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At least 253 records · Page 14Linked to original sources
PubMed2000

Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray.

cDNA microarray technology has been increasingly used to monitor global gene expression patterns in various tissues and cell types. However, applications to mammalian development have been hampered by the lack of appropriate cDNA collections, particularly for early developmental stages. To overcome this problem, a PCR-based cDNA library construction method was used to derive 52,374 expressed sequence tags from pre- and peri-implantation embryos, embryonic day (E) 12.5 female gonad/mesonephros, and newborn ovary. From these cDNA collections, a microarray representing 15,264 unique genes (78% novel and 22% known) was assembled. In initial applications, the divergence of placental and embryonic gene expression profiles was assessed. At stage E12.5 of development, based on triplicate experiments, 720 genes (6.5%) displayed statistically significant differences in expression between placenta and embryo. Among 289 more highly expressed in placenta, 61 placenta-specific genes encoded, for example, a novel prolactin-like protein. The number of genes highly expressed (and frequently specific) for placenta has thereby been increased 5-fold over the total previously reported, illustrating the potential of the microarrays for tissue-specific gene discovery and analysis of mammalian developmental programs.

Amino Acid Sequence↗
PubMed1999

cDNA expression array reveals heterogeneous gene expression profiles in three glioblastoma cell lines.

Tumor cell lines are an indispensable tool for cancer research. However, among cell lines of the same pathological group, heterogeneity has been detected in gene expression, gene mutation, and cellular response to various treatments. In this study, we systematically investigated the extent of heterogeneity of gene expression in three glioblastoma cell lines using cDNA array technology in which the expression of 588 cellular genes is studied simultaneously. Comparison of the expression profiles revealed substantial qualitative and quantitative heterogeneity. Among the 588 genes, 197 genes were expressed in all three lines and 56 genes were not expressed in any of the three lines; total of 222 genes were expressed in only two of the three cell lines, and 113 genes were expressed in only one of the three cell lines. These results provide molecular evidence that cell lines of the same pathological origin can be highly heterogeneous.

DNA, Complementary↗
PubMed2000

Gene expression profiling of advanced lung cancer.

Lung cancer is a highly aggressive neoplasm with 85% mortality. To identify new tumor-associated genes, we compared the expression profile of a primary metastasizing adenocarcinoma with normal airway epithelial cells. Two cDNA libraries of up- and downregulated genes were generated, comprising 253 and 299 clones, respectively. The sequence analysis revealed 205 different known genes and 314 cDNA fragments of unknown functions. Northern-blot analysis of 167 clones confirmed differential expression in 58%, and indicated a similar expression pattern in additional lung-cancer cell lines for selected clones, strengthening the value of this model for the identification of new candidate genes in lung carcinogenesis.

Chromosome Mapping↗
PubMed2000

Direct quantitative transcript analysis of the agr regulon of Staphylococcus aureus during human infection in comparison to the expression profile in vitro.

Bacteria possess a repertoire of distinct regulatory systems promoting survival in disparate environments. Under in vitro conditions it was demonstrated for the human pathogen Staphylococcus aureus that the expression of most virulence factors is coordinated by the global regulator agr. To monitor bacterial gene regulation in the host, we developed a method for direct transcript analysis from clinical specimens. Quantification of specific transcripts was performed by competitive reverse transcription-PCR, and results were normalized against the constitutively expressed gene for gyrase (gyr). Using sputum from cystic fibrosis (CF) patients infected with S. aureus we examined the transcription of the effector molecule RNAIII of agr, of spa (protein A), generally repressed by agr, and of hla (alpha-toxin), generally activated by agr. In the CF lung RNAIII was expressed poorly, indicating an inactive agr in vivo. Despite the low level of RNAIII expression, spa was detectable only in minute amounts and an irregular transcription of hla was observed in all sputum samples. After subculturing of patient strains agr-deficient isolates and isolates with unusual expression profiles, i.e., not consistent with those obtained from prototypic strains, were observed. In conclusion, the agr activity seems to be nonessential in CF, and from the described expression pattern of spa and hla, other regulatory circuits aside from agr are postulated in vivo.

Bacterial Proteins↗
PubMed1998

Expression profiling of single cells using 3 prime end amplification (TPEA) PCR.

The ability to relate the physiological status of individual cells to the complement of genes they express is limited by current methodological approaches for performing these analyses. We report here the development of a robust and reproducible method for amplifying 3' sequences of mRNA derived from single cells and demonstrate that the amplified cDNA, derived from individual human lymphoblastoma cells, can be used for the expression profiling of up to 40 different genes per cell. In addition, we show that 3 prime end amplification (TPEA) PCR can be used to enable the detection of both high and low abundance mRNA species in samples harvested from live neurons in rat brain slices. This procedure will facilitate the study of complex tissue function at the cellular level.

Animals↗
PubMed2001

Expression profile of human defensins and antimicrobial proteins in oral tissues.

Antimicrobial peptides and proteins are an important part of the innate host defense. In the present study, the expression profile of three human alpha-defensins, of two human beta-defensins (hBD) and of phospholipase A-2 (PLA-2) and lysozyme was determined by reverse transcription-polymerase chain reaction (RT-PCR) in 56 non-inflamed and 18 inflamed oral tissue samples and primary oral keratinocytes and fibroblasts. The transcripts for hBD-1 and -2 as well as for PLA-2 and lysozyme were found to be widely expressed. In the group of the alpha-defensins, the message for the human neutrophil peptide-1 (HNP-1) was frequently detected, whereas an expression of human Paneth's cell defensin-5 (HD-5) was identified in only a minority of samples. Transcripts for HD-6 were not detectable in any sample. Oral keratinocytes but not fibroblasts contained transcripts for the beta-defensins, suggesting that these defensins are produced in the epithelial compartment. In contrast, mRNA expression of neutrophil-derived HNP-1 and PLA-2 was not observed in any of these cells. These results suggest an important role for hBD-1 and hBD-2 in the innate oral epithelial host defense.

DNA, Complementary↗
PubMed2026

Genome-wide identification of the superoxide dismutase gene family in Lycium barbarum and their expression profiles under abiotic stress and phytohormone treatment.

BACKGROUND: Superoxide dismutases (SODs) are crucial metalloenzymes that constitute the first line of defense against reactive oxygen species in plants under abiotic stress. Wolfberry (Lycium barbarum) is an economically important medicinal plant with notable stress tolerance, however, a comprehensive genome-wide analysis of its SOD gene family has not yet been performed. RESULTS: We identified ten wolfberry SOD genes (LbaSODs) and classified them into three subfamilies: iron-SODs (Fe-SODs), manganese-SODs (Mn-SODs), and copper/zinc-SODs (Cu/Zn-SODs). Members within each subfamily shared conserved gene structures and motifs. Segmental duplication was the primary driver of LbaSOD expansion, with three paralogous pairs identified. Analysis of cis-regulatory elements in the promoter region revealed a predominance of stress- and hormone-responsive cis-elements, particularly ABA-responsive elements (ABREs) (22 copies) and LTR (17 copies) motifs. Tissue-specific expression profiling revealed that LbaSOD2 and LbaSOD5 expression peaked during early fruit development, whereas LbaSOD6, LbaSOD9, and LbaSOD10 were progressively upregulated through fruit maturation. Under abiotic conditions, Fe-SOD members were markedly suppressed during prolonged drought, whereas LbaSOD9 and LbaSOD10 were rapidly induced in response to salt stress. Among the phytohormone treatments, methyl jasmonate (MeJA) elicited the most pronounced response, with LbaSOD5 expression increasing by approximately 60-fold after 24 hours. Notably, abscisic acid (ABA) triggered an exceptionally strong transcriptional induction of LbaSOD5 (2.5 × 105-fold), LbaSOD10 (6 × 105-fold), and LbaSOD6 (70-fold). In addition, LbaSOD3 and LbaSOD7 transcripts were undetectable in any of the tested conditions. CONCLUSIONS: This study provides the first comprehensive characterization of the LbaSOD gene family and elucidates its hormone- and stress-responsive regulatory landscape, providing a valuable foundation for future functional investigations of LbaSOD genes in abiotic stress adaptation. The extraordinarily strong ABA-mediated induction of specific LbaSOD members, together with their tissue- and stress-specific expression patterns, highlights their potential as targets for genetic improvement of stress tolerance in wolfberry.

Lycium barbarum↗
PubMed1995

Comparative expressed-sequence-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment.

Nerve growth factor-induced differentiation of adrenal chromaffin PC-12 cells to a neuronal phenotype involves alterations in gene expression and represents a model system to study neuronal differentiation. We have used the expressed-sequence-tag approach to identify approximately 600 differentially expressed mRNAs in untreated and nerve growth factor-treated PC-12 cells that encode proteins with diverse structural and biochemical functions. Many of these mRNAs encode proteins belonging to cellular pathways not previously known to be regulated by nerve growth factor. Comparative expressed-sequence-tag analysis provides a basis for surveying global changes in gene-expression patterns in response to biological signals at an unprecedented scale, is a powerful tool for identifying potential interactions between different cellular pathways, and allows the gene-expression profiles of individual genes belonging to a particular pathway to be followed.

Animals↗
PubMed1999

The hairless gene of the mouse: relationship of phenotypic effects with expression profile and genotype.

Various mutations of the hairless (hr) gene of mice result in hair loss and other integument defects. To examine the role of the hr gene in mouse development, the expression profile of hr has been determined by in situ hybridisation and correlated to the nature of genetic changes and morphological abnormalities in different mutant animals. Four variant alleles have been characterised at the molecular level. hr/hr mice produce reduced, but significant, levels of hr mRNA whereas other alleles contain mutations which would be expected to preclude the synthesis of functional product, demonstrating a correlation between allelic variation at the hr locus and phenotypic severity. hr expression was shown to be widespread and temporally regulated. It was identified in novel tissues such as cartilage, developing tooth, inner ear, retina, and colon as well as in skin and brain. Analysis of mice homozygous for the rhino allele of hairless revealed that, although no morphological defects were detectable in many tissues normally expressing hr, previously undescribed abnormalities were present in several tissues including inner ear, retina, and colon. These findings indicate that the hairless gene product plays a wider role in development than previously suspected. Dev Dyn 1999;216:113-126.

Animals↗
PubMed1998

The human gene encoding the lectin-type oxidized LDL receptor (OLR1) is a novel member of the natural killer gene complex with a unique expression profile.

LOX-1 is an endothelial receptor for oxidized low-density lipoprotein that plays essential roles in atherogenesis. LOX-1 has the highest homology with C-type lectin receptors expressed on natural killer cells. In the present study, we cloned and characterized the human LOX-1 gene (HGMW-approved symbol OLR1). The gene structure of LOX-1 resembles that of the natural killer cell receptors. Fluorescence in situ hybridization and analyses of a yeast artificial chromosome contig revealed that the human LOX-1 gene is located in the natural killer gene complex on chromosome 12p12-p13, where the genes of the natural killer cell receptors cluster. In contrast, the expression pattern of LOX-1 is different from that of the natural killer cell receptors; LOX-1 is expressed in vascular-rich organs, but not in lymphocytes. A 1753-bp fragment of the 5' flanking region of the LOX-1 gene had a functional promoter activity. This region contains binding sites for several transcription factors, including the STAT family and NF-IL6, and the expression of LOX-1 was upregulated by several cytokines. These results demonstrate that the human LOX-1 gene is a new member of the natural killer gene complex with a unique expression profile.

Amino Acid Sequence↗
PubMed1992

Integrin expression profiles during erythroid differentiation.

To study the expression of integrins at the erythroid progenitor level we isolated selected populations of cells from human fetal liver after immunoadherence to anti-beta 2 integrin (CD18) coated plates. These CD18 adherent cells (CD18-Ad), in contrast to CD18 nonadherent cells (CD18-NAd), have a blastlike cell morphology and are highly enriched in all progenitor types (14% to 37% progenitors). By several criteria progenitor cells present in CD18-Ad cells appear to have a higher proliferative potential and diversity than the ones found in CD18-NAd, which were mostly later erythroid progenitors. Positivity of CD18-Ad cells with the common beta 2 integrin (CD18) is largely attributable to expression of alpha L (CD11a) chain, rather than alpha M (CD11b). CD11a is present in all types of progenitors, but it is selectively lost at later stages of erythroid differentiation/maturation. By contrast, CD11b appears to be virtually absent from all progenitors but it has an enhanced expression during granulomonocytic differentiation/maturation. In addition to beta 2 integrins, CD18-Ad cells express several other cytoadhesion molecules (VLA-4, VLA-5, I-CAM, H-CAM) as well as other progenitor cell antigens (CD34, HLA-DR, CD38). Cells expressing all these antigens were selectively enriched in CD18-Ad cells. Our data add new information on the regulation of CD11a and CD11b molecules in hematopoiesis and on the composite profile of integrin expression at several stages of erythroid differentiation.

Antigens, CD↗
PubMed2001

Gene expression profile in a case of primary cutaneous CD30-negative large T-cell lymphoma with a blastic phenotype.

A 65-year-old Japanese woman presented with disseminated erythematous patches, plaques, and nodules on the trunk and limbs. Histological examination showed diffuse and dense infiltrates located in the dermis and subcutis, composed of large pleomorphic T lymphocytes. Immunohistochemically, neoplastic cells were positive for blastic T-cell markers, but negative for CD30 (Ki-1) antigen. Based on the clinicopathological findings, a diagnosis of primary cutaneous large T-cell lymphoma was made. Despite systemic chemotherapy, the patient died 7 months after diagnosis. Gene expression profiling using complementary DNA microarrays indicated significantly increased expression of an apoptosis-inhibitory protein and certain cyokines and cytokine receptors (e.g. MCP-1, MCP-2, IP-10, and IL-2R gamma) in the tumour-indurated skin. Comprehensive gene expression patterning in additional cases may provide useful information regarding the biological and clinical behaviour of aggressive cutaneous lymphomas such as CD30-negative large T-cell lymphoma.

Aged↗
PubMed1999

Neural expression profile of alpha-synuclein in developing human cortex.

Alpha-synuclein is a predominantly neuronal presynaptic protein that may play an important role during synaptogenesis and CNS development. In order to elucidate the human developmental expression profile, we used a polyclonal antiserum against the NAC domain of alpha-synuclein. In normal fetal cortex neuroectodermal precursor cells elicited staining in the soma, whereas, in adult cortex, we observed a staining pattern compatible with synaptic function. The same developmental intraneuronal redistribution was found in neurodegenerative disorders, i.e. somatic staining in neuroectodermal precursors in fetal (trisomy 21) and a synaptic pattern in adult (Down's syndrome, Alzheimer's disease) brains. RT-PCR and Western blot analysis revealed expression at all time points studied (4-7.5 months) during human brain development.

Adult↗
PubMedDate not supplied

Neural expression profile of Elav-like genes in human brain.

BACKGROUND: Hel-N1 and HuD belong to the elav gene family and have a considerable role in neuronal development. However, there is only limited information available on the expression profile in human brain and neural tumor cell lines. METHOD: Therefore, RT-PCR analysis has been performed on human fetal, normal adult, and psychiatric brains (from patients with schizophrenia, Alzheimer's disease, and alcoholism) as well as 20 glioblastoma and 9 medulloblastoma cell lines. RESULTS: Both, Hel-N1 and HuD were abundantly expressed in all brain samples with no obvious difference. However, the neural tumor cell lines showed a differential expression pattern. The medulloblastoma cell lines expressed at least one of the genes in a frequency of 67% for HuD and 78% for Hel-N1 transcripts, respectively. In contrast to the glioblastoma cell lines, which revealed no evidence for HuD RT-PCR products. Surprisingly, 55% of the glioblastoma cell lines showed Hel-N1 expression. CONCLUSION: These observations indicate that Hel-N1 and HuD participate in molecular processes in human brain, both during development and in the mature adult brain. Hel-N1 and HuD transcriptional activity are stable markers for medulloblastoma cell lines, a tumor, which is thought to be derived from a neuronal precursor cell. The role of Hel-N1 in glioblastomas, the most prominent representative of the glial tumors is presently unclear. This finding is the first indication for a possible involvement of an Elav-like gene product in the glial cell lineage.

Alcoholism↗
PubMed2000

Expression profiles of 22 novel molecular markers for organogenetic pathways acting in alfalfa nodule development.

During symbiotic nodule development, a variety of molecular signals of rhizobia and plant origin are likely to be involved in the control of the expression of specific genes in the legume Medicago sativa (alfalfa). Twenty-two new, nodule-associated Expressed Sequence Tags (ESTs, MsNod clones) as well as 16 clones for previously reported alfalfa nodulins were identified by cold-plaque screening. Protein homologs were found for 10 of the 22 MsNod-encoded polypeptides, revealing putative novel functions associated with this symbiosis. Expression of these MsNod genes was investigated in spontaneous nodules (generated in the absence of bacteria), in nodules induced by a Sinorhizobium meliloti wild-type strain and Eps- and Bac- mutant derivatives, as well as in roots inoculated with a Nod- mutant strain. This analysis enabled us to correlate plant gene expression with the different stages of nodule ontogeny and invasion. The effect of phytohormones on MsNod gene expression was analyzed in cytokinin- and auxin-treated alfalfa roots. Cytokinin induced the accumulation of seven MsNod transcripts, four of them were also regulated by the synthetic auxin 2,4-D (2,4-dichlorophenoxyacetic acid). Comparison of MsNod expression profiles in wild-type and transgenic M. truncatula roots overexpressing the early nodulin Enod40 suggested that one clone, the M. sativa L3 ribosomal protein homolog (MsNod377), is a putative component of an Enod40-dependent pathway acting during nodule development. These novel molecular markers may help in the investigation of gene networks and regulatory circuits controlling nodule organogenesis.

Cytokinins↗
PubMedDate not supplied

Gene expression profiling during erythroid differentiation of K562 cells.

We studied the temporal changes in gene expression in K562 cells at intervals from 2 to 48 h following induction using differential display polymerase chain reaction and gene expression arrays. More than 110 cDNA fragments representing 86 unique mRNAs were either up- or downregulated during erythroid differentiation. Sixty-one of the differentially expressed cDNA fragments had more than 95% homology to known GenBank sequences; 21 represented cDNA sequences with only dbEST or high-throughput gene-screening database matches. Four fragments had no database matches. Using gene expression arrays, 73 differentially expressed genes were observed. Unique expressed sequence tags (ESTs) were used to "clone" two novel genes from available databases and their tissue expression was examined. Erythroid maturation in induced K562 cells is associated with differential expression of many genes. Some differentially expressed clones were transcription factors and 25 expressed fragments with open reading frames were found whose function remains unknown.

Base Sequence↗
PubMed2001

Gene expression profiling of cultured human bronchial epithelial and lung carcinoma cells.

Lung cancer is a complex collection of diseases that is thought to begin with single mutated progenitor cells and culminates in any of several clinically described pathologies. Our knowledge of the molecular events that lead to different lung cancer types--small cell carcinoma, squamous cell carcinoma, adenocarcinoma, and large cell carcinoma--is incomplete. Nonetheless, it is evident that genetic changes that impact multiple molecular networks are involved in the generation of each specific phenotype. Due to the obvious complexity of these processes, the simultaneous quantitative monitoring of changes in the expression of genes that define these networks can provide mechanistic information to increase our understanding of the molecular basis for human pulmonary carcinogenesis. To this end, we have employed a commercially available human cDNA array (Atlas Human Array, Clontech Laboratories) to systematically screen for alterations in the expression of 600 genes in normal human bronchial epithelial (NHBE) cells as well as in several lung carcinoma lines. Studies on the reproducibility and variability of array results indicate that a 2-fold or greater difference in the expression of a particular gene could be considered a real difference in transcript abundance. Accuracy of gene expression as measured in the array was verified by comparing mRNA levels of the proto-oncogene c-myc in the array with results obtained by traditional Northern blot analysis and by quantitative RT-PCR. Gene expression profiles were compared within and among cell types. The differential expression of 17 genes, including downregulation of MRP8 and MRP14 and upregulation of CYP1B1, was observed in all four carcinoma lines compared to NHBE cells. The direction of all 17 gene expression differences, either upregulation or downregulation relative to NHBE cells, was the same for all four carcinoma lines, underscoring their common molecular features. Each lung tumor line also exhibited a number of unique differences compared to both normal cells and the other tumor cell lines. These differences may be due to differences in the cellular origin and/or pathology of the cell lines studied.

Adenocarcinoma↗