interfering (si)RNA to canonical transient receptor potential protein-1. Genes regulated by SOCE are involved in signal transduction, transcription, apoptosis, metabolism, and membrane transport. These data provide insight into the physiological role of SOCE. In addition, a potential regulator of SOCE, insulin receptor substrate (IRS)-2, has been identified. A reduction of IRS-2 levels by siRNA methods in two high clones dramatically reduced SOCE, whereas overexpression of IRS-2 in a low SOCE clone elevated SOCE.

Apoptosis↗

PubMed2004

Deciphering gene expression profiles generated from DNA microarrays and their applications in oral medicine.

Genome-wide monitoring of gene expression profiles using DNA microarrays provides a unique approach to exploring the biological processes underlying oral diseases and disorders by providing a comprehensive survey of a cell's or tissue's transcriptional mapping. This revolutionary technology allows for the simultaneous assessment of the transcription levels of tens of thousands of genes, and of their relative expression between normal and diseased cells. As microarray data analysis evolves, there is a widespread hope that microarrays will significantly impact our ability to explore the genetic changes associated with disease etiology and development, ultimately leading to the discovery of new biomarkers for disease diagnosis and prognosis prediction as well as new therapeutic tools. The goal of this manuscript is to review 2 of the most commonly used microarray technologies, provide an overview of data analyses involved in a typical microarray experiment, and comment upon the application of microarrays to oral medicine.

Biomarkers↗

PubMed2002

Gene expression profiling following BMP-2 induction of mesenchymal chondrogenesis in vitro.

OBJECTIVE: This study aims to apply gene expression profiling technology to gain insight into the molecular regulation of mesenchymal chondrogenesis. METHODS: The experimental system consists of micromass cultures of C3H10T1/2 cells, a murine multipotential embryonic cell line, treated with the chondroinductive growth factor, bone morphogenetic factor-2 (BMP-2). In this system, chondrogenic differentiation characterized by both morphological changes and cartilage matrix gene expression has been shown to be completely dependent upon BMP-2 treatment and the high cell plating density of micromass cultures. To identify candidate genes that may have key functional roles in chondrogenesis, we have applied subtractive hybridization to isolate genes whose expression is significantly up- or down-regulated during chondrogenesis. RNA was isolated from micromass cultures treated with BMP-2 for 24 h and analysed for representational differences by means of a subtractive hybridization screening method. RESULTS: Sixteen different genes were identified whose expression was up-regulated between two- and 12-fold by B,P-2, and twelve different genes were identified whose expression was down-regulated between two- and seven-fold by BMP-2. CONCLUSIONS: The potential of this screening methodology to identify new BMP-2 regulated genes is suggested by the fact that a majority of the identified genes are indeed novel. Identification and characterization of these genes should provide insight as to how chondrogenesis is regulated and also should provide important new markers for the study of osteoarthritis.

Animals↗

PubMed2005

Alternative life histories shape brain gene expression profiles in males of the same population.

Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative 'sneaker' tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the 'default' life cycle, may actually result from an active inhibition of development into a sneaker.

Adaptation, Physiological↗

PubMed2006

Expression profiles of high voltage-activated calcium channels in sympathetic and parasympathetic pelvic ganglion neurons innervating the urogenital system.

Among the autonomic ganglia, major pelvic ganglia (MPG) innervating the urogenital system are unique because both sympathetic and parasympathetic neurons are colocalized within one ganglion capsule. Sympathetic MPG neurons are discriminated from parasympathetic ones by expression of low voltage-activated Ca2+ channels that primarily arise from T-type alpha1H isoform and contribute to the generation of low-threshold spikes. Until now, however, expression profiles of high voltage-activated (HVA) Ca2+ channels in these two populations of MPG neurons remain unknown. Thus, in the present study, we dissected out HVA Ca2+ channels using pharmacological and molecular biological tools. Reverse transcription-polymerase chain reaction analysis showed that MPG neurons contained transcripts encoding all of the known HVA Ca2+ channel isoforms (alpha1B, alpha1C, alpha1D and alpha1E), with the exception of alpha1A. Western blot analysis and pharmacology with omega-agatoxin IVA (1 microM) confirmed that MPG neurons lack the alpha1A Ca2+ channels. Unexpectedly, the expression profile of HVA Ca2+ channel isoforms was identical in the sympathetic and parasympathetic neurons of the MPG. Of the total Ca2+ currents, omega-conotoxin GVIA-sensitive N-type (alpha1B) currents constituted 57 +/- 5% (n = 9) and 60 +/- 3% (n = 6), respectively; nimodipine-sensitive L-type (alpha1C and alpha1D) currents made up 17 +/- 4% and 14 +/- 2%, respectively; and nimodipine-resistant and omega-conotoxin GVIA-resistant R-type currents were 25 +/- 3% and 22 +/- 2%, respectively. The R-type Ca2+ currents were sensitive to NiCl2 (IC50 = 22 +/- 0.1 microM) but not to SNX-482, which was able to potently (IC50 = 76 +/- 0.4 nM) block the recombinant alpha1E/beta2a/alpha2delta Ca2+ currents expressed in human embryonic kidney 293 cells. Taken together, our data suggest that sympathetic and parasympathetic MPG neurons share a similar but unique profile of HVA Ca2+ channel isoforms.

Animals↗

PubMed2006

Gene expression profiling reveals consistent differences between clinical samples of human leukaemias and their model cell lines.

Microarray gene expression profiles of fresh clinical samples of chronic myeloid leukaemia in chronic phase, acute promyelocytic leukaemia and acute monocytic leukaemia were compared with profiles from cell lines representing the corresponding types of leukaemia (K562, NB4, HL60). In a hierarchical clustering analysis, all clinical samples clustered separately from the cell lines, regardless of leukaemic subtype. Gene ontology analysis showed that cell lines chiefly overexpressed genes related to macromolecular metabolism, whereas in clinical samples genes related to the immune response were abundantly expressed. These findings must be taken into consideration when conclusions from cell line-based studies are extrapolated to patients.

Gene Expression↗

PubMed2004

The expression profile of lectin differs from that of seed storage proteins in Castanea crenata trees.

Using Northern blot analysis, the expression of the Japanese chestnut (Castanea crenata Sieb. et Zucc.) agglutinin (CCA) gene was compared with that of its seed storage protein (SSP) gene. After cDNA cloning of SSP, the expression profile of SSP mRNA and CCA mRNA were compared. SSP mRNA was seed-specific, while CCA mRNA was expressed in the stems and flowers (both male and female) as well as in the seeds. Whereas extracts from all organs observed using Western blot analysis exhibited positive signals, in seeds, large expressions of SSP mRNA were restricted to the late maturation and harvest stages. Levels were maintained during the dormant period. No expression was observed during the germination stage. In contrast, CCA mRNA expression was maintained at a high level during development, was at a relatively low level during dormancy, and showed subsequent high expression during germination. These results suggest that one of the physiological roles of CCA is to act as a vegetative storage protein. But since protein expression did not coincide with that of mRNA, the expression of CCA may be regulated both at the transcription and the translation levels.

Agglutinins↗

PubMed2004

Identification of maspin and S100P as novel hypomethylation targets in pancreatic cancer using global gene expression profiling.

DNA hypomethylation is one of the major epigenetic alterations in human cancers. We have previously shown that genes identified as hypomethylated in pancreatic cancer are expressed in pancreatic cancer cell lines, but not in normal pancreatic ductal epithelium and can be reexpressed in nonexpressing cells using 'epigenetic modifying agents' such as DNA methyltransferase inhibitors. To identify additional targets for aberrant hypomethylation in pancreatic cancer, we used oligonucleotide microarrays to screen for genes that displayed expression patterns associated with hypomethylation. This analysis identified a substantial number of candidates including previously reported hypomethylated genes. A subset of eight genes were selected for further methylation analysis, and two cancer-related genes, maspin and S100P, were found to be aberrantly hypomethylated in a large fraction of pancreatic cancer cell lines and primary pancreatic carcinomas. Combined treatment with 5-aza-2'-deoxycytidie and trichostatin A resulted in synergistic induction of maspin and S100P mRNA in MiaPaCa2 cells where both genes were methylated. Furthermore, there was an inverse correlation between methylation and mRNA expression level for maspin and S100P in a large panel of pancreatic cancer cell lines. We also found a significant difference in the methylation patterns of maspin and two previously identified hypomethylated genes (trefoil factor 2 and lipocalin 2) between pancreatic and breast cancer cell lines, suggesting cancer-type specificity for some hypomethylation patterns. Thus, our present results confirm that DNA hypomethylation is a frequent epigenetic event in pancreatic cancer, and suggest that gene expression profiling may help to identify potential targets affected by this epigenetic alteration.

Calcium-Binding Proteins↗

PubMed2006

Use of self-quenched, fluorogenic LUX primers for gene expression profiling.

Application of a real-time detection system based on a novel primer design in gene expression profiling is described. In this system, called LUX (Light Upon eXtension), the generation of signal is based on a single fluorescent dye molecule that is attached to an oligonucleotide close to the 3'-end. A primer design software is available that identifies LUX primer pairs based on a set of rules for optimum signal development. The use of LUX fluorogenic primers to determine the expression patterns of various transcripts during differentiation in the P-19 mouse neuronal model is described.

Animals↗

PubMed2001

A gene expression profile of embryonic stem cells and embryonic stem cell-derived neurons.

Embryonic stem (ES) cells have the ability to differentiate into a variety of cell lineages. We are examining ES cell differentiation in vitro by using cDNA microarrays to generate a molecular phenotype for each cell type. El4 ES cells induced by retinoic acid after forming embryoid bodies differentiate almost exclusively to neurons. We obtained expression patterns for about 8500 gene sequences by comparing mRNAs from undifferentiated ES cells and their differentiated derivatives in a competitive hybridization. Our results indicate that the genes expressed by ES cells change dramatically as they differentiate (58 gene sequences up-regulated, 34 down-regulated). Most notably, totipotent ES cells expressed high levels of a repressor of Hox expression (the polycomb homolog Mphl) and a co-repressor (CTBP2). Expression of these genes was undetectable in differentiated cells; the ES cell-derived neurons expressed a different set of transcriptional regulators, as weil as markers of neurogenesis. The gene expression profiles indicate that ES cells actively suppress differentiation by transcriptional repression; cell-cell contact in embryoid bodies and retinoic acid treatment may overcome this suppression, allowing expression of Hox genes and inducing a suite of neuronal genes. Gene expression profiles will be a useful outcome measure for comparing in vitro treatments of differentiating ES cells and other stem cells. Also, knowing the molecule phenotype of transplantable cells will allow correlation of phenotype with the success of the transplant.

Cell Differentiation↗

PubMed2002

[cDNA array approach to cytokine expression profile of aseptic loosened hip arthroplasty].

FACTS: Aseptic loosening of hip arthroplasties are the main reason for revision operations. Basic research indicates a significant relevance of the interface membrane formed between the implant an the surrounding bone. Their cellular composition and the influence of various factors on the process of aseptic loosening has attracted scientific interest. Cytokines are essential for intracellular communication. QUESTION: Is it possible to reveal differences in the expression profile of cytokines between well-fixed and failed hip arthroplasties using the cDNA array approach? AIM. Generation of a cytokine expression profile characteristic for failed hip arthroplasty. METHODS AND RESULTS: Radioactively labeled cDNA probes were synthesised from mRNA isolated from the interface membrane of six patients with aseptic loosened hip arthroplasty. Using a phosphorimager the analysis of the cDNA arrays revealed nine cytokines which were overexpressed compared with the reference tissue (Calgranulin A, Calgranulin B, IL-10, MCP-1, RANTES, TFDG1, TNFR2, RAI, THYB10). CONCLUSION: In this study four out of these nine cytokines were found to be connected with the process of aseptic loosening for the first time.

Arthroplasty, Replacement, Hip↗

PubMed2003

Gene expression profiling of malignant mesothelioma.

PURPOSE: Malignant mesothelioma is a uniformly fatal cancer of the pleural and peritoneal spaces. Several challenging clinical problems include poor understanding of the pathophysiology, inaccurate diagnosis from tissue samples, and unsuccessful treatment strategies. The purpose of this study was to use microarray analysis to identify specific gene expression changes in mesothelioma compared with normal mesothelium. EXPERIMENTAL DESIGN: We performed gene expression analysis on mesothelioma tissue specimens from 16 patients and compared these to 4 control pleural tissue samples using cDNA microarray filters with 4132 clones. Multiple normalization and analysis approaches were used. Quantitative reverse transcription-PCR and immunohistochemistry were used to validate results. RESULTS: Genes (166) were significantly up-regulated, and 26 were down-regulated. Validation of 18 genes using real-time PCR confirmed array predictions in every case. Analysis revealed activation of several key pathways including genes involved in glucose metabolism, mRNA translation, and cytoskeletal remodeling. Expression profiling identified processes likely responsible for 18-fluoro-2-deoxy-glucose uptake and tumor localization by positron emission tomography, and a role for hypoxia-inducible factor-1 was suggested. Potentially important up-regulated genes included gp96, lung resistance-related protein, galectin-3 binding protein, the M(r) 67,000 laminin receptor (on tumor vessels), and voltage-dependent anion channels. Prospective testing using reverse transcription-PCR confirmed up-regulation of these novel markers. CONCLUSIONS: Expression profiling revealed marked up-regulation of energy, protein translation, and cytoskeletal remodeling pathways in mesothelioma. Additional genes that could be important in our understanding of the pathogenesis of mesothelioma, aiding in diagnosis, or improving targets for therapy were also identified.

Aged↗

PubMed2003

Comparison of gene expression profiles of lymphoma cell lines from transformed follicular lymphoma, Burkitt's lymphoma and de novo diffuse large B-cell lymphoma.

To determine the specific gene expression in B-cell lymphoma subtypes, we compared expression profiles of cell lines from transformed follicular lymphoma (tFL), Epstein-Barr virus-negative (EBV(-)) Burkitt's lymphoma (BL) and EBV(+)BL. Complementary DNAs were synthesized from these cell lines and hybridized with the Atlas Human 1.2 Array membrane. Hierarchical clustering analysis based upon the levels of 43 genes highlighted characteristic expression patterns of the 3 lymphoma subtypes. Genes expressed at higher levels in tFL than EBV(-)BL and EBV(+)BL included calcium/calmodulin-dependent protein kinase I (CAMK1) and mitogen-activated protein kinase 10 (MAPK10). EBV(-)BL was characterized by high-level expression of amyloid beta precursor protein (APP), heat shock 27 kD protein 1 (HSPB1) and mothers against decapentaplegic homolog 1 (MADH1). Gardner-Rasheed feline sarcoma viral oncogene homolog (FGR) was the most significant gene to delineate EBV(+)BL. A subtype prediction algorithm using 34 genes correctly classified 22 (92%) of 24 lymphomas into FL/tFL, EBV(-)BL or EBV(+)BL. By comparison with normal reference B-cell materials, the expression patterns of the selected genes were characteristic of lymphomas. We extended the clustering analysis to cell lines from de novo diffuse large B-cell lymphoma (DLBCL). The DLBCL cell lines were either separated from the former 3 lymphoma subtypes or segregated with EBV(+)BL, possibly reflecting variable genetic abnormalities. The associations of CAMK1 with tFL, APP and MADH1 with EBV(-)BL, FGR with EBV(+)BL, and BCL2 with tFL and DLBCL were confirmed by real-time quantitative reverse transcriptase-mediated polymerase chain reaction assays. This study has provided new molecular markers, expressions of which are closely associated with B-cell lymphoma subtypes.

B-Lymphocytes↗

PubMed2005

New insights into MLL gene rearranged acute leukemias using gene expression profiling: shared pathways, lineage commitment, and partner genes.

Rearrangements of the MLL gene occur in both acute lymphoblastic and acute myeloid leukemias (ALL, AML). This study addressed the global gene expression pattern of these two leukemia subtypes with respect to common deregulated pathways and lineage-associated differences. We analyzed 73 t(11q23)/MLL leukemias in comparison to 290 other acute leukemias and demonstrate that 11q23 leukemias combined are characterized by a common specific gene expression signature. Additionally, in unsupervised and supervised data analysis algorithms, ALL and AML cases with t(11q23) segregate according to the lineage they are derived from, that is, myeloid or lymphoid, respectively. This segregation can be explained by a highly differing transcriptional program. Through the use of novel biological network analyses, essential regulators of early B cell development, PAX5 and EBF, were shown to be associated with a clear B-lineage commitment in lymphoblastic t(11q23)/MLL leukemias. Also, the influence of the different MLL translocation partners on the transcriptional program was directly assessed. Interestingly, gene expression profiling did not reveal a clear distinct pattern associated with one of the analyzed partner genes. Taken together, the identified molecular expression pattern of MLL fusion gene samples and biological networks revealed new insights into the aberrant transcriptional program in 11q23/MLL leukemias.

Acute Disease↗