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PubMed2004

GenePaint.org: an atlas of gene expression patterns in the mouse embryo.

High-throughput instruments were recently developed to determine gene expression patterns on tissue sections by RNA in situ hybridization. The resulting images of gene expression patterns, chiefly of E14.5 mouse embryos, are accessible to the public at http://www.genepaint.org. This relational database is searchable for gene identifiers and RNA probe sequences. Moreover, patterns and intensity of expression in approximately 100 different embryonic tissues are annotated and can be searched using a standardized catalog of anatomical structures. A virtual microscope tool, the Zoom Image Server, was implemented in GenePaint.org and permits interactive zooming and panning across approximately 15,000 high-resolution images.

Animals↗

PubMed2002

A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ.

We apply the fast redundant dyadic wavelet transform to the spatial registration of two-dimensional gene expression patterns of 736 Drosophila melanogaster embryos. This method is superior to the Fourier transform or windowed Fourier transform because of its ability to reduce noise and is of high resolution. In registration of the dataset we use two cost functions based on computing the Euclidean or Mahalanobis distance. The algorithm shows a high level of accuracy. For early temporal classes the cost function based on Mahalanobis distance gives better results. We have reported a method for construction of an integrated dataset elsewhere. In this paper the method is extended to the two-dimensional case. The procedure for data assembly provides for the preservation of some aspects of the nuclear structure of a two-dimensional gene expression pattern. It is based on creating an averaged model that reproduces the spatial distribution of nuclei over the embryo image. The average concentrations of each protein in each averaged nucleus are computed from the series of embryos of the same age.

Algorithms↗

PubMed2004

Atlas of Hox gene expression in the developing kidney.

Hox genes often play important roles in segment identity determination and organogenesis. To better understand the roles of Hox genes during kidney development, we performed an extensive analysis of their expression patterns. Section in situ hybridizations were used to define the expression of 37 Hox genes at embryonic day (E) 12.5, E13.5, E15.5, and E17.5 of kidney development. Several interesting principles emerged. First, the concept of colinearity was preserved. Hox genes from the more 3' positions in clusters were more often expressed in the ureteric bud, which is derived from the anterior of the intermediate mesoderm. Second, Hox genes were expressed throughout the ureteric bud without any segment specificity. Third, in the different segments of the forming nephron we did observe overlapping domains of Hox gene expression, which initiated distally at the junction between the nephron and ureteric bud, and extended proximally variable distances. Finally, we observed that paralogous Hox genes often showed surprisingly diverse expression patterns. Indeed, contiguous genes on a single cluster more often showed similar expression patterns than paralogs. In summary, the resulting atlas of Hox gene expression provides a foundation for further study of the overlapping functions Hox genes in the developing kidney.

Animals↗

PubMed2006

[The effects of CT120B over-expression on growth suppression and changes of gene expression profiles in lung adenocarcinoma cells].

OBJECTIVE: CT120B gene is a splicing variant of CT120A, which deletes 96 nucleotides and leads to an in-frame loss of 32 amino acids between the codon 136 and 167 as compared with CT120A. This study was undertaken to assess the effects of CT120B expression on lung cancer cell growth and to explore the gene expression profiles. METHODS: CT120B cDNA was transfected into the human lung adenocarcinoma SPC-A-1 cells, and stable cell lines overexpressing CT120B were established. CCK-8 assay and tumorigenecity in a xenograft model were performed to analyze cell proliferation in vitro and in vivo. The differential gene expression induced by overexpressed CT120B was investigated using Atlas cDNA expression array. Flow cytometry was performed to analyze cell cycle and cell apoptosis. RESULTS: Overexpression of CT120B in SPC-A-1 cells resulted in a reduced cell growth rate in vitro, and decrease of the tumorigenicity in nude mice. A total of 38 genes were identified as differential expressions with more than a 2.0-fold change by Atlas cDNA expression array analysis, including downregulated cyclin E1, cdk 2, c-kit, CXCR4 and upregulated caspase 8 gene. Overexpression of CT120B also induced G1 phase arrest, but had no effect on cell apoptosis. CONCLUSION: The G1 cell cycle arrest, but not apoptosis, underlay the growth inhibitory activities of CT120B. The down-regulation of c-kit and CXCR4 expression might also contribute to the suppressive effects on cell growth of CT120B.

Adenocarcinoma↗

PubMed2002

Cellular signaling, AGE accumulation and gene expression in hepatocytes of lean aging rats fed ad libitum or food-restricted.

The effects of food restriction on liver glucagon and vasopressin V1a receptors, on AGE accumulation and on gene expression were investigated in 10- and 30-month-old WAG/Rij female rats fed ad libitum or chronically food-restricted by 30%. The age-related increase in glucagon and vasopressin V1a receptor density, as well as the rise in glucagon-induced cAMP generation was prevented by the restriction. AGE accumulation, characteristic of the aging process, was normalized in food-restricted animals. Gene expression determined with rat Atlas cDNA Expression Arrays containing 1176 cDNA indicates that a few genes exhibited a greater than twofold change in mRNA ratios with age. Most down-regulated genes were related to oxidative metabolism of lipids, and most of the up-regulated genes were concerned with the cell cycle and transcription factors. Chronic food restriction partially prevents these changes in gene expression and induces up- and down-regulation of several mRNAs which are not modified with age in ad libitum fed rats.

Aging↗

PubMed2004

Expression of TN4 gene and its role in human hepatocarcinogenesis from Qidong, a liver cancer risk area.

BACKGROUND: We investigated the expression and role of TN4 in the oncogenesis of human hepatocellular carcinoma (HCC) from Qidong which is a HCC risk area. METHODS: The expression of TN4 in HCC was observed using immunohistochemical staining (IHC). TN4 levels were manipulated in human liver cancer cell SMMC7721, using pcDNA3.1 eukaryotic expression constructs designed to express the complete TN4 cDNA. The biological changes of the cells were observed before and after transfection of TN4 and the change of gene expression was analysed by atlas cDNA expression array. RESULTS: Among 100 pairs of samples of HCC, TN4 down-regulation expression and up-regulation expression positive rate were 81% (81/100), 19% (19/100), respectively (P < 0.01). TN4 protein was mainly localized in cytoplasm and membrane. The positive rate of TN4 were 10% (3/30), 100% (70/70) in lymph node metastasis and no lymph node metastasis, respectively (P < 0.01). The growth rates of the derivative SMMC7721-TN4 cell lines were decreased in comparison with that of normal SMMC7721 cells and pcDNA-SMMC7721. Some gene expression was changed before and after transfection of TN4. At 30 days of post-implantation of SMMC7721-TN4, SMMC7721-pcDNA3, SMMC7721 group produced tumors of (301.9 +/- 143.4) mm(3), (2418.7 +/- 362.8) mm(3), (2317.4 +/- 587.8) mm(3), respectively, (P < 0.01). Tumor inhibiting rate was 82.4% in TN4 transfection group. Sections of tumors were observed for their degree of tissue necrosis and there was higher degree of necrosis in tumors of the TN4-SMMC7721 cell group than those of the SMMC7721, SMMC7721-pcDNA groups. CONCLUSIONS: TN4 may play an important role in the oncogenesis of human HCC, especially in Qidong, the HCC risk area and TN4 could be a candidate tumor suppressor gene for HCC.

Adult↗

PubMed2001

Radiation-induced apoptosis of human peripheral T cells: analyses with cDNA expression arrays and mitochondrial membrane potential assay.

We examined sequential changes in post-irradiated peripheral blood T cells taken from normal volunteers, by using targeted Atlas cDNA Expression Arrays and mitochondrial membrane potential assay. At 1 and 3 hours after 5 Gy irradiation, changes of gene expression were examined by targeted Atlas cDNA Expression Arrays using Apoptosis Array. The Atlas Human Apoptosis Array includes 205 key genes that are known to control apoptosis, including extracellular and cytoplasmic effectors. Concerning Fas, no significant changes of spot intensities were identified between irradiated T cells and non-irradiated ones at both 1 h and 3 h after 5 Gy irradiation. Caspase families, including caspases 9 and 3 also showed no changes between these two groups. An apoptosis regulator bclw showed a remarkable decrease in irradiated T cells. These results suggested that irradiation induced direct apoptosis of T cells by changing the membrane potential of mitochondria. Using a CCD camera-equipped fluorescence microscope and MitoCapture, a mitochondrial membrane potential indicator, we demonstrated 5 Gy radiation induced loss of membrane potential, i.e., an early stage of apoptosis, in human peripheral blood T cells at 10 hours after irradiation.

Apoptosis↗

PubMed2004

An atlas of differential gene expression during early Xenopus embryogenesis.

We have carried out a large-scale, semi-automated whole-mount in situ hybridization screen of 8369 cDNA clones in Xenopus laevis embryos. We confirm that differential gene expression is prevalent during embryogenesis since 24% of the clones are expressed non-ubiquitously and 8% are organ or cell type specific marker genes. Sequence analysis and clustering yielded 723 unique genes displaying a differential expression pattern. Of these, 18% were already described in Xenopus, 47% have homologs and 35% are lacking significant sequence similarity in databases. Many of them encode known developmental regulators. We classified 363 of the 723 genes for which a Gene Ontology annotation for molecular function could be attributed and found 'DNA binding' and 'enzyme' the most represented terms. The most common protein domains encoded in these embryonic, differentially expressed genes are the homeobox and RNA Recognition Motif (RRM). Fifty-nine putative orthologs of human disease genes, and 254 organ or cell specific marker genes were identified. Markers were found for nasal placode and archenteron roof, organs for which a specific marker was previously unavailable. Markers were also found for novel subdomains of various other organs. The tissues for which most markers were found are muscle and epidermis. Expression of cell cycle regulators fell in two classes, containing proliferation-promoting and anti-proliferative genes, respectively. We identified 66 new members of the BMP4, chromatin, endoplasmic reticulum, and karyopherin synexpression groups, thus providing a first glimpse of their probable cellular roles. Cluster analysis of tissues to measure tissue relatedness yielded some unorthodox affinities besides expectable lineage relationships. In conclusion, this study represents an atlas of gene expression patterns, which reveals embryonic regionalization, provides novel marker genes, and makes predictions about the functional role of unknown genes.

Animals↗

PubMed2005

Influence of sex on gene expression in the mouse lacrimal gland.

Significant, sex-associated differences exist in the physiology and pathophysiology of the lacrimal gland. We hypothesize that many of these differences are due to fundamental variations in gene expression. The purpose of this study was to determine the extent to which sex-related differences in gene expression are present in the lacrimal gland. Lacrimal glands were obtained from adult male and female BALB/c mice (n=5-10mice/sex/experiment), pooled according to sex and processed for the isolation of RNA. Samples were analyzed for differentially expressed mRNAs by using Atlas Mouse cDNA Expression Arrays, cDNA amplification techniques, GEM 1 and 2 gene chips, CodeLink bioarrays and quantitative real-time PCR (qPCR) procedures. Quantitative evaluation of Atlas Array gene expression was performed with an image analysis system developed in our laboratory, whereas gene chip data were analyzed with Rosetta Resolver and GeneSifter.Net software. Statistical significance was determined by using Student's t-test. Our results with CodeLink bioarrays show that sex has a significant influence on the expression of over 490 genes in the mouse lacrimal gland. These genes are involved in a wide range of biological processes, molecular functions and cellular components, including such activities as development, growth, transcription, metabolism, signal transduction, transport, receptor activity and protein and nucleic acid binding. The expression of selected genes was confirmed by the use of GEM gene chips and qPCR. Our findings also demonstrate that certain methodological approaches are less useful in attempting to assess the magnitude of sex-associated differences in the lacrimal gland. These results support our hypothesis that sex-related differences in gene expression play a role in the sexual dimorphism of the lacrimal gland.

Animals↗

PubMed1995

An atlas of aromatase mRNA expression in the zebra finch brain.

Neural conversion of androgen to estrogen by aromatase is an important step in the development and expression of masculine behavior in mammals and birds. In contrast to the low telencephalic levels of aromatase in adult mammals and nonsongbirds, the zebra finch telencephalon possesses high aromatase activity. This study maps, by in situ hybridization, cells that express aromatase mRNA in the adult zebra finch telencephalon, diencephalon, midbrain, and pons. High aromatase mRNA expression was observed in the caudal neostriatum, limbic archistriatum, and hypothalamus. The hippocampus, parahippocampal area, and hyperstriatum accessorium contained cells expressing moderate amounts of aromatase message. Weakly labeled cells were found in the rostral neostriatum, lobus parolfactorius, and mesencephalic reticular formation. These findings are consistent with aromatase activity measurements of zebra finch tissue and document with anatomical precision both the widespread expression of aromatase mRNA in the brain and novel sites of brain aromatase. This study identifies the caudal neostriatum as a major site of telencephalic aromatase. A previous survey (Gahr et al., 1993: J. Comp. Neurol. 327:112-122) of several avian species found that the presence of estrogen receptors in parts of the caudal neostriatum is unique to songbirds, which are the only birds to possess the elaborated telencephalic song system. Together, these findings suggest that the heightened estrogen synthesis and estrogen sensitivity of the passerine caudal neostriatum may have some functional relation with the telencephalic circuits responsible for song.

Animals↗

PubMed2002

Gene expression of cell surface antigens in the early phase of murine influenza pneumonia determined by a cDNA expression array technique.

BACKGROUND: Influenza virus is a worldwide health problem with significant economic consequences. To study the gene expression pattern induced by influenza virus infection, it is useful to reveal the pathogenesis of influenza virus infection; but this has not been well examined, especially in vivo study. AIMS: To assess the influence of influenza virus infection on gene expression in mice, mRNA levels in the lung and tracheal tissue 48 h after infection were investigated by cDNA array analysis. METHODS: Four-week-old outbred, specific pathogen free strain, ICR female mice were infected by intra-nasal inoculation of a virus solution under ether anesthesia. The mice were sacrificed 48 h after infection and the tracheas and lungs were removed. To determine gene expression, the membrane-based microtechnique with an Atlas cDNA expression array (mouse 1.2 array II) was performed in accordance with the manual provided. RESULTS AND CONCLUSIONS: We focused on the expression of 46 mRNAs for cell surface antigens. Of these 46 mRNAs that we examined, four (CD1d2 antigen, CD39 antigen-like 1, CD39 antigen-like 3, CD68 antigen) were up-regulated and one (CD36 antigen) was down-regulated. Although further studies are required, these data suggest that these molecules play an important role in influenza virus infection, especially the phase before specific immunity.

Adenosine Triphosphatases↗

PubMed2005

An atlas of human gene expression from massively parallel signature sequencing (MPSS).

We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences in gene expression between cell and tissue types are largely determined by transcripts derived from a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little more than half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the idea that most human genes have been mapped, if not functionally characterized. This data set should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance. The data are available on the Web at http://mpss.licr.org and http://sgb.lynxgen.com.

Algorithms↗

PubMed2005

Down-regulation of CT120A by RNA interference suppresses lung cancer cells growth and sensitizes to ultraviolet-induced apoptosis.

CT120A gene was isolated from chromosome 17p13.3 by using positional cloning and RACE by our laboratory. Here, we reported the evidence that CT120A protein was a potential molecular target for treatment of lung cancers. CT120A was overexpressed in 15 cases of the 16 primary lung cancer specimens. Knockdown of CT120A by small hairpin RNA in the human lung adenocarcinoma cell line SPC-A-1 cells resulted in a reduced cell growth rate in vitro and decrease of the capacity for anchorage-independent growth and tumorigenicity in nude mice. The suppression of CT120A expression also sensitized cells to ultraviolet-induced apoptosis. Atlas cDNA expression array revealed that the expressions of several apoptosis- and growth-associated genes were altered underlying the molecular mechanisms of these cell biological behaviors. These results suggested that CT120A was a novel lung cancer-related gene and CT120A might be a potential target for therapeutic anti-cancer drugs.

Adenocarcinoma↗

PubMed2026

TCGA-based identification of prognostic biomarkers and candidate traditional Chinese medicine compounds in papillary thyroid carcinoma: An observational study.

This study aimed to identify prognostic genes associated with papillary thyroid carcinoma (PTC) and explore candidate traditional Chinese medicine (TCM) compounds using integrated bioinformatics and molecular docking. In this observational study, PTC gene expression profiles and clinical data were obtained from The Cancer Genome Atlas. Differentially expressed genes were screened using differential-expression sequencing (DESeq2), followed by protein-protein interaction network analysis to identify hub genes. Their expression, diagnostic value, immune relevance, prognostic significance, protein-level validation, and single-cell distribution were assessed using gene expression profiling interactive analysis, receiver operating characteristic analysis, immune infiltration analysis, Kaplan-Meier survival analysis, the human protein atlas, and single-cell RNA-sequencing data. Candidate TCM compounds were predicted using symptom mapping (SymMap) and the TCM Systems Pharmacology Database and Analysis Platform, and molecular docking was performed to evaluate potential ligand-target interactions. Five hub genes, colony-stimulating factor 2, apolipoprotein E, fibronectin 1 (FN1), collagen type I alpha 1 chain (COL1A1), and intercellular adhesion molecule 1, were identified and found to be significantly upregulated in PTC tissues, with diagnostic value in receiver operating characteristic analysis. Immune infiltration analysis showed associations with macrophages, dendritic cells, and T helper 1 cells, whereas single-cell analysis demonstrated heterogeneous expression across immune and stromal cell populations, including fibroblasts. Higher FN1 and COL1A1 expression was associated with poorer outcomes. Immunohistochemistry supported the expression patterns, while single-cell analysis provided exploratory cell-type-level context for the cellular distribution of selected genes. Ginseng and Smilax glabra were predicted as common candidate TCMs, and docking suggested favorable binding between their active compounds and selected hub targets. Colony-stimulating factor 2, apolipoprotein E, FN1, COL1A1, and intercellular adhesion molecule 1 may be biologically relevant hub genes in PTC, while FN1 and COL1A1 may have prognostic value. Predicted TCM compounds provide preliminary computational evidence for possible compound-target interactions, requiring experimental and clinical validation.

Female↗

PubMed2003

cDNA array analysis of alterations in gene expression in the promyelocytic leukemia cell line, HL-60, after apoptosis induction with etoposide.

Alterations in gene expression during apoptosis in HL-60 cells were identified by a cDNA based array analysis. Apoptosis was induced in the human promyelocytic leukemia cell line, HL-60, by incubation with 30 microM etoposide for 5 hours. Changes in gene expression occurring during apoptosis in these cells were detected using the "ATLAS cDNA Expression Array" technique. 40 genes were identified as differentially expressed in the apoptotic cells by at least a factor of two. 30 of these genes were down-regulated during apoptosis. Many of the down-regulated genes reflected decreased proliferative activity in the cells as well as decreased activity of survival pathways. Most of the genes, which were up-regulated during apoptosis, were genes involved in pathways leading to cell death and suppression of proliferation. Based on the up-regulations observed at the mRNA level, it is speculated that etoposide-induced apoptosis in the HL-60 cells proceeds via pathways involving factors such as TNFalpha, IGFBP3, SAPK1, AP-1 and GADD153/CHOP10. Four genes, which showed changes at the mRNA level, were also analyzed by Western blotting in order to confirm the observed differences at the protein level.

Animals↗

PubMed2000

Inhibition of COX-2 and induction of apoptosis: two determinants of nonsteroidal anti-inflammatory drugs' chemopreventive efficacies in mouse lung tumorigenesis.

Recent studies suggested that nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit lung tumorigenesis under conditions that are immunosuppressive. We hypothesized that this inhibition of mouse lung tumorigenesis requires induction of apoptosis and inhibition of COX (cyclooxygenase)-1, COX-2, and the incidence of K-ras mutation. The NSAIDs used in this study include acetylsalicylic acid (ASA) that is anti-inflammatory with COX-1 and COX-2 inhibition and N-[2-(cyclohexyloxy)-4-nitrophenyl]-methanesulfonamide (NS398) that is a specific COX-2 inhibitor. We have previously demonstrated that ASA (147 and 294 mg/kg diet) and NS398 (7 mg/kg diet) inhibited lung tumorigenesis by 31%, 44%, and 34%, respectively, in 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-treated A/J mice. No difference in the incidence and types of K-ras mutations was found between the lung tumors treated with NNK and those treated with NNK/ASA and NNK/NS398. In NNK-treated mice, ASA (394 mg/kg diet) or NS398 significantly increased the apoptotic index, from 0.07 to 0.30 or to 0.33, respectively. ASA (294 mg/kg diet) and NS398 also inhibited the expression of COX-2. Finally, modulation of gene expression by NS398 and ASA (294 mg/kg diet) was determined using Atlas cDNA expression arrays. Expression of cyclin B2 was decreased and expression of Fas-L and BAD were increased in lung tissues treated with both NS398 and ASA. Treatment with NS398 also increased expression of p57kip2 and myosin. These genes modulated by NSAIDs may play a role in mediating the observed chemopreventive effects of the NSAIDs in the mouse lung. Our results demonstrate that lung tumor prevention with NSAIDs involve both the induction of apoptosis and the inhibition of COX-2 expression.

Adenoma↗

PubMed2001

[Gene apoptosis expression profiles in liver cancer and their comparison to normal peri-cancerous liver tissues].

OBJECTIVE: To describe a few gene expression profiles related to apoptosis and to demonstrate their difference between the liver cancer and its adjacent normal tissues. METHODS: cDNA, labeled as a-32P dATP was synthesized from the total RNA of cancer and adjacent normal tissues and, then, hybridized individually with two identical array membranes of Atlas human cancer dDNA expression containing 588 known genes. The method involving gene-specific semi-quantitative reverse transcription in the polymerase chain reaction (RT-PCR) was used to confirm the expression pattern of three known genes. RESULTS: Autoradiographic results were analyzed by specific AtlasImage (version 1.01a) software. Among 69 genes that were found to be related to apoptosis, 4 were up-related, including Aktl, and 19 were down-related, including BAK, Caspase-3, etc., all being related to cancer. The RT-PCR results showed that the expression pattern of all genes was in agreement with the results of Atlas expression array. CONCLUSION: The result obtained from Atlas microarray provides a liver cancer-specific expression profile related to apoptosis. The discovery about the apoptosis related genes may yield some clues on the oncogenetic mechanism of liver cancer in the future. The differential hybridization technique of cDNA expression array involving the Atlas human cancer can become a useful method in the understanding of the development and progression of human cancer.

Apoptosis↗

PubMed2002

[Effects of two haplotypes of HCAP1 gene on cellular gene expression levels in a human hepatocarcinoma cell line Hep3B].

BACKGROUND AND OBJECTIVE: HCAP1 gene is a novel gene cloned in our laboratory, which has two haplotypes(N and M). This study was designed to investigate the effects of two haplotypes of HCAP1 gene on cellular gene expression levels in a human hepatocarcinoma cell line Hep3B. METHODS: The Hep3B-Tet-on cells were transfected with HCAP1N or HCAP1M using liposome transfection reagent. In order to obtain the cells with high inducible expression of HCAP1N or HCAP1M, the transfected cells were screened by Western blot. Then, human atlas cDNA expression arrays were used to analyze the cellular gene expression profiles before and after HCAP1N or HCAP1M over-expression. The hybridization results were analyzed with FR-200 image system. RESULTS: The profiles of differential gene expression before and after HCAP1N or HCAP1M over-expression were established. These data indicated that over-expression of HCAP1M resulted in an up-regulation of genes involved in cellular proliferation (e.g., c-erbB2 receptor and transcription factor DP2) and a down-regulation of genes involved in cell apoptosis (caspase9) or DNA excision repair (ERCC5). While overexpression of HCAP1N resulted in an up-regulation of genes involved in cellular suppressors (e.g., snoN and WAF1) or DNA excision repair (ERCC5) and a down-regulation of genes involved in anti-apoptosis (HSPs). CONCLUSION: Over-expression of HCAP1M may promote cell proliferation. Over-expression of HCAP1N may suppress cell growth.

Amino Acid Sequence↗