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Identification of differentially expressed mRNA during pancreas regeneration of rat by mRNA differential display.

Pancreatectomy (Px) is known to cause islet hypertrophy and is a putative method to mimic hyperglycemia representing type II diabetes mellitus. Therefore, finding new genes related to pancreatectomy will help to understand the molecular mechanism of hypertrophy and hyperglycemia, and may provide new diagnostic markers of type II diabetes. To this end, mRNA differential display was used to isolate genes that show transcriptional changes in pancreas of rat after 90% partial pancreatectomy. Forty-nine candidate pancreas regeneration-associated transcripts were isolated. cDNA sequencing and subsequent database analysis revealed that 15 transcripts showed no significant sequence similarity to previously reported genes, whereas 34 transcripts showed significant similarity with genes deposited in the GenBank. The differential mRNA expression of 49 transcripts was confirmed using screening of slot blots and Northern blot analysis was performed to several genes. It was noteworthy that the Wnt-1 inducible signaling pathway protein-1 (WISP-1), Ras-associated protein 1B (Rap1B), vascular cell adhesion molecule-1 (VCAM-1), and huntingtin interacting protein genes (HIP) were observed to be over-expressed during pancreas regeneration. Several genes' expression was modified by pancreatectomy. Profiling of gene expression in response to pancreatectomy may lead to new insights into hypertrophy and hyperglycemia representing type II diabetes, as well as into the identification of novel diagnostic markers of type II diabetes.

Animals↗

Differential expression of oxidative phosphorylation genes in patients with Alzheimer's disease: implications for early mitochondrial dysfunction and oxidative damage.

In Alzheimer's disease (AD) pathogenesis, increasing evidence implicates mitochondrial dysfunction resulting from molecular defects in oxidative phosphorylation (OXPHOS). The objective of the present study was to determine the role of mRNA expression of mitochondrial genes responsible for OXPHOS in brain specimens from early AD and definite AD patients. In the present article, using quantitative real-time polymerase chain reaction (PCR) techniques, we studied mRNA expression of 11 mitochondrial-encoded genes in early AD patients (n = 6), definite AD patients (n = 6), and control subjects (n = 6). Using immunofluorescence techniques, we determined differentially expressed mitochondrial genes NADH 15-kDa subunit (complex I), cytochrome oxidase subunit 1 (complex IV), and ATPase delta-subunit (complex V) in the brain sections of AD patients and control subjects. Our quantitative reverse transcription (RT)-PCR analysis revealed a downregulation of mitochondrial genes in complex I of OXPHOS in both early and definite AD brain specimens. Further, the decrease of mRNA fold changes was higher for subunit 1 compared to all other subunits studied, suggesting that subunit 1 is critical for OXPHOS. Contrary to the downregulation of genes in complex I, complexes III and IV showed increased mRNA expressions in the brain specimens of both early and definite AD patients, suggesting a great demand on energy production. Further, mitochondrial gene expression varied greatly across AD patients, suggesting that mitochondrial DNA defects may be responsible for the heterogeneity of the phenotype in AD patients. Our immunofluorescence analyses of cytochrome oxidase and of the ATPase delta-subunit suggest that only subpopulations of neurons are differentially expressed in AD brains. Our double-labeling immunofluorescence analyses of 8-hydroxyguanosine and of cytochrome oxidase suggest that only selective, overexpressed neurons with cytochrome oxidase undergo oxidative damage in AD brains. Based on these results, we propose that an increase in cytochrome oxidase gene expression might be the result of functional compensation by the surviving neurons or an early mitochondrial alteration related to increased oxidative damage.

Aged↗

Differential expression of ubiquitous and neuronal kinesin heavy chains during differentiation of human neuroblastoma and PC12 cells.

Kinesin is a microtubule-based motor protein involved in intracellular organelle transport. Neurons are characterized by the presence of at least two isoforms of conventional kinesin: ubiquitous kinesin, expressed in all cells and tissues, and neuronal kinesin, whose pattern of expression is confined to neuronal cells. In order to investigate whether the two kinesin motors, which are encoded by different genes, may play distinct biological roles in neurons, we studied their expression during neuronal differentiation. Human neuroblastoma SH-SY5Y and IMR32 cells and rat phaeochromocytoma PC12 cells were used as an in vitro system for neuronal differentiation and were induced to differentiate in the presence of retinoic acid, a combination of dibutyryl cAMP and 5-bromodeoxyuridine, and nerve growth factor respectively. The expression level of each kinesin isoform was evaluated by quantitative immunoblot before and after pharmacological treatment. We found that in all cell types the expression level of neuronal kinesin, but not of ubiquitous kinesin, is stimulated during differentiation. In particular, SH-SY5Y cells show a 4.5-fold, IMR32 cells a 3-fold and PC12 cells a 7-fold increase in the level of expression of neuronal kinesin. By Northern blot analysis we found that the selective increase in the expression of neuronal kinesin is paralleled by an increase in its mRNA, indicating that there is a transcriptional control of the expression of this kinesin isoform during differentiation of neuroblastoma and PC12 cells. Our results suggest that these cells represent an adequate model to study the function of conventional kinesin and its isoforms.

Animals↗

Ectopeptidases are differentially expressed in hepatocellular carcinomas.

We investigated the expression pattern of neprilysin (CD10), aminopeptidase N (CD13) and angiotensin-I converting enzyme (CD143) in hepatocellular carcinomas (HCC), and their putative roles in hepatocarcinogenesis. Tissue samples were obtained from 31 patients with HCC. Tissue samples obtained from non-neoplastic liver, fetal livers and focal nodular hyperplasias (FNH) were used by comparison. Transcription and expression of CD10, CD13, and CD143 were studied by quantitative RT-PCR, Western blotting, and immunohistochemistry. Cell proliferation assays were performed with the C3A hepatoma cell line. The mRNA and protein of each of CD10, CD13 and CD143 were differentially expressed in HCCs. CD10 was decreased in HCCs as compared to non-neoplastic liver tissue, while CD13 and CD143 were mildly increased. In fetal liver and FNHs, the expression of CD10 was less intense than in the surrounding non-tumorous liver. The expression patterns of CD13 and CD143 in fetal livers and FNHs were similar to HCCs and were predominantly localized in bile canaliculi (CD13) and endothelial cells (CD143). CD10 and CD13 mRNAs were expressed by C3A cells and blocking either CD10 or CD13 ectopeptidase activity retarded cell growth significantly in vitro. We demonstrate that ectopeptidases are differentially expressed in HCCs and may have influence on tumor biology. Overall, expression of CD10 in non-neoplastic and neoplastic hepatocytes appears to correlate inversely with their state of proliferation or differentiation. CD13 shows a characteristic canalicular distribution pattern and may be important for cell polarization and bile compartmentalization in HCCs, while CD143 may influence angiogenesis.

Adult↗

Differential expression of antioxidant enzymes in various hepatocellular carcinoma cell lines.

Recent evidence suggests that reactive oxygen species (ROS) play an important role in the pathogenesis of various illnesses, and the ROS and antioxidant enzymes are highly associated with cell differentiation and diseases. In this study, we tested the hypothesis that specific antioxidant enzymes are differentially expressed in hepatocellular carcinoma (HCC) cell lines with various degrees of differentiation. We compared the expression of several antioxidant enzymes including catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GRx), and glutathione peroxidase (GPx) in five HCC cell lines with well (Hep G2 and Hep 3B) or poor (HA22T/VGH, HA55T/VGH, and SK-Hep-1) differentiation. Our results showed that both well-differentiated HCC cell lines expressed extremely higher CAT and GRx enzyme activities than all three poorly differentiated ones. Moreover, the protein and mRNA levels of CAT were much higher in two well-differentiated HCC cell lines than in all three poorly differentiated ones. Both well-differentiated HCC cell lines also showed a higher protein or mRNA expression of Cu/ZnSOD and MnSOD than three poorly differentiated ones. Our results demonstrate that specific antioxidant enzymes (especially, CAT and GRx) are differentially expressed in HCC cell lines with well or poor differentiation. These findings suggest that CAT and GRx are two potential differentiation markers for HCC.

Antioxidants↗

Differential expression of cyclin D1 in the human hair follicle.

The proliferation of keratinocytes in the hair follicle varies from slowly cycling, intermittently proliferating stem cells in the bulge to rapidly proliferating, transient cells in the bulb. To better understand the biological differences between these two compartments, we sought to identify differentially expressed genes using cDNA macroarray analysis. Cyclin D1 was one of 13 genes increased in the bulge compared to the bulb, and its differential expression was corroborated by quantitative real-time polymerase chain reaction (PCR) on the original samples. Using immunohistochemical staining, laser-capture microdissection (LCM) and quantitative real-time PCR, we localized cyclin D1 to the suprabasal cells of the telogen bulge and anagen outer root sheath (ORS). Surprisingly, cyclin D1, D2, and D3 were not detectable by immunohistochemistry in the rapidly proliferating hair-producing cells of the anagen bulb (matrix cells), while these cells were strongly positive for Ki-67 and retinoblastoma protein. In contrast, pilomatricoma, a tumor thought to be derived from matrix cells, was positive for cyclin D1, D2, and D3. Our results suggest that cyclin D1 may mediate the proliferation of stem cells in the bulge to more differentiated transient amplifying cells in the suprabasal ORS. In contrast, non-cyclin D1-proteins appear to control cell division of the highly proliferative bulb matrix cells. This non-cyclin D1-mediated proliferation may provide a protective mechanism against tumorigenesis, which is overridden in pilomatricomas. Our data also demonstrate that the combination of DNA macroarray, LCM and quantitative real-time PCR is a powerful approach for the study of gene expression in defined cell populations with limited starting material.

Computer Systems↗

cDNA array analysis of the differential expression change in virulence-related genes during the development of resistance in Candida albicans.

Candida albicans is the most frequently isolated fungus in immunocompromised patients associated with mucosal and deep-tissue infections. To investigate the correlation between virulence and resistance on a gene expression profile in C. albicans, we examined the changes in virulence-related genes during the development of resistance in C. albicans from bone marrow transplant patients using a constructed cDNA array representing 3096 unigenes. In addition to the genes known to be associated with azole resistance, 16 virulence-related genes were identified, whose differential expressions were newly found to be associated with the resistant phenotype. Differential expressions for these genes were confirmed by RT-PCR independently. Furthermore, the up-regulation of EFG1, CPH2, TEC1, CDC24, SAP10, ALS9, SNF1, SPO72 and BDF1, and the down-regulation of RAD32, IPF3636 and UBI4 resulted in stronger virulence and invasiveness in the resistant isolates compared with susceptible ones. These findings provide a link between the expression of virulence genes and development of resistance during C. albicans infection in bone marrow transplant (BMT) patients, where C. albicans induces hyphal formation and expression change in multiple virulence factors.

Candida albicans↗

Multiple cDNAs of wheat voltage-dependent anion channels (VDAC): isolation, differential expression, mapping and evolution.

The mitochondrial outer membrane of eukaryotic cells contains voltage-dependent anion channels (VDAC) also termed porins. Three cDNAs from wheat (Triticum aestivum) were isolated and sequenced (Tavdac 1-3). They share 65% similarity of their amino acid sequences, and therefore they probably represent isoforms. The deduced amino acid sequence of one of the cDNAs was found to be identical to the purified VDAC protein from wheat mitochondria [8]. Secondary structure analysis of the deduced amino acid sequences of the three vdac cDNAs revealed a characteristic alpha helix at their N-terminal and beta-barrel cylinders characteristic of VDAC channels. The Tavdac cDNAs are differentially expressed in meristematic tissues. The transcript levels of Tavdac 1 in all wheat tissues is at least 2.5-fold higher than Tavdac 2 and Tavdac 3. Tavdac 2 has a low level of expression in all floral tissues whereas Tavdac 3 is highly expressed in anthers. This is the first report on differential expression of vdac genes in plants. The Tavdac genes have been mapped on the wheat genome. Tavdac 1 is located on the long arm of chromosome 5, Tavdac 2 on the long arm of chromosome 1 and Tavdac 3 on the long arm of chromosome 3. A phylogenetic reconstruction indicates that vdac genes underwent numerous duplication events throughout their evolution. All duplications occurred after the separation of plants from animals and fungi, and no orthologous genes are shared among phyla. Within plants, some of the vdac gene duplications probably occurred before the monocotydelon-dicotydelon split.

Amino Acid Sequence↗

Differential expression in normal-adenoma-carcinoma sequence suggests complex molecular carcinogenesis in colon.

The majority of colon cancers develop from pre-existing adenomas. We analyzed the expression profiles in the sequence of normal colon crypts, adenomas and early-stage carcinomas using microdissected cells from tubular adenomas with foci of malignant transformation. Differentially expressed genes were detected between normal-adenoma and adenoma-carcinoma, and were grouped according to the patterns of expression changes in the sequence. Down-regulated genes in the sequence included PLA2G2A, TSPAN1, PDCD4, FCGBP, AATK, EPLIN, FABP1, AGR2, MTUS1, TSC1, galectin 4 and MT1F. PLA2G2A has been shown to suppress colon tumorigenesis in mice, but the pathobiological role in humans has been controversial. Our data showed continuous down-regulation of PLA2G2A in the sequence supporting an implication in human colon cancer. Tumor suppressor and/ or proapoptotic activities have also been reported in other genes. Up-regulated genes included ribosomal proteins, IER3 and TPR. TGF-beta2 and matrix metalloproteinase 23B were up-regulated in carcinoma but not in adenoma, supporting the pathobiological roles in malignant transformation. Differentially expressed genes partly coincided with those in the adenoma-carcinoma sequence of the stomach, which was published previously, suggesting a partial overlap between the adenoma-carcinoma sequences of the colon and stomach.

Adenoma↗

Molecular cloning of a new gene which is differentially expressed in breast and prostate cancers.

OBJECTIVE: The chromosomal region 19q13 is non-randomly rearranged in many solid tumors. METHODS: Using the positional candidate gene approach, we cloned a new gene, tentatively named cancer-associated gene (CAG), which is differentially expressed in breast and prostate cancers. RESULTS: The gene is formed of 3 exons and 2 intervening introns. Its coding region is 1,047 bp in length and is predicted to encode a 348-amino-acid polypeptide. The new gene maps to chromosome 19q13.4 and is located 14 kb telomeric to the kallikrein gene locus (KLK14 gene) and 17 kb centromeric from the Siglec family of genes (Siglec-9). The gene is expressed in a wide variety of tissues including the brain, colon, kidney and pancreas. The CAG protein shows a high degree of conservation among species and phylogenetically is most closely related to its mouse ortholog. In silico analysis indicates that this gene is differentially expressed in a variety of tumors including brain, colon, ovarian and prostate cancers. CONCLUSIONS: Our preliminary experimental data show that CAG is upregulated in prostate cancer tissues compared to normal prostatic tissues. CAG also appears to be downregulated in breast cancer tissues. The physiological function of the CAG protein is currently unknown.

Amino Acid Sequence↗

Differential expression of glutaredoxin and thioredoxin during monocytic differentiation.

Macrophages generate reactive oxygen intermediates (ROIs) as the effectors of anti-bacterial defense mechanism. Intracellular ROIs and reduction/oxidation (redox) status play crucial roles in signal transduction. We therefore investigated the expression of redox-regulating proteins such as glutaredoxin (GRX) and thioredoxin (TRX) during the differentiation of murine monocytic leukemia cell line M1 cells and human monocytic leukemia cell line U937 cells. When M1 cells were treated by IL-6, GRX mRNA markedly increased and TRX mRNA also increased slightly. In contrast, there was no increase of GRX mRNA in D-cell, which is a sub-cell line derived from M1 lacking in the capacity of differentiation. GRX mRNA also increased in U937 cells differentiated by phorbol 12-myristate 13-acetate (PMA). By immunohistochemistry, unstimulated M1 cells showed strong staining of TRX and marginal staining of GRX. In contrast, TRX expression in IL-6 treated M1 cells is as strong as in unstimulated M1 cells, whereas GRX expression is slightly enhanced in IL-6 treated M1 cells. Phagocytosis is markedly enhanced and hydrogen peroxide production is slightly enhanced in IL-6 treated M1 cells. These results showed that TRX is steadily expressed whereas GRX is induced in association with the differentiation in macrophage-like cell line cells, suggesting differential roles of these redox regulators in macrophage lineage.

Animals↗

Differential expression of oocyte-type class III genes with fraction TFIIIC from immature or mature oocytes.

The Xenopus OAX genes can be expressed in oocytes but are virtually inactive in somatic tissues. The tRNA(Met1) (tMET) genes also appear to be developmentally regulated. We have examined the reason for the differential expression of these class III genes. Analysis of the transcriptional activities of extracts derived from immature and mature oocytes revealed that the developmental regulation of these genes can be reproduced in vitro. We have partially purified the required transcription factors B and C from these extracts to ascertain the components responsible for this differential activity. The immature oocyte C fraction activates the tMET and OAX genes when reconstituted with either the immature or mature oocyte-derived B fraction. In contrast, the mature oocyte C fraction fails to activate these genes regardless of which B fraction is used. Both C fractions activated the somatic 5S gene. Purification of the oocyte C fractions by phosphocellulose or B box DNA affinity chromatography failed to separate additional activities responsible for the differential expression of OAX or tMET. By using template exclusion assays, the inability of the mature oocyte C fraction to activate transcription was correlated with an inability to form stable transcription complexes with the tMET or OAX gene.

Animals↗

Antibody potential of human peripheral blood lymphocytes differentially expressing surface membrane IgM.

The appearance of circulating pokeweed mitogen-reactive B lymphocyte subpopulations responsible for the synthesis of IgM and IgG anti-tetanus toxoid antibody after in vivo booster immunization has been analyzed for differential expression of surface membrane IgM. B cells were rosetted with human mu-chain specific antiglobulin-coupled ox red blood cells and separated by density centrifugation into mu+ and mu- populations. After 8 days in vitro culture with irradiated T cells and pokeweed mitogen, antibody synthesis was assessed by quantitative radioimmunoassay. Mu+ cells synthesized both IgG and IgM anti-tetanus toxoid antibodies, whereas mu- cells predominantly synthesized IgG anti-tetanus toxoid antibodies. Limiting dilution analysis revealed a greater number of IgG anti-tetanus toxoid precursors in the mu+ population at all times after immunization compared with mu- cells. However, the activity, as measured by the amount of antibody produced per IgG anti-tetanus toxoid antibody precursor, was 2 to 4 times greater in the mu- population than that in the mu+ population. These results indicate that functionally distinct human circulating B lymphocytes can be identified by their differential expression of surface membrane IgM.

Animals↗

Differential expression of Fas ligand in Th1 and Th2 cells is regulated by early growth response gene and NF-AT family members.

Inducible expression of Fas ligand (CD95 ligand) by activated T cells and the resulting apoptosis of CD95-bearing cells is a critical component of peripheral T cell homeostasis and cytotoxic effector mechanisms. Transcriptional control of the expression of Fas ligand has been attributed to a number of factors, including early growth response gene 2 (Egr2), Egr3, Sp1, and NF-AT, although a direct contribution of NF-AT is controversial. The present study confirms a role for Egr factors and indicates that NF-AT is essential for optimal expression of murine Fas ligand through a direct interaction with an NF-AT consensus element. The role of these factors was further defined by studying the differential expression of Fas ligand in Th1 and Th2 lines derived from DO11.10 TCR transgenic mice. EMSA analyses of a composite Egr/NF-AT site showed recruitment of Sp1 to this site in Th2 cells, but not in Th1 cells. Furthermore, gel-shift analyses demonstrated the binding of Egr1, 2, and 3 in Th2 cells and Egr1 and 2, but not Egr3 in Th1 cells at a known Egr site. Northern analysis corroborated the lack of Egr3 in Th1 cells. Differential usage of these transcription factors by Th1 and Th2 cells suggests a potential mechanism underlying the differential expression of Fas ligand by distinct T cell lineages.

Animals↗

Application of restriction fragment differential display-polymerase chain reaction in study on differential expression profiles of human diseases.

OBJECTIVE: To establish the restriction fragment differential display-polymerase chain reaction (RFDD-PCR) as an efficient technique for constructing and studying the gene expression profile of human tissues. METHODS: The tissues of mamma adenocarcinoma (T), cancerometastasis lymph node (L) and normal mammary (N) from one mammary infiltrating ductal carcinoma case were collected, and the gene expression profile of each kind of tissue was constructed using RFDD-PCR technique at equal pace according to the operating manual of Qbio-gene Company. Then all fragments of the three gene expression profiles were separated and displayed by electrophoresis. With the use of gene database at the website http://www.Qbio-gene.com/display, the authors identified the names of the probable fragments by bioinformatics analysis. Through comparison of the three profiles, the numbers and types of most differentially expressed gene fragments were displayed. RESULTS: The expression profiles of the three kinds of tissue have been constructed covering 1716 fragments of mammary adenocarcinoma, 1769 of cancerometastasis lymph nodes and 1922 of normal mammary tissue. Among these 5407 fragments, 39.39% were exactly the same. While 33.9% sequences of T and L showed differences in abundance or presence, 40.9% of T and N and 39.6% fragments of L and N were observed differentially expressed. These differentially expressed gene fragments were found to relate with metastasis, differentiation, inflammation and so on. CONCLUSION: RFDD-PCR is an efficient technique for research in human diseases genomics as a mass screening for complete gene expression profile with high-flux. Through comparison among three or more profiles, the screening for candidate genes of a certain disease can be accomplished, and there is probably a chance to identify novel gene or expressed sequence tag.

Adenocarcinoma↗

Differential expression of two cell adhesion molecules, Ephrin-A5 and Integrin alpha6, during cranial neurulation in the chick embryo.

The formation of the neural tube (neurulation) depends on the physical properties of the cells and tissues both inside and outside the neural plate. One such important physical property is cell adhesion. Theoretical and biological evidence support a role for cell adhesion in neurulation, but few specific cell adhesion molecules have been identified during this process. Ephrin-A5 and Integrin alpha6 are two of the known genes encoding cell adhesion molecules that are likely to be directly involved in neurulation because neural tube defects result when they are knocked out in mice. Yet it remains unclear how they can act on the cell and tissue behaviors of neurulation, because their domains of expression in neurulating tissues have not been reported. We report here the detailed pattern of expression of these two cell adhesion molecules in the chick embryo throughout the stages of neurulation at the mRNA and protein level. We show that Ephrin-A5 and Integrin alpha6 are differentially expressed in the ectoderm, outside and inside the neural plate, respectively, and that they are both restricted to neurulation at cranial (brain) levels. We discuss the potential contribution of this differential expression to the cell adhesion mechanisms involved in cranial neurulation and anencephaly.

Animals↗

p23 transplantation antigen mRNA is differentially expressed in human fetal brain.

As gene expression governs development, we attempted to isolate differentially expressed genes in fetal and adult human brain. RNA samples extracted from adult and 18-24-week-old fetal human brain were reverse transcribed, amplified using twenty combinations of 3'-anchored primers and degenerate 5'-primers, and the resulting cDNA fragments separated on denaturing polyacrylamide gels. Thereafter, 45 (H1-H45) differentially displayed cDNA bands were extracted from the gels, amplified by polymerase chain reaction, and used as probes to detect their mRNA by northern blotting. One of these fragments, H8, confirmed on northern blotting to be highly expressed in fetal brain, was cloned and sequenced. This fragment was homologous to wild type p23 human transplantation antigen. This is phylogenetically a well conserved gene and appears to play an important role in cell growth. Even a single point mutation in the mouse gene results in cell destruction secondary to a cytotoxic T-lymphocyte response. Therefore, our finding that normal human fetal brain expresses high levels of wild type p23 transplantation antigen may have importance in maintaining cell growth during human brain development.

Antigens, Neoplasm↗

Differential expression of alkaline phosphatase and ATPase activities in human colon carcinoma cell line HT-29.18 during differentiation.

The expression and cytochemical localization of alkaline phosphatase and Na+-pump sites were investigated in the human adenocarcinoma cell line HT-29.18 during differentiation. In the undifferentiated state, HT-29.18 cells expressed ATPase activity on plasma membrane whereas they displayed no alkaline phosphatase activity. In differentiated HT-29.18 cells, strong alkaline phosphatase activity was present on the apical membrane, whereas ATPase activity was restricted to the basolateral membrane. Intra- and intercellular lumina (cysts) observed in undifferentiated cells were devoid of both enzyme activities. In differentiated cells, cysts bearing well developed microvilli were strongly positive for alkaline phosphatase activity, while this activity seemed to be lacking in cysts without microvilli. ATPase activity was not found in either type of structure. Finally, HT-29.18 differentiated cells expressed, at pH 9.0, a p-nitrophenylphosphatase activity six-fold greater than that of undifferentiated cells.

Adenocarcinoma↗