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ABSTRACT: A variety of technical errors have arisen in data analysis when using cDNA or oligonucleotide microarrays. One of the most insidious problems is the saturation of the hybridization signal of high-abundant transcripts. This problem arises from the truncation of the laser fluorescence signal. When the hybridization signal on the microarray is very strong, this truncation can result in serious consequences that may not be readily apparent to the user. As an illustration of this problem, two subclasses of normal human tissue samples (six liver and six lung samples) were analyzed with GeneChip probe arrays to evaluate the patterns of expression for approximately 7000 human genes. Five of these data sets were found to suffer from signal truncation. This caused several tissues to be incorrectly classified using hierarchical clustering. To rectify this problem so that the gene expression data could be properly compared and clustered, we developed a "filtering" procedure that identifies a subset of genes least affected by the signal saturation. This filtering procedure can be obtained at www.hugeindex.org.
BioTechniques 03/2002; 32(2):330-2, 334, 336. · 2.67 Impact Factor
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L L Hsiao,
F Dangond,
T Yoshida,
R Hong,
R V Jensen,
J Misra,
W Dillon,
K F Lee,
K E Clark,
P Haverty, [......],
M P Frosch,
M E MacDonald,
E L Milford,
C P Crum,
R Bueno,
R E Pratt,
M Mahadevappa,
J A Warrington,
G Stephanopoulos, S R Gullans
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ABSTRACT: This study creates a compendium of gene expression in normal human tissues suitable as a reference for defining basic organ systems biology. Using oligonucleotide microarrays, we analyze 59 samples representing 19 distinct tissue types. Of approximately 7,000 genes analyzed, 451 genes are expressed in all tissue types and designated as housekeeping genes. These genes display significant variation in expression levels among tissues and are sufficient for discerning tissue-specific expression signatures, indicative of fundamental differences in biochemical processes. In addition, subsets of tissue-selective genes are identified that define key biological processes characterizing each organ. This compendium highlights similarities and differences among organ systems and different individuals and also provides a publicly available resource (Human Gene Expression Index, the HuGE Index, http://www.hugeindex.org) for future studies of pathophysiology.
Physiological Genomics 01/2002; 7(2):97-104. · 2.73 Impact Factor
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ABSTRACT: The properties and functions of gamma-aminobutyric acid (GABA(A)) receptors in the mammalian central nervous system are well studied. However, the presence and significance of GABA(A) receptors in nonneural tissue is less clear. The goal of this study was to examine the expression and localization of the GABA(A) receptor beta(2) and beta(3) subunits in the kidney. Reverse transcriptase products from RNA isolated from rat and rabbit kidney cortex and cerebellum and rabbit S(2) segments were amplified by use of PCR and GABA(A) beta(2) and beta(3) subunit-specific primers. Sequencing of the kidney PCR products revealed that the rat kidney cortex and rat neuronal GABA(A) receptor beta(2) subunit were identical in nucleotide composition. The rabbit kidney and rabbit neuronal GABA(A) receptor beta(2) subunit were 99% identical in nucleotide composition. Sequencing of the kidney PCR products revealed that the rat kidney cortex and rat neuronal GABA(A) receptor beta(3) subunits were 93% and 95% identical in nucleotide and amino acid composition, and rabbit kidney cortex and rabbit neuronal GABA(A) receptor beta(3) subunits were 95% and 98% identical in nucleotide and amino acid composition, respectively. PCR screening of a human kidney cDNA library and sequencing revealed that the human kidney cortex and neuronal beta(3) subunits were identical in nucleotide composition. Immunoblot analysis of rat kidney cortex and brain identified immunoreactive proteins in the 55 to 57 kD region, corresponding to the GABA(A) receptor beta(2) and beta(3) subunits. Immunohistochemistry revealed cytosolic and basolateral staining of the proximal convoluted and straight tubule. These results provide compelling evidence for the expression of the GABA(A) receptor beta(2) and beta(3) subunits in the kidney of multiple species and the localization of the beta(2)/beta(3) subunits to the renal proximal tubule.
Journal of the American Society of Nephrology 07/2001; 12(6):1107-13. · 9.66 Impact Factor
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ABSTRACT: DNA microarrays, or gene chips, allow surveys of gene expression, (i.e., mRNA expression) in a highly parallel and comprehensive manner. The pattern of gene expression produced, known as the expression profile, depicts the subset of gene transcripts expressed in a cell or tissue. At its most fundamental level, the expression profile can address qualitatively which genes are expressed in disease states. However, with the aid of bioinformatics tools such as cluster analysis, self-organizing maps, and principle component analysis, more sophisticated questions can be answered. Microarrays can be used to characterize the functions of novel genes, identify genes in a biologic pathway, analyze genetic variation, and identify therapeutic drug targets. Moreover, the expression profile can be used as a tissue or disease "fingerprint." This review details the fabrication of arrays, data management tools, and applications of microarrays to the field of renal research and the future of clinical practice.
Journal of the American Society of Nephrology 06/2001; 12(5):1072-8. · 9.66 Impact Factor
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ABSTRACT: To improve signal detection on cDNA microarrays, we adapted a fluorescent oligonucleotide dendrimeric signal amplification system to microarray technology. This signal detection method requires 16-fold less RNA for probe synthesis, does not depend on the incorporation of fluorescent dNTPs into a reverse transcription reaction, generates a high signal-to-background ratio, and can be used to allow for multichannel detection on a single chip. Furthermore, since the dendrimers can be detected individually, it may be possible, by employing dendrimer-binding standards, to calculate the numbers of bound cDNAs can be estimated. These features make the dendrimer signal detection reagent ideal for high-throughput functional genomics research.
Physiological Genomics 09/2000; 3(2):93-9. · 2.73 Impact Factor
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ABSTRACT: At the forefront of the revolution in human genomics is DNA microarray technology, which evaluates expression levels or genotypes of thousands of genes simultaneously, by means of miniaturization and parallel processing. Furthermore, advances in bioinformatics will result in the creation of large databases, which will require complex software programming for structural analysis. Over the next decade, DNA microarrays, combined with sophisticated informatics and genomic databases, will provide molecular fingerprints of disease processes and prognoses. This review provides an update on DNA microarray technology and its application to renal diseases.
Current Opinion in Nephrology and Hypertension 06/2000; 9(3):253-8. · 4.33 Impact Factor
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ABSTRACT: Histone deacetylases (HDACs) are enzymes that play a pivotal role in transcription, differentiation, and cell cycle progression. We previously cloned human HDAC3 cDNA and showed that its transfection into THP-1 cells results in G2/M cell cycle accumulation. Using bioinformatic screening and PCR, we have now cloned the murine Hdac3 cDNA, which encodes a 428-amino-acid protein with near complete identity to its human ortholog. To establish a link to a potential disease locus, we performed PCR-based chromosomal mapping for the mHdac3 gene and chromosomal fluorescence in situ hybridization (FISH) for the human gene. mHdac3 localizes to chromosome 18 and human HDAC3 gene localizes to a syntenic region in chromosome 5 at band q31.3-q32 telomeric to the cytokine gene cluster. Transfection of mHdac3 into HeLa cells led to accumulation in G2/M. Our results suggest a cell cycle function for murine Hdac3, reflecting the complex regulatory roles of this gene family.
Molecular Cell Biology Research Communications 09/1999; 2(2):91-6.
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ABSTRACT: A novel human membrane protein, TIRC7, was recently identified and demonstrated to be essential in T cell activation. Here we report on the genomic organization of the TIRC7 gene, which is composed of 15 exons and spans 7.9 kb. The seven predicted transmembrane-spanning domains of the TIRC7 protein coincide well with exon-intron boundaries. TIRC7 and OC116, a recently described putative subunit of the vacuolar proton pump that was demonstrated to be expressed in an osteoclastoma tumor as well as in a human pancreatic adenocarcinoma cell line, are demonstrated to be alternative transcripts of the same gene. OC116 consists of 20 exons with the last 14 introns and exons being identical with those of TIRC7. The chromosomal locus for both transcripts was identified on chromosome 11q13.4-q13.5. In human alloactivated T lymphocytes, mRNA expression of TIRC7, but not OC116, is demonstrated, indicating that OC116 is not involved in regular T cell proliferation.
Genomics 06/1999; 57(3):398-406. · 3.02 Impact Factor
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N Utku,
G C Bulwin,
S Beinke,
T Heinemann,
F Beato,
J Randall,
B Schnieders,
K Sandhoff,
H D Volk,
E Milford, S R Gullans
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ABSTRACT: To identify novel genes induced in the early stage of T-cell activation, mRNA expression in alloactivated human lymphocytes was examined. Differential display-reverse transcription PCR analysis revealed a 207-bp cDNA fragment which was upregulated 24 h after allostimulation of a human T-cell line. The corresponding complete 1396 bp cDNA, named TGAM77, encodes a predicted 134 amino acid protein which shares 63% homology with the cornichon (cni) protein of Drosophila melanogaster. Upregulation of TGAM77 mRNA in the early phase of T-cell activation was confirmed by Northern blot and RT-PCR analysis of activated human lymphocytes. TGAM77 mRNA is expressed in a variety of human tissues with various expression levels. In analogy to cni which is involved in an epidermal growth factor-like signaling pathway inducing cellular asymmetry in Drosophila oogenesis, TGAM77 might function in similar signaling establishing vectorial re-localization and concentration of signaling events in T-cell activation.
Biochimica et Biophysica Acta 05/1999; 1449(3):203-10. · 4.66 Impact Factor
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N Utku,
T Heinemann,
S G Tullius,
G C Bulwin,
S Beinke,
R S Blumberg,
F Beato,
J Randall,
R Kojima,
L Busconi,
E S Robertson,
R Schülein,
H D Volk,
E L Milford, S R Gullans
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ABSTRACT: A novel 75 kDa membrane protein, TIRC7, is described that exhibits a central role in T cell activation in vitro and in vivo. Modulation of TIRC7-mediated signals with specific anti-TIRC7 antibodies in vitro efficiently prevents human T cell proliferation and IL-2 secretion. Moreover, anti-TIRC7 antibodies specifically inhibit type 1 subset specific IFN-gamma expression but spare the type 2 cytokine IL-4. Diminished proliferation but not IFN-gamma secretion is reversible by exogenous rIL-2. An anti-TIRC7 antibody that cross-reacts with the 75 kDa rat homolog exhibits inhibition of rat alloimmune response in vitro and significantly prolongs kidney allograft survival in vivo. Targeting of TIRC7 may provide a novel therapeutic approach for modulation of the immune response.
Immunity 11/1998; 9(4):509-18. · 21.64 Impact Factor
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ABSTRACT: The reversible acetylation of histones by histone deacetylases (HDACs) and acetyltransferases (HATs) plays a fundamental role in gene transcription. We previously showed that HDAC mRNA is upregulated in immune cells upon PHA-induced activation. Little is known, however, about the differential regulation of HDAC mRNAs by the HDAC inhibitors Trichostatin A (TSA) and butyrate, agents known to block proliferation and induce apoptosis. We report that apoptosis-inducing concentrations of TSA and butyrate upregulate the expression of HDAC mRNAs in a differential manner and act synergistically with PHA to induce HDAC expression, suggesting the presence of independent HDAC regulatory mechanisms. Moreover, we show that HDAC inhibitor-induced apoptosis is associated with early abrogation of gamma-IFN production by Th1 lymphocytes and with p53 mRNA downregulation. Our findings highlight the dynamic interplay of cell cycle-, activation- and apoptosis-related proteins in association with time-dependent expression of HDACs and are suggestive of different specific roles for these enzymes.
Biochemical and Biophysical Research Communications 07/1998; 247(3):833-7. · 2.48 Impact Factor
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ABSTRACT: Physiological adaptation to the hyperosmolar milieu of the renal medulla involves a complex series of signaling and gene expression events in which NaCl and urea activate different cellular processes. In the present study, we evaluated the effects of NaCl and urea, individually and in combination, on the viability of murine inner medullary collecting duct (mIMCD3) cells. Exposure to hyperosmolar NaCl or urea caused comparable dose- and time-dependent decreases in cell viability, such that 700 mosmol/kgH2O killed >90% of the cells within 24 h. In both cases, cell death was an apoptotic event. For NaCl, loss of viability at 24 h paralleled decreases in RNA and protein synthesis at 4h, whereas lethal doses of urea had little or no effect on these biosynthetic processes. Cell cycle analysis showed both solutes caused a slowing of the G2/M phase. Surprisingly, cells exposed to a combination of NaCl + urea were significantly more osmotolerant such that 40% survived 900 mosmol/kgH2O. Madin-Darby canine kidney cells but not human umbilical vein endothelial cells also exhibited a similar osmotolerance response. Enhanced survival was not associated with a restoration of normal biosynthetic rates or cell cycle progression. However, the combination of NaCl + urea resulted in a shift in Hsp70 expression that appeared to correlate with survival. In conclusion, hyperosmolar NaCl and urea activate independent and complementary cellular programs that confer enhanced osmotolerance to renal medullary epithelial cells.
The American journal of physiology 07/1998; 274(6 Pt 2):F1167-73.
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ABSTRACT: Hsp110, Osp94, and Hsp70RY are members of the recently described Hsp110/SSE subfamily of (heat and osmotic) stress proteins whose members are structurally related to the Hsp70/BiP gene superfamily. To date, little is known about the response of this gene family to stresses in vitro or in vivo. In this study, an analysis of mRNA expression showed that Hsp110 and Osp94, like Hsp70, are induced in renal murine inner medullary collecting duct (mIMCD3) epithelial cells by heat shock, hyperosmotic NaCl, and cadmium, whereas low pH had a suppressive effect on Osp94. H2O2 decreased expression of Osp94 while inducing levels of Hsp110 and Hsp70 message. Tunicamycin, hypertonic urea, and tumor necrosis factor- had no effects. Hsp70RY was responsive exclusively to cadmium chloride. Moreover, enhanced expression of Hsp110 and Osp94 was subsequent to induction of Hsp70 and was suppressed by inhibition of protein synthesis by cycloheximide. RT-PCR analysis showed Hsp110, Osp94, and Hsp70RY are ubiquitously expressed in mouse tissues. In murine kidney, there was a corticomedullary gradient of expression of Hsp110, Osp94, Hsp70RY, and Hsp70 but not Hsc70 or BiP. Furthermore, dehydration increased inner medullary expression of Hsp110 and Osp94. An analysis of stress tolerance in mIMCD3 cells showed that heat shock and hyperosmotic NaCl stress are cross-tolerant stresses, suggesting hyperosmolality is a physiological correlate of heat shock in mammalian kidney. Thus Hsp110 and Osp94 behave as heat shock proteins, although they are regulated differently than Hsp70.
The American journal of physiology 07/1998; 274(6 Pt 2):F1054-61.
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ABSTRACT: Monocytic infiltration of the vessel wall is a hallmark of injury in a variety of vascular diseases. In the present study, we explored the relationship between endothelial apoptosis and hyperadhesiveness for monocytic cells. Apoptosis of human umbilical vein endothelial cells (HUVECs) was induced by either growth factor deprivation (GFD) for 24 hours or by incubation with mitomycin C (MMC) at 0.01 mg/ml for 24 hours and confirmed by light microscopy and DNA laddering. In parallel assessments of cell-cell adhesion, GFD and MMC induced hyperadhesiveness of HUVECs for the THP-1 monocytic cell line. Hyperadhesiveness developed in association with induction of intercellular adhesion molecule (ICAM)-1 and vascular cell adhesion molecule (VCAM)-1 on HUVECs and was attenuated by monoclonal antibodies directed against these ligands. Culture medium conditioned by apoptotic HUVECs up-regulated the expression of adhesion molecules on normal HUVECs, suggesting that paracrine factors in the apoptotic milieu led to induction of adhesion molecules. Interleukin (IL)-1beta was implicated as a putative mediator in this setting because 1) exogenous IL-1beta up-regulates ICAM-1 and VCAM-1 with kinetics similar to those noted during endothelial cell apoptosis, 2) endothelial apoptosis was associated with increased expression of IL-1beta converting enzyme, and 3) the adhesion-promoting actions of GFD and MMC were attenuated by an anti-IL-1beta antibody.
American Journal Of Pathology 03/1998; 152(2):523-32. · 4.89 Impact Factor
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Contributions to nephrology 02/1998; 123:110-20. · 1.49 Impact Factor
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ABSTRACT: The nucleosomal histones can be modified through reversible acetylation by histone acetyltransferases (HATs) and deacetylases (HDACs). HATs induce nucleosomal relaxation and allow DNA-binding by transcriptional activators. HDACs from corepressor complexes which negatively regulate cell growth. However, the HDAC inhibitors butyrate and Trichostatin A block T cell proliferation, suggesting that not all effects of HDACs lead to repression. Using mRNA differential display and 5'RACE we isolated human HDAC3, a novel gene that is upregulated in PHA-activated T cell clones. HDAC3 is homologous to other human HDACs and yeast RPD3. In peripheral blood mononuclear cells (PBMCs), activation by PHA, PMA and alpha-CD3 increased HDAC mRNA but no effect was seen with IFN-gamma, LPS, or IL-4. In contrast, GMCSF downregulated PBMC levels of HDAC3 mRNA. All HDACs were found to be ubiquitously expressed in immune and non-immune tissues. In human myeloid leukemia THP-1 cells, HDAC3 transfection resulted in increased size, aberrant nuclear morphology and cell cycle G2/M cell accumulation. Functional activity of the expressed HDAC3 protein was confirmed in alpha-HDAC3 antibody immunoprecipitates by a histone deacetylase assay. Our study suggests the participation of HDACs in cell cycle progression and activation.
Biochemical and Biophysical Research Communications 02/1998; 242(3):648-52. · 2.48 Impact Factor
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ABSTRACT: The extreme hyperosmotic conditions that exist in the renal inner medulla enable the urinary concentrating mechanism to function. In this study, we evaluated whether stress-related molecular chaperones are induced in response to hyperosmotic stress in mouse inner medullary collecting duct (mIMCD3) cells. Exposure of cells to medium supplemented with 100 mM NaCl for 4 or 24 h resulted in an increase in heat shock protein-72 (HSP-72) (inducible form) by Western blot. Immunocytochemistry confirmed the increase of HSP-72 and showed that hyperosmotic stress resulted in a localization of HSP-72 predominantly to the nucleoplasm that surrounds the nucleoli and to the cytoplasm, a subcellular distribution pattern different from that seen with heat shock. Using a denatured protein (casein)-affinity column with ATP elution, we identified a number of putative molecular chaperones (46, 60, 78, and 200 kDa) that are upregulated in response to 4 h of hyperosmotic NaCl treatment. Microsequencing identified one of these proteins to be the mitochondrial chaperone mtHSP-70, a member of HSP-70 family, and another to be similar to beta-actin. We also found high levels of HSP-72 in cells chronically adapted to hypertonicity, indicating that chaperones are still required to maintain certain cellular functions even after nonperturbing organic osmolytes are known to accumulate. These results suggest an important role for molecular chaperones in the adaptation of renal medullary epithelial cells to the hyperosmotic conditions that exist in the inner medulla in vivo.
The American journal of physiology 08/1997; 273(1 Pt 2):F9-17.
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ABSTRACT: We used in situ hybridization and immunocytochemistry with polyclonal antibodies against the mouse bumetanide-sensitive Na(+)-K(+)-2Cl- cotransporter (mBSC2) to determine the location of this cotransporter in rat brain. Northern blots and in situ hybridization showed the presence of cotransporter mRNA in the brain, with an especially high level of expression in the choroid plexus (CP). Affinity-purified anti-BSC2 antibody identified proteins of 145-155 kDa on Western blot analysis and immunoprecipitation of brain and CP membrane protein. Indirect immunofluorescence demonstrated that BSC2 protein is located on the apical surface of the CP and is heterogeneously distributed in cell bodies and dendrites of neurons in the central and peripheral nervous system. The apical localization of BSC2 in the CP was confirmed by 86Rb+ uptakes in primary cultures of CP cells grown on permeable filters and confocal immunofluorescence microscopy. The apical localization of the cotransporter in CP epithelium suggests a role for the cotransporter in cerebrospinal fluid K+ homeostasis. In neurons, the cotransporter may help regulate intracellular Cl- concentration and thereby affect neuronal response to gamma-aminobutyric acid.
The American journal of physiology 02/1997; 272(1 Pt 1):C173-83.
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The American journal of physiology 12/1996; 271(5 Pt 2):F957-9.
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ABSTRACT: A thiazide sensitive Na-Cl cotransporter, rTSC1, has recently been cloned from a rat kidney cortex cDNA library. The molecular regulation and nephron localization of this protein is unknown. The purpose of this study was to examine the nephron distribution and subcellular localization of the rTSC1 protein in the rat kidney. In situ hybridization showed rTSC1 transcripts were localized to short, convoluted tubule segments in the kidney cortex. Polyclonal antibodies raised against a 110 amino acid segment from the amino terminus of rTSC1 recognized three major bands of 135, 140 and 155 kDa on Western blotting of membrane protein from cortex but not outer medulla of the rat kidney. Immunofluorescence studies using the antibody alone and in double labeling experiments with antibodies against the H+ ATPase and calbindin D28, showed intense labeling of apical membranes in the distal nephron beginning in the initial distal convoluted tubule and terminating within the connecting tubule. The intensity of labeling diminished from proximal to distal sites along the distal tubule. Ultrastructural studies by immunoelectron microscopy showed the cotransporter protein to be localized predominately on apical microvilli of the distal convoluted tubule cells. These results are consistent with rTSC1 encoding the apical thiazide sensitive Na-Cl cotransporter in the distal tubule.
Kidney International 08/1996; 50(1):174-83. · 6.61 Impact Factor
