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PubMed1994

Targeted RNA fingerprinting: the cloning of differentially-expressed cDNA fragments enriched for members of the zinc finger gene family.

We have developed and applied a modification of an 'RNA Fingerprinting' protocol previously published by Welsh and McClelland (Nucleic Acids Research 19: 5275-5279 1991) such that cDNA fragments which are both differentially-expressed and enriched for members of a specific gene family can readily be identified. cDNA fragments were amplified with an arbitrary primer initially used in the reverse transcription reaction in combination with a member of a primer set which corresponded to a conserved region within a specific gene family. This technique was used to isolate cDNAs encoding a recently described protein kinase as well as an unknown gene that contained a zinc finger. Several other known genes that contained a zinc finger domain and that were differentially-expressed were also isolated.

Amino Acid Sequence↗
PubMed2005

Microarray analysis of differentially expressed genes of primary tumors in the canine central nervous system.

The pathophysiologic similarities of many human and canine cancers support the role of the domestic dog as a model for brain tumor research. Here we report the construction of a custom canine brain-specific cDNA microarray and the analysis of gene expression patterns of several different types of canine brain tumor. The microarray contained 4000 clones from a canine brain specific cDNA library including 2161 clones that matched known genes or expressed sequence tags (ESTs) and 25 cancer-related genes. Our study included 16 brain tumors (seven meningiomas, five glial tumors, two ependymomas, and two choroid plexus papillomas) from a variety of different dog breeds. We identified several genes previously found to be differentially expressed in human brain tumors. This suggests that human and canine brain tumors share a common pathogenesis. In addition, we also found differentially expressed genes unique to either meningiomas or the glial tumors. This report represents the first global gene expression analysis of different types of canine brain tumors by cDNA microarrays and might aid in the identification of potential candidate genes involved in tumor formation and progression.

Animals↗
PubMed2000

Identification of four human cDNAs that are differentially expressed by early hematopoietic progenitors.

The molecular processes that maintain the stem cell pool are largely unknown. Using polymerase chain reaction-driven subtraction, we examined genes that are differentially expressed by early hematopoietic progenitors. We expected that identifying genes that are uniquely expressed by the earliest precursors would provide insight into the mechanism(s) through which stem cell number is maintained and differentiation is regulated. Using CD34(+)CD38(-) cells as starting material, we identified four mRNAs, expressed by these cells, that are either absent or present in reduced amounts in more mature CD34(+)CD38(+) cells. One of these cDNAs (C40) encodes a known member of the subfamily of protein phosphatases (CL100) that exhibits dual substrate specificity for phosphotyrosine- and phosphoserine/threonine-containing substrates and specifically inactivates MAP kinases. This phosphatase has been shown to play a role in regulating the differentiation of several cell types. The second cDNA (C23) is identical to LR11 (gp250), a member of the low-density lipoprotein receptor family. LR11 is unusual in that, in addition to 11 ligand-binding repeats, it contains a series of fibronectin type III repeats near its carboxyl terminal end that are similar to those found in cytokine receptors. It is highly expressed in developing brain, but hematopoietic expression has not been reported. The 178-bp fragment that we originally cloned is part of a 4,145-bp 3' untranslated region (UTR) that had not been previously sequenced and is among the largest human 3' UTRs ever reported. The other isolates (C21 and C12) do not correspond to known protein sequences. They are homologous to EST sequences from a fetal brain library. C21 encodes a previously unknown gene that is a member of the WD-40 family. An open reading frame encoding a 515 amino acid protein has been identified. Four mRNAs, differentially expressed by CD34(+)CD38(-) human bone marrow cells, have been identified. Although this population is highly enriched for early hematopoietic progenitors, none of these genes encodes a message whose expression is limited to the hematopoietic system. They all are expressed in a variety of tissues, suggesting that they are involved in processes that are fundamental to the development of many cell types. All of these cDNAs possess atypically long 3' UTRs, and one of them is among the longest ever described. Their differential expression by immature hematopoietic cells, in contrast to more mature cells, suggest that long 3' UTRs may be characteristic of genes that play a regulatory role during development.

Base Sequence↗
PubMed2002

The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data.

BACKGROUND: The biomedical community is developing new methods of data analysis to more efficiently process the massive data sets produced by microarray experiments. Systematic and global mathematical approaches that can be readily applied to a large number of experimental designs become fundamental to correctly handle the otherwise overwhelming data sets. RESULTS: The gene selection model presented herein is based on the observation that: (1) variance of gene expression is a function of absolute expression; (2) one can model this relationship in order to set an appropriate lower fold change limit of significance; and (3) this relationship defines a function that can be used to select differentially expressed genes. The model first evaluates fold change (FC) across the entire range of absolute expression levels for any number of experimental conditions. Genes are systematically binned, and those genes within the top X% of highest FCs for each bin are evaluated both with and without the use of replicates. A function is fitted through the top X% of each bin, thereby defining a limit fold change. All genes selected by the 5% FC model lie above measurement variability using a within standard deviation (SDwithin) confidence level of 99.9%. Real time-PCR (RT-PCR) analysis demonstrated 85.7% concordance with microarray data selected by the limit function. CONCLUSION: The FC model can confidently select differentially expressed genes as corroborated by variance data and RT-PCR. The simplicity of the overall process permits selecting model limits that best describe experimental data by extracting information on gene expression patterns across the range of expression levels. Genes selected by this process can be consistently compared between experiments and enables the user to globally extract information with a high degree of confidence.

Animals↗
PubMed2005

[Inflammatory reactions in the wear particle induced and infectious periprosthetic membrane of loosened hip- and knee endoprostheses: pathogenetic relevance of differentially expressed genes cd9, cd11b, cd18, cd52 and pdgfrbeta].

BACKGROUND: A previous cDNA-microarray analysis described constantly differentially expressed genes in wear particle induced and infectious SLIM (synovial-like interface membrane). This study aims to validate the cDNA microarray data in order to approve differences of the gene expression profiles of RNA and proteins. METHODS: Tissue from 16 wear particle induced and 20 infectious periprosthetic membranes were analyzed by RT-PCR and immunohistology with regard to the expression of inflammatoric associated genes. RESULTS: RT-PCR showed the genes cd9, cd11b, cd18, cd52 as well as pdgfrbeta in interface membranes. In the wear particle induced membrane the immunohistochemical analysis showed a significantly weaker gene expression of PDGFRbeta, whereas the differential overexpression of CD9, CD11b and CD52 was confirmed. For CD18, there was no difference in expression between wear induced and infectious periprosthetic tissue. CONCLUSION: Different pathomechanisms, which are reflected by different gene expression profiles, might produce different types of periprosthetic membranes. By RT-PCR and immunohistochemical analysis the micro array data of the genes cd9, cd11b, cd52 and pdgfrbeta could be validated. Identifying the gene products of cd9, cd11b and cd52 in blood or tissue may help to differentiate between wear induced and infectious loosening.

Adult↗
PubMed2002

Differential expression of cytokeratins 8 and 20 distinguishes craniopharyngioma from rathke cleft cyst.

BACKGROUND: Craniopharyngiomas are epithelial neoplasms usually located in the sellar and suprasellar regions. Distinguishing craniopharyngioma from Rathke cleft cyst is sometimes difficult, and the distinction is clinically significant because Rathke cleft cysts have a better prognosis than craniopharyngiomas. DESIGN: We retrieved 10 cases with a primary diagnosis of craniopharyngioma and 5 cases with a diagnosis of Rathke cleft cyst for analysis. Five cases of normal pars intermedia of pituitary glands from autopsy served as controls. We evaluated the expression patterns of a broad range of low- to intermediate-molecular weight cytokeratins (CK7, CK8, CK10, CK17, CK18, CK19, and CK20) and high-molecular weight cytokeratins (K903: a combination of CK1, CK5, CK10, and CK14; and CK5/6) in these cases. RESULTS: Craniopharyngiomas had a cytokeratin expression pattern distinct from that of Rathke cleft cysts and pituitary gland pars intermedia: craniopharyngiomas did not express cytokeratins 8 and 20, whereas Rathke cleft cysts and pars intermedia of pituitary glands both expressed cytokeratins 8 and 20. CONCLUSION: The differential expression of cytokeratins distinguishes between craniopharyngioma and Rathke cleft cyst, and this difference could be useful for identifying craniopharyngioma in difficult cases in which only a small biopsy is available. The different cytokeratin profiles of craniopharyngioma and Rathke cleft cyst suggest that these lesions do not come from the same origin, or that they come from a different developmental stage of the pouch epithelium.

Adolescent↗
PubMed2002

Identification of low-abundance differentially expressed transcripts using arrayed cDNA clones.

Analysis of comparative gene expression by the use of DNA microarrays has become a widely used tool. However, this technique is only readily applied to organisms where sequence information is known. This paper describes the development of a low-cost method of gene discovery by enrichment of differentially expressed transcripts, which uses cDNA library arrays of bacterial clones on nylon membranes (macroarrays) coupled with a subtractive probe preparation method to discover differentially expressed genes. The method requires no prior knowledge of the organism's genome sequence and overcomes the inherent insensitivity of standard methods of macroarray hybridisation.

Animals↗
PubMed2006

Genetic variability for physiological traits under drought conditions and differential expression of water stress-associated genes in sunflower (Helianthus annuus L.).

Genotypic variation for water status and gas exchange parameters under different water treatments (well-watered and water-stressed plants before and after rehydration) were investigated in a population of recombinant inbred lines (RILs) of sunflower (Helianthus annuus L.). Afterwards, four RILs and parental lines presenting contrasting responses to dehydration and rehydration were selected to determine the differential expression of four water-stress associated genes: aquaporin, dehydrin, leafy cotyledon1-like protein and fructose-1,6 bisphosphatase. Water stress revealed a high genetic variability for water status and gas exchange parameters when compared with well-watered genotypes. Genetic gain when selected RILs were compared with the best parent was significant for most traits due to transgressive segregation. QTL mapping and graphical genotyping showed that RILs carrying different genomic regions for some QTLs presented also physiological different characteristics as well as gene expression patterns. The expression level of aquaporin genes in leaves of four RILs and their parents was down regulated by water stress and was associated with relative water content (RWC). Down-regulation was also associated with genomic regions having alleles with negative effects on plant water status. The level of dehydrin transcripts increased in leaves of all studied RILs in response to water stress. Transcript accumulations of dehydrin and leafy cotyledon1-like genes, likely involved in protective tolerance processes, were not correlated directly with plant water status or QTL effects. Down-regulation of fructose-1,6 bisphosphatase was observed under water stress. Net photosynthesis rate (P(n)) and the fructose-1,6 bisphosphatase gene expression levels were associated mainly after rehydration. This phenomenon indicates an association between physiological response to water stress and differential expression of water-stress related genes.

Dehydration↗
PubMed2005

The use of cDNA microarray to identify differentially expressed labor-associated genes within the human myometrium during labor.

OBJECTIVE: Microarray technology was used to comprehensively analyze gene expression during human labor in the myometrium. STUDY DESIGN: cDNA micro-array was used to compare the transcriptomes of myometrium obtained from patients in spontaneous labor and those not in labor. Expression of four labor-specific genes was confirmed in the myometrium obtained from patients in spontaneous labor using RT-PCR, Northern blot analysis, and in-situ hybridization. RESULTS: Of the >6000 cDNAs evaluated, 56 were found to be differentially expressed during labor. The labor-specific expression of 4 genes was confirmed using RT-PCR and Northern blot analysis. The relative increased expression of thrombospondin-1 in myometrium obtained from patients in spontaneous labor was also confirmed using in-situ hybridization. CONCLUSION: cDNA microarray was used to identify 56 differentially expressed genes in myometrium obtained from patients in spontaneous labor. The up-regulation of four genes was confirmed by multiple methods. Elucidation of the role(s) of the genes identified by microarray should improve our understanding of normal labor physiology and may ultimately lead to more effective treatments for abnormal labor.

Blotting, Northern↗
PubMed2002

Differential expression of a novel gene in response to hsp27 and cell differentiation in human keratinocytes.

The 27 kDa heat shock protein (hsp27) is expressed in keratinocytes in a differentiation-related pattern. Keratinocyte differentiation involves a coordinated program of expression and interaction of specific differentiation-related genes and proteins. To investigate the functional role of hsp27 in these processes we used a differential display approach to identify genes that might be regulated by the expression of hsp27 in human keratinocytes. mRNA was extracted from the human squamous carcinoma cell line A431 and a subclone stably transfected with human hsp27. Reverse transcriptase differential display polymerase chain reaction was performed using one base anchored oligo-dT and arbitrary primers. Differentially expressed genes were confirmed by northern blot analysis and further characterized by sequencing. Their expression in human skin and other tissues was investigated by northern blot and in situ hybridization. Out of five fragments detected with the initial reverse transcriptase differential display polymerase chain reaction screen one could be confirmed by northern blot to be downregulated in hsp27-overexpressing A431. This mRNA (G24) is not only downregulated by overexpression of hsp27 in A431 but also during differentiation in normal human keratinocytes in culture and in situ, situations where hsp27 is known to be induced. According to sequence analysis G24 represents a novel gene that does not code for a protein and thus might belong to the growing family of noncoding RNAs. These results not only demonstrate for the first time that overexpression of hsp27 by gene transfer is associated with regulation of gene expression but also reveal a novel differentiation-associated gene in human keratinocytes.

Base Sequence↗
PubMed2004

Identification of genes with differential expression in acquired drug-resistant gastric cancer cells using high-density oligonucleotide microarrays.

PURPOSE: A major obstacle in chemotherapy is treatment failure due to anticancer drug resistance. The emergence of acquired resistance results from host factors and genetic or epigenetic changes in the cancer cells. The purpose of this study was to identify differentially expressed genes associated with acquisition of resistance in human gastric cancer cells. EXPERIMENTAL DESIGN: We performed global gene expression analysis in the acquired drug-resistant gastric cancer cell lines to the commonly used drugs 5-fluorouracil, doxorubicin, and cisplatin using Affymetrix HG-U133A microarray. The gene expression patterns of 10 chemoresistant gastric cancer cell lines were compared with those of four parent cell lines using fold-change and Wilcoxon's test for data analysis. RESULTS: We identified over 250 genes differentially expressed in 5-fluorouracil-, cisplatin-, or doxorubicin-resistant gastric cancer cell lines. Our expression analysis also identified eight multidrug resistance candidate genes that were associated with resistance to two or more of the tested chemotherapeutic agents. Among these, midkine (MDK), a heparin-binding growth factor, was overexpressed in all drug-resistant cell lines, strongly suggesting that MDK might contribute to multidrug resistance in gastric cancer cells. CONCLUSIONS: Our investigation provides comprehensive gene information associated with acquired resistance to anticancer drugs in gastric cancer cells and a basis for additional functional studies.

Antineoplastic Agents↗
PubMed1998

Differential expression and androgen regulation of the human selenium-binding protein gene hSP56 in prostate cancer cells.

Low levels of dietary selenium are associated with increased risk of malignancy of several organs, including the prostate. Using a subtractive approach called linker capture subtraction, we have found that the human selenium-binding protein gene hSP56 is differentially expressed by the relatively slow-growing, androgen-sensitive prostate cancer cell line LNCaP but not by the more rapidly growing androgen-insensitive lines PC-3 and DU145. We confirmed this differential expression by Northern blot analysis. Importantly, hSP56 expression by LNCaP cells was reversibly down-regulated by exogenous androgen in a concentration-dependent manner. Marked differences in steady-state hSP56 mRNA levels were found in a variety of normal and neoplastic human cells that were examined. hSP56 expression was especially high in normal tissues that appear to benefit from the cancer-protective action of dietary selenium and was low in many neoplastic cells. The results suggest that hSP56 may play a role in determining the neoplastic phenotype.

Androgens↗
PubMed2000

Differential Expression of Myoepithelial Markers in Salivary, Sweat and Mammary Glands.

Myoepithelial cells (MECs) are contractile elements showing a combined epithelial and smooth muscle phenotype. Among the numerous immunohistochemical markers employed to detect MECs, smooth muscle actin (SMA) is the most widely used. Recently, other markers of smooth muscle differentiation have been demonstrated in MECs, such as calponin, heavy caldesmon (h-caldesmon), and smooth muscle myosin heavy chain (SMM-HC). In the present study normal salivary, mammary, and sweat glands have been studied with four markers of smooth muscle differentiation (SMA, calponin, h-caldesmon, and SMM-HC). The four markers were differentially expressed in the various types of glands. In parotid glands MECs mainly expressed calponin and caldesmon; in submandibular and in cutaneous apocrine and eccrine glands, MECs strongly expressed SMA, calponin, and caldesmon; in minor salivary glands all four markers were equally strongly expressed; and in mammary glands SMA, calponin, and SMM-HC were present both in periductal and periacinar MECs while caldesmon was present in periductal MECs only. In addition to MECs, SMA stained stromal myofibroblasts, sometimes hampering the identification of MECs. Among the other markers, calponin stained only rare stromal myofibroblasts, while caldesmon and SMM-HC were confined to MECs. In conclusion, these latter markers are very useful for identifying MECs. It is suggested that the differential expression of smooth muscle contractile proteins might reflect different functions of MECs in the various sites. Int J Surg Pathol 8(1):29-37, 2000

Journal Article↗
PubMed2004

[Differential expression of motility-related protein-1/CD9 gene in gastric cancers and premalignant lesions].

OBJECTIVE: To clone and identify gastric cancer-related genes and explore the possible pathogenic mechanism of gastric cancer. METHODS: The differentially expressed cDNA bands were isolated by fluorescent mRNA differential display in gastric cancer specimens, matched normal gastric mucosa and premalignant lesions. The motility-related protein-1 (MRP-1/CD9) gene was one of the down-regulated genes. MRP-1/CD9 gene expression in different kinds of gastric tissue was analyzed by Northern blot and reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: MRP-1/CD9 expression was down-regulated in all gastric cancer tissues. Northern blot analysis confirmed this differential expression. RT-PCR analysis showed that the MRP-1/CD9 gene expression was much lower in gastric cancers(0.31+/-0.18) than in the matched normal gastric tissue (0.49+/-0.24) and in the premalignant lesions (0.47+/-0.18) (P<0.05), and its expression in intestinal type gastric cancer (0.38+/-0.16) was higher than that in diffuse type gastric cancer (0.22+/-0.17) (P<0.05). CONCLUSION: The MRP-1/CD9 gene expression was down-regulated in gastric cancer, its expression was probably related to the carcinogenesis and histology types of gastric cancer.

Antigens, CD↗
PubMed2000

Identification and characterization of differentially expressed genes in the early response phase during liver regeneration.

It has been suggested that the early response was a critical regulator of the remaining quiescent liver cells reentering the cell cycle after partial hepatectomy. The identification of genetic factors and function important in the early response phase during liver regeneration after partial hepatectomy will help in understanding the underlying molecular mechanisms of hepatic injuries. Through the application of complementary DNA representational difference analysis (RDA), we have identified genes that are up-regulated in early response phase during liver regeneration. Results from slot blot and Northern blot analysis confirmed that the RDA products were truly differentially expressed. In addition to well-characterized up-regulated genes during liver regeneration, including IGFBP-1, LRF-1, and metallothionein, we demonstrate the differential expression of at least 6 genes previously not known to be associated with liver regeneration. PC3 and TEC genes were identified as immediate-early response genes and were dramatically increased following partial hepatectomy. Ribosomal protein L6, ribosomal protein S7, chaperonin 10, and cytochrome oxidase I were identified to be up-regulated 4- to 5-fold after 70% partial hepatectomy. In addition to the known genes, 7 novel genes were isolated. Among them, two genes showed their up-regulation in liver regeneration by Northern blot analysis. One was exclusively expressed in liver, and no expression was observed in other tissues. Peak expression, 30-fold above baseline, occurred 60 min after 70% hepatectomy. Cycloheximide pretreatment could not suppress the induction of this gene, indicating that this gene as a novel immediate-early response gene following partial hepatectomy. The novel gene, which was represented three times in the differential clones, may be one of the highly up-expressed genes in regenerating liver. Its transcript is undetectable in normal liver; its level of mRNA increased by 0.5 h after 2/3 partial hepatectomy, reaching a maximum at 2 h. This gene is similar to human alpha-1-beta-glycoprotein (40%). These results suggest a role of these genes in the early response phase of liver regeneration.

Animals↗
PubMed1994

Differential expression of membrane currents in dissociated mouse primary sensory neurons.

The whole cell configuration of the patch clamp technique has been applied to identify the membrane currents expressed by populations of dissociated mouse primary sensory neurons. Three discrete populations of cells were distinguished on the basis of cell size and the array of currents expressed. Group 1 cells (capacitance 10-30 pF) expressed a Na+ current resistant to tetrodotoxin (1 microM) and a prominent, low threshold, inactivating, K+ current sensitive to 4-aminopyridine (IA). A population (53%) of these small cells responded to capsaicin (10 microM) with an inward current, suggesting a functional correlate with nociceptive "C"-cells. The cells of Group 2 (capacitance 55-85 pF) were characterized by the expression of a Na+ current sensitive to tetrodotoxin and a prominent inward current activated by hyperpolarization (IH). They also showed a variant of the A-type K+ current, which was a low threshold, but sustained K+ current, sensitive to dendrotoxin (30 nM). Group 3 cells, of intermediate size (capacitance 30-55 pF) were similar to Group 2 cells, in that they expressed a tetrodotoxin-sensitive Na+ current and (through reduced in amplitude), IH. The most notable feature of Group 3 cells was the expression of a transient, low threshold Ca2+ current. The differential expression of these conductances was reflected in the behaviour of cells under current clamp control. Each group of cells could thus be distinguished by the selective expression of specific ionic conductances which correlated clearly with cell size, suggesting a correlation with well recognised functional differentiation of sensory neurons. The selective expression of specific subsets of membrane channels may provide valuable markers in studying the developmental regulation of phenotype in this population of cells.

Action Potentials↗
PubMed2005

[Screening of differential expression genes between primary breast cancer and its lymph node metastasis using single primer amplification of cDNA for microarray].

OBJECTIVE: To screen genes related to breast cancer metastasis by comparing difference of expression profile between primary breast cancer and its lymph node metastasis. METHODS: The cell total RNA was extracted from 10 breast cancer specimens, including the primary cancer and metastatic cancer tissues of axillary lymph nodes resected during operation. Single primer amplification (SPA) was used to prepare fluorescence-labeled targets and then Oligo microarray concluding 21 000 human functional genes was used to screen out 1.5 fold or more differential expression genes in at least 5 pairs of samples. The screened-out genes were identified by real-time PCR. RESULTS: Preparing targets by using SPA reduced the initial RNA to 0.25 microg, with 57 genes screened out, the expression of 19 of which were up-regulated and the expression of 38 of which were down-regulated in the metastatic tissues. Eight differentially expressed genes were related to cell migration and adhesion, 14 to signal transduction, and 14 to cell growth or metabolism. Real-time PCR showed that the fibronectin (FN) mRNA expression in the lymph node metastasis was only 1/3.6 of that in the matched primary breast cancer in 30 cases (t = -3.188, P = 0.003). CONCLUSION: SPA is a sensitive method for preparing targets. Genes related to cell migration and adhesion, signal transduction, and cell growth or metabolism, which are associated with the biology process of metastasis have been screened out. FN as a potent marker may contribute to diagnosis of metastasis and prognosis for breast cancer patients.

Adult↗
PubMed2006

Proteins differentially expressed in response to nicotine in five rat brain regions: identification using a 2-DE/MS-based proteomics approach.

To determine protein expression patterns within the central nervous system (CNS) in response to nicotine, 2-DE/MS was performed on samples from five brain regions of rats that had received nicotine bitartrate by osmotic minipump infusion at a dose of 3.15 mg/kg/day for 7 days. After spot matching and statistical analysis, 41 spots in the amygdala, 49 in the nucleus accumbens (NA), 46 in the prefrontal cortex (PFC), 36 in the striatum, and 28 in the ventral tegmental area (VTA) showed significant differences in the nicotine-treated compared with control samples. Using MALDI-TOF MS peptide fingerprinting, 14 proteins in the amygdala, 11 in the NA, 19 in the PFC, 13 in the striatum, and 19 in the VTA were identified. Several proteins (e.g. dynamin 1, laminin receptors, aldolase A, enolase 1 alpha, Hsc70-ps1, and N-ethylmaleimide-sensitive fusion protein) were differentially expressed in multiple brain regions. By gene ontology analysis, these differentially expressed proteins were grouped into biological process categories, such as energy metabolism, synaptic function, and oxidative stress metabolism. These data, in combination with microarray analysis of mRNA transcripts, have the potential to identify the CNS gene products that show coordinated changes in expression at both the RNA and protein levels in response to nicotine.

Animals↗