Publications

@article{pmid19687011,

title = {Interferon-resistant Daudi cell line with a Stat2 defect is resistant to apoptosis induced by chemotherapeutic agents},

author = {Ziyun Du and Meiyun Fan and Jong-Gwan Kim and Dara Eckerle and Leonard Lothstein and Lai Wei and Lawrence M Pfeffer},

doi = {10.1074/jbc.M109.028324},

issn = {1083-351X},

year  = {2009},

date = {2009-10-01},

journal = {J Biol Chem},

volume = {284},

number = {41},

pages = {27808--27815},

abstract = {Interferon-alpha (IFNalpha) has shown promise in the treatment of various cancers. However, the development of IFN resistance is a significant drawback. Using conditions that mimic in vivo selection of IFN-resistant cells, the RST2 IFN-resistant cell line was isolated from the highly IFN-sensitive Daudi human Burkitt lymphoma cell line. The RST2 cell line was resistant to the antiviral, antiproliferative, and gene-induction actions of IFNalpha. Although STAT2 mRNA was present, STAT2 protein expression was deficient in RST2 cells. A variant STAT2 mRNA, which resulted from alternative splicing within the intron between exon 19 and 20, was expressed in several human cell lines but at relatively high levels in RST2 cells. Most importantly, the RST2 line showed an intrinsic resistance to apoptosis induced by a number of chemotherapeutic agents (camptothecin, staurosporine, and doxorubicin). Expression of STAT2 in RST2 cells not only rescued their sensitivity to the biological activities of IFNs but also restored sensitivity to apoptosis induced by these chemotherapeutic agents. The intrinsic resistance of the RST2 cells to IFN as well as chemotherapeutic agents adds a new dimension to our knowledge of the role of STAT2 as it relates to not only biological actions of IFN but also resistance to chemotherapy-induced apoptosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19501869,

title = {Antiviral activity and host gene induction by tamarin and marmoset interferon-alpha and interferon-gamma in the GBV-B primary hepatocyte culture model},

author = {Deborah Chavez and Bernadette Guerra and Robert E Lanford},

doi = {10.1016/j.virol.2009.05.005},

issn = {1096-0341},

year  = {2009},

date = {2009-08-01},

journal = {Virology},

volume = {390},

number = {2},

pages = {186--196},

abstract = {GBV-B induces hepatitis in tamarins and marmosets and is a surrogate model for HCV infections. Here, we cloned and characterized the antiviral activity of tamarin and marmoset interferon (IFN)alpha and IFN gamma. Potent antiviral activity was observed for tamarin and marmoset IFN alpha in primary hepatocyte cultures infected with GBV-B. The antiviral activity was greater in cultures exposed to IFN alpha prior to GBV-B infection, suggesting that either GBV-B was capable of inhibition of the antiviral activity of exogenous IFN alpha or that the preexisting endogenous IFN response to the virus reduced efficacy to exogenous IFN alpha. IFN gamma also exhibited antiviral activity in GBV-B infected hepatocytes. The transcriptional response to IFN alpha in marmoset hepatocytes was characterized using human genome microarrays. Since the GBV-B hepatocyte culture model possesses a functional innate immune response, it will provide opportunities to explore the nature of the antiviral response to a virus closely related to HCV.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19265796,

title = {Hepatic gene expression in morbidly obese women: implications for disease susceptibility},

author = {Marshall B Elam and George S Cowan and Robert J Rooney and M Lloyd Hiler and Chandrahasa R Yellaturu and Xiong Deng and George E Howell and Edwards A Park and Ivan C Gerling and Divyan Patel and J Christopher Corton and Lauren M Cagen and Henry G Wilcox and Malay Gandhi and Micheal H Bahr and Micheal C Allan and Linus A Wodi and George A Cook and Thomas A Hughes and Rajendra Raghow},

doi = {10.1038/oby.2009.49},

issn = {1930-7381},

year  = {2009},

date = {2009-08-01},

journal = {Obesity (Silver Spring)},

volume = {17},

number = {8},

pages = {1563--1573},

abstract = {The objective of this study was to determine the molecular bases of disordered hepatic function and disease susceptibility in obesity. We compared global gene expression in liver biopsies from morbidly obese (MO) women undergoing gastric bypass (GBP) surgery with that of women undergoing ventral hernia repair who had experienced massive weight loss (MWL) following prior GBP. Metabolic and hormonal profiles were examined in MO vs. MWL groups. Additionally, we analyzed individual profiles of hepatic gene expression in liver biopsy specimens obtained from MO and MWL subjects. All patients underwent preoperative metabolic profiling. RNAs were extracted from wedge biopsies of livers from MO and MWL subjects, and analysis of mRNA expression was carried out using Affymetrix HG-U133A microarray gene chips. Genes exhibiting greater than twofold differential expression between MO and MWL subjects were organized according to gene ontology and hierarchical clustering, and expression of key genes exhibiting differential regulation was quantified by real-time-polymerase chain reaction (RT-PCR). We discovered 154 genes to be differentially expressed in livers of MWL and MO subjects. A total of 28 candidate disease susceptibility genes were identified that encoded proteins regulating lipid and energy homeostasis (PLIN, ENO3, ELOVL2, APOF, LEPR, IGFBP1, DDIT4), signal transduction (MAP2K6, SOCS-2), postinflammatory tissue repair (HLA-DQB1, SPP1, P4HA1, LUM), bile acid transport (SULT2A, ABCB11), and metabolism of xenobiotics (GSTT2, CYP1A1). Using gene expression profiling, we have identified novel candidate disease susceptibility genes whose expression is altered in livers of MO subjects. The significance of altered expression of these genes to obesity-related disease is discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19306956,

title = {New insights into BMP-7 mediated osteoblastic differentiation of primary human mesenchymal stem cells},

author = {Karen Lavery and Sara Hawley and Pamela Swain and Robert Rooney and Dean Falb and Moulay Hicham Alaoui-Ismaili},

doi = {10.1016/j.bone.2009.03.656},

issn = {1873-2763},

year  = {2009},

date = {2009-07-01},

journal = {Bone},

volume = {45},

number = {1},

pages = {27--41},

abstract = {Bone Morphogenetic Proteins (BMPs) are members of the TGF-beta superfamily of growth factors. Several BMPs exhibit osteoinductive bioactivities, and are critical for bone formation in both developing and mature skeletal systems. BMP-7 (OP-1) is currently used clinically in revision of posterolateral spine fusions and long bone non-unions. The current study characterizes BMP-7 induced gene expression during early osteoblastic differentiation of human mesenchymal stem cells (hMSC). Primary hMSC were treated with BMP-7 for 24 or 120 h and gene expression across the entire human genome was evaluated using Affymetrix HG-U133 Plus 2.0 Arrays. 955 probe sets representing 655 genes and 95 ESTs were identified as differentially expressed and were organized into three major expression profiles (Profiles A, B and C) by hierarchical clustering. Genes from each profile were classified according to biochemical pathway analyses. Profile A, representing genes upregulated by BMP-7, revealed strong enrichment for established osteogenic marker genes, as well as several genes with undefined roles in osteoblast function, including MFI2, HAS3, ADAMTS9, HEY1, DIO2 and FGFR3. A functional screen using siRNA suggested roles for MFI2, HEY1 and DIO2 in osteoblastic differentiation of hMSC. Profile B contained genes transiently downregulated by BMP-7, including numerous genes associated with cell cycle regulation. Follow-up studies confirmed that BMP-7 attenuates cell cycle progression and cell proliferation during early osteoblastic differentiation. Profile C, comprised of genes continuously downregulated by BMP-7, exhibited strong enrichment for genes associated with chemokine/cytokine activity. Inhibitory effects of BMP-7 on cytokine secretion were verified by analysis of enriched culture media. Potent downregulation of CHI3L1, a potential biomarker for numerous joint diseases, was also observed in Profile C. A focused evaluation of BMP, GDF and BMP inhibitor expression elucidated feedback loops modulating BMP-7 bioactivity. BMP-7 was found to induce BMP-2 and downregulate GDF5 expression. Transient knockdown of BMP-2 using siRNA demonstrated that osteoinductive properties associated with BMP-7 are independent of endogenous BMP-2 expression. Noggin was identified as the predominant inhibitor induced by BMP-7 treatment. Overall, this study provides new insight into key bioactivities characterizing early BMP-7 mediated osteoblastic differentiation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19627265,

title = {Oxidative stress and longevity in Caenorhabditis elegans as mediated by SKN-1},

author = {Sang-Kyu Park and Patricia M Tedesco and Thomas E Johnson},

doi = {10.1111/j.1474-9726.2009.00473.x},

issn = {1474-9726},

year  = {2009},

date = {2009-06-01},

journal = {Aging Cell},

volume = {8},

number = {3},

pages = {258--269},

abstract = {Oxidative stress has been hypothesized to play a role in normal aging. The response to oxidative stress is regulated by the SKN-1 transcription factor, which also is necessary for intestinal development in Caenorhabditis elegans. Almost a thousand genes including the antioxidant and heat-shock responses, as well as genes responsible for xenobiotic detoxification were induced by the oxidative stress which was found using transcriptome analysis. There were also 392 down-regulated genes including many involved in metabolic homeostasis, organismal development, and reproduction. Many of these oxidative stress-induced transcriptional changes are dependent on SKN-1 action; the induction of the heat-shock response is not. When RNAi to inhibit genes was used, most had no effect on either resistance to oxidative stress or longevity; however two SKN-1-dependent genes, nlp-7 and cup-4, that were up-regulated by oxidative stress were found to be required for resistance to oxidative stress and for normal lifespan. nlp-7 encodes a neuropeptide-like protein, expressed in neurons, while cup-4 encodes a coelomocyte-specific, ligand-gated ion channel. RNAi of nlp-7 or cup-4 increased sensitivity to oxidative stress and reduced lifespan. Among down-regulated genes, only inhibition of ent-1, a nucleoside transporter, led to increased resistance to oxidative stress; inhibition had no effect on lifespan. In contrast, RNAi of nhx-2, a Na(+)/H(+) exchanger, extended lifespan significantly without affecting sensitivity to oxidative stress. These findings showed that a transcriptional shift from growth and maintenance towards the activation of cellular defense mechanisms was caused by the oxidative stress; many of these transcriptional alterations are SKN-1 dependent.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19094237,

title = {Alterations in cell growth and signaling in ErbB3 binding protein-1 (Ebp1) deficient mice},

author = {Yuexing Zhang and Yan Lu and Hua Zhou and Myounghee Lee and Zhenqiu Liu and Bret A Hassel and Anne W Hamburger},

doi = {10.1186/1471-2121-9-69},

issn = {1471-2121},

year  = {2008},

date = {2008-12-01},

journal = {BMC Cell Biol},

volume = {9},

pages = {69},

abstract = {BACKGROUND: The ErbB3 binding protein-1 (Ebp1) belongs to a family of DNA/RNA binding proteins implicated in cell growth, apoptosis and differentiation. However, the physiological role of Ebp1 in the whole organism is not known. Therefore, we generated Ebp1-deficient mice carrying a gene trap insertion in intron 2 of the Ebp1 (pa2g4) gene.



RESULTS: Ebp1-/- mice were on average 30% smaller than wild type and heterozygous sex matched littermates. Growth retardation was apparent from Day 10 until Day 30. IGF-1 production and IGBP-3 and 4 protein levels were reduced in both embryo fibroblasts and adult knock-out mice. The proliferation of fibroblasts derived from Day 12.5 knock out embryos was also decreased as compared to that of wild type cells. Microarray expression analysis revealed changes in genes important in cell growth including members of the MAPK signal transduction pathway. In addition, the expression or activation of proliferation related genes such as AKT and the androgen receptor, previously demonstrated to be affected by Ebp1 expression in vitro, was altered in adult tissues.



CONCLUSION: These results indicate that Ebp1 can affect growth in an animal model, but that the expression of proliferation related genes is cell and context specific. The Ebp1-/- mouse line represents a new in vivo model to investigate Ebp1 function in the whole organism.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid18852121,

title = {EBP1, an ErbB3-binding protein, is decreased in prostate cancer and implicated in hormone resistance},

author = {Yuexing Zhang and Douglas Linn and Zhenqiu Liu and Jonathan Melamed and Fabio Tavora and Charles Y Young and Angelika M Burger and Anne W Hamburger},

doi = {10.1158/1535-7163.MCT-08-0526},

issn = {1535-7163},

year  = {2008},

date = {2008-10-01},

journal = {Mol Cancer Ther},

volume = {7},

number = {10},

pages = {3176--3186},

abstract = {Aberrant activation of the androgen receptor (AR) by the ErbB2/ErbB3 heterodimer contributes to the development of hormone resistance in prostate cancer. EBP1, an ErbB3-binding protein, acts as an AR corepressor. As EBP1 is decreased in preclinical models of hormone-refractory prostate cancer, we studied the expression of EBP1 in human prostate cancer. We found that the expression of the EBP1 gene was significantly decreased in prostate cancer tissues compared with benign prostate at both mRNA and protein levels. Restoration of EBP1 expression in the hormone-refractory LNCaP C81 cell line led to an amelioration of the androgen-independent phenotype based on established biological criteria and a reduction in the expression of a cohort of AR target genes. The ability of the ErbB3 ligand heregulin (HRG) to stimulate growth and AKT phosphorylation of hormone-refractory prostate cancer cells was abolished. Abrogation of EBP1 expression by short hairpin RNA in hormone-dependent LNCaP cells, which undergo apoptosis in response to HRG, resulted in HRG-stimulated cell growth. Restoration of EBP1 expression decreased the tumorigenicity of C81 xenografts in female mice, whereas elimination of EBP1 expression enhanced the ability of LNCaP cells to grow in female mice. Our data support a role for EBP1 in the development of hormone-refractory prostate cancer via inhibition of both AR- and HRG-stimulated growth and present a novel strategy for treating androgen-refractory prostate cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid18632874,

title = {Comparative effects of estradiol, methyl-piperidino-pyrazole, raloxifene, and ICI 182 780 on gene expression in the murine uterus},

author = {Angela M Davis and Jiude Mao and Bushra Naz and Jessica A Kohl and Cheryl S Rosenfeld},

doi = {10.1677/JME-08-0029},

issn = {1479-6813},

year  = {2008},

date = {2008-10-01},

journal = {J Mol Endocrinol},

volume = {41},

number = {4},

pages = {205--217},

abstract = {Selective estrogen receptor modulators (SERMs) are potentially useful in treating various endometrial disorders, including endometrial cancer, as they block some of the detrimental effects of estrogen. It remains unclear whether each SERM regulates a unique subset of genes and, if so, whether the combination of a SERM and 17beta-estradiol has an additive or synergistic effect on gene expression. We performed microarray analysis with Affymetrix Mouse Genome 430 2.0 short oligomer arrays to determine gene expression changes in uteri of ovariectomized mice treated with estradiol (low and high dose), methyl-piperidino-pyrazole (MPP), ICI 182 780, raloxifene, and combinations of high dose of estradiol with one of the SERM and dimethyl sulfoxide (DMSO) vehicle control. The nine treatments clustered into two groups, with MPP, raloxifene, and high dose of estradiol in one, and low dose of estradiol, ICI + estradiol, ICI, MPP + estradiol, and raloxifene + estradiol in the second group. Surprisingly, combining a high dose of estradiol with a SERM markedly increased (P<0.02) the number of regulated genes compared with each individual treatment. Analysis of expression for selected genes in uteri of estradiol and SERM-treated mice by quantitative (Q)RT-PCR generally supported the microarray results. For some cancer-associated genes, including Klk1, Ihh, Cdc45l, and Cdca8, administration of MPP or raloxifene with estradiol resulted in greater expression than estradiol alone (P<0.05). By contrast, ICI 182 780 suppressed more genes governing DNA replication compared with MPP and raloxifene treatments. Therefore, ICI 182 780 might be superior to MPP and raloxifene to treat estrogen-induced endometrial cancer in women.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid18817551,

title = {Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: mouse forebrain weight},

author = {Lu Lu and Lai Wei and Jeremy L Peirce and Xusheng Wang and Jianhua Zhou and Ramin Homayouni and Robert W Williams and David C Airey},

doi = {10.1186/1471-2164-9-444},

issn = {1471-2164},

year  = {2008},

date = {2008-09-01},

journal = {BMC Genomics},

volume = {9},

pages = {444},

abstract = {BACKGROUND: Successful strategies for QTL gene identification benefit from combined experimental and bioinformatic approaches. Unique design aspects of the BXD recombinant inbred line mapping panel allow use of archived gene microarray expression data to filter likely from unlikely candidates. This prompted us to propose a simple five-filter protocol for candidate nomination. To filter more likely from less likely candidates, we required candidate genes near to the QTL to have mRNA abundance that correlated with the phenotype among the BXD lines as well as differed between the parental lines C57BL/6J and DBA/2J. We also required verification of mRNA abundance by an independent method, and finally we required either differences in protein levels or confirmed DNA sequence differences.



RESULTS: QTL mapping of mouse forebrain weight in 34 BXD RI lines found significant association on chromosomes 1 and 11, with each C57BL/6J allele increasing weight by more than half a standard deviation. The intersection of gene lists that were within +/- 10 Mb of the strongest associated location, that had forebrain mRNA abundance correlated with forebrain weight among the BXD, and that had forebrain mRNA abundance differing between C57BL/6J and DBA/2J, produced two candidates, Tnni1 (troponin 1) and Asb3 (ankyrin repeat and SOCS box-containing protein 3). Quantitative RT-PCR confirmed the direction of an increased expression in C57BL/6J genotype over the DBA/2J genotype for both genes, a difference that translated to a 2-fold difference in Asb3 protein. Although Tnni1 protein differences could not be confirmed, a 273 bp indel polymorphism was discovered 1 Kb upstream of the transcription start site.



CONCLUSION: Delivery of well supported candidate genes following a single quantitative trait locus mapping experiment is difficult. However, by combining available gene expression data with QTL mapping, we illustrated a five-filter protocol that nominated Asb3 and Tnni1 as candidates affecting increased mouse forebrain weight. We recommend our approach when (1) investigators are working with phenotypic differences between C57BL/6J and DBA/2J, and (2) gene expression data are available on http://www.genenetwork.org that relate to the phenotype of interest. Under these circumstances, measurement of the phenotype in the BXD lines will likely also deliver excellent candidate genes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid18500935,

title = {Transcriptome profile of the vascular endothelial cell response to Candida albicans},

author = {Katherine S Barker and Hyunsook Park and Quynh T Phan and Lijing Xu and Ramin Homayouni and P David Rogers and Scott G Filler},

doi = {10.1086/589516},

issn = {0022-1899},

year  = {2008},

date = {2008-07-01},

journal = {J Infect Dis},

volume = {198},

number = {2},

pages = {193--202},

abstract = {BACKGROUND: During hematogenously disseminated candidiasis, bloodborne Candida albicans interacts with vascular endothelial cells (ECs), which have the capacity to influence the local inflammatory response to this organism.



METHODS: To elucidate the EC response to C. albicans, we determined the transcriptional profile of ECs infected with wild-type C. albicans strain SC5314 and a hypovirulent cph1Delta/cph1Delta efg1Delta/efg1Delta mutant, CAN34. These EC responses were also compared to our previously published data on the response of the macrophage-like THP-1 cell line to C. albicans.



RESULTS: Infection with strain SC5314 induced upregulation of EC genes involved in chemotaxis, stress response, angiogenesis, and inhibition of apoptosis. Infection with CAN34 induced weaker expression of fewer genes. The angiogenic and anti-apoptotic response of ECs to C. albicans did not occur in THP-1 cells. However, there was upregulation of CCL3 and CCL4 expression in both cell types. Because CCR5 is the receptor for CCL3 and CCL4, we tested the susceptibility of CCR5(-/-) mice to disseminated candidiasis. The survival and renal fungal burden of the CCR5(-/-) mice were similar to that of wild-type control mice.



CONCLUSIONS: ECs respond significantly differently to infection with C. albicans, compared with THP-1 cells. CCR5 is dispensable for the host defense against disseminated candidiasis in immunocompetent mice.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid18487346,

title = {A gain-of-function mutation in the transcription factor Upc2p causes upregulation of ergosterol biosynthesis genes and increased fluconazole resistance in a clinical Candida albicans isolate},

author = {Nico Dunkel and Teresa T Liu and Katherine S Barker and Ramin Homayouni and Joachim Morschhäuser and P David Rogers},

doi = {10.1128/EC.00103-08},

issn = {1535-9786},

year  = {2008},

date = {2008-07-01},

journal = {Eukaryot Cell},

volume = {7},

number = {7},

pages = {1180--1190},

abstract = {In the pathogenic yeast Candida albicans, the zinc cluster transcription factor Upc2p has been shown to regulate the expression of ERG11 and other genes involved in ergosterol biosynthesis upon exposure to azole antifungals. ERG11 encodes lanosterol demethylase, the target enzyme of this antifungal class. Overexpression of UPC2 reduces azole susceptibility, whereas its disruption results in hypersusceptibility to azoles and reduced accumulation of exogenous sterols. Overexpression of ERG11 leads to the increased production of lanosterol demethylase, which contributes to azole resistance in clinical isolates of C. albicans, but the mechanism for this has yet to be determined. Using genome-wide gene expression profiling, we found UPC2 and other genes involved in ergosterol biosynthesis to be coordinately upregulated with ERG11 in a fluconazole-resistant clinical isolate compared with a matched susceptible isolate from the same patient. Sequence analysis of the UPC2 alleles of these isolates revealed that the resistant isolate contained a single-nucleotide substitution in one UPC2 allele that resulted in a G648D exchange in the encoded protein. Introduction of the mutated allele into a drug-susceptible strain resulted in constitutive upregulation of ERG11 and increased resistance to fluconazole. By comparing the gene expression profiles of the fluconazole-resistant isolate and of strains carrying wild-type and mutated UPC2 alleles, we identified target genes that are controlled by Upc2p. Here we show for the first time that a gain-of-function mutation in UPC2 leads to the increased expression of ERG11 and imparts resistance to fluconazole in clinical isolates of C. albicans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid18431470,

title = {The T7-primer is a source of experimental bias and introduces variability between microarray platforms},

author = {Ron M Kerkhoven and Daoud Sie and Marja Nieuwland and Mike Heimerikx and Jorma De Ronde and Wim Brugman and Arno Velds},

doi = {10.1371/journal.pone.0001980},

issn = {1932-6203},

year  = {2008},

date = {2008-04-01},

journal = {PLoS One},

volume = {3},

number = {4},

pages = {e1980},

abstract = {Eberwine(-like) amplification of mRNA adds distinct 6-10 bp nucleotide stretches to the 5' end of amplified RNA transcripts. Analysis of over six thousand microarrays reveals that probes containing motifs complementary to these stretches are associated with aberrantly high signals up to a hundred fold the signal observed in unaffected probes. This is not observed when total RNA is used as target source. Different T7 primer sequences are used in different laboratories and platforms and consequently different T7 primer bias is observed in different datasets. This will hamper efforts to compare data sets across platforms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17699737,

title = {Catechol-o-methyltransferase and methoxyestradiols participate in the intraoviductal nongenomic pathway through which estradiol accelerates egg transport in cycling rats},

author = {Alexis Parada-Bustamante and Pedro A Orihuela and Mariana Ríos and Patricia A Navarrete-Gómez and Catherina A Cuevas and Luis A Velasquez and Manuel J Villalón and Horacio B Croxatto},

doi = {10.1095/biolreprod.107.061622},

issn = {0006-3363},

year  = {2007},

date = {2007-12-01},

journal = {Biol Reprod},

volume = {77},

number = {6},

pages = {934--941},

abstract = {Estradiol (E(2)) accelerates oviductal egg transport through intraoviductal nongenomic pathways in cyclic rats and through genomic pathways in pregnant rats. This shift in pathways, which we have provisionally designated as intracellular path shifting (IPS), is caused by mating-associated signals and represents a novel and hitherto unrecognized phenomenon. The mechanism underlying IPS is currently under investigation. Using microarray analysis, we identified several genes the expression levels of which changed in the rat oviduct within 6 hours of mating. Among these genes, the mRNA level for the enzyme catechol-O-methyltransferase (COMT), which produces methoxyestradiols from hydroxyestradiols, decreased 6-fold, as confirmed by real-time PCR. O-methylation of 2-hydroxyestradiol was up to 4-fold higher in oviductal protein extracts from cyclic rats than from pregnant rats and was blocked by OR486, which is a selective inhibitor of COMT. The levels in the rat oviduct of mRNA and protein for cytochrome P450 isoforms 1A1 and 1B1, which form hydroxyestradiols, were detected by RT-PCR and Western blotting. We explored whether methoxyestradiols participate in the pathways involved in E(2)-accelerated egg transport. Intrabursal application of OR486 prevented E(2) from accelerating egg transport in cyclic rats but not in pregnant rats, whereas 2-methoxyestradiol (2ME) and 4-methoxyestradiol mimicked the effect of E(2) on egg transport in cyclic rats but not in pregnant rats. The effect of 2ME on egg transport was blocked by intrabursal administration of the protein kinase inhibitor H-89 or the antiestrogen ICI 182780, but not by actinomycin D or OR486. We conclude that in the absence of mating, COMT-mediated formation of methoxyestradiols in the oviduct is essential for the nongenomic pathway through which E(2) accelerates egg transport in the rat oviduct. Yet unidentified mating-associated signals, which act directly on oviductal cells, shut down the E(2) nongenomic signaling pathway upstream and downstream of methoxyestradiols. These findings highlight a physiological role for methoxyestradiols in the female genital tract, thereby confirming the occurrence of and providing a partial explanation for the mechanism underlying IPS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17905926,

title = {Genome-wide expression and location analyses of the Candida albicans Tac1p regulon},

author = {Teresa T Liu and Sadri Znaidi and Katherine S Barker and Lijing Xu and Ramin Homayouni and Saloua Saidane and Joachim Morschhäuser and André Nantel and Martine Raymond and P David Rogers},

doi = {10.1128/EC.00327-07},

issn = {1535-9778},

year  = {2007},

date = {2007-11-01},

journal = {Eukaryot Cell},

volume = {6},

number = {11},

pages = {2122--2138},

abstract = {A major mechanism of azole resistance in Candida albicans is overexpression of the genes encoding the ATP binding cassette transporters Cdr1p and Cdr2p due to gain-of-function mutations in Tac1p, a transcription factor of the zinc cluster family. To identify the Tac1p regulon, we analyzed four matched sets of clinical isolates representing the development of CDR1- and CDR2-mediated azole resistance by using gene expression profiling. We identified 31 genes that were consistently up-regulated with CDR1 and CDR2, including TAC1 itself, and 12 consistently down-regulated genes. When a resistant strain deleted for TAC1 was examined similarly, expression of almost all of these genes returned to levels similar to those in the matched azole-susceptible isolate. Using genome-wide location (ChIP-chip) analysis (a procedure combining chromatin immunoprecipitation with hybridization to DNA intergenic microarrays), we found 37 genes whose promoters were bound by Tac1p in vivo, including CDR1 and CDR2. Sequence analysis identified nine new genes whose promoters contain the previously reported Tac1p drug-responsive element (CGGN(4)CGG), including TAC1. In total, there were eight genes whose expression was modulated in the four azole-resistant clinical isolates in a TAC1-dependent manner and whose promoters were bound by Tac1p, qualifying them as direct Tac1p targets: CDR1, CDR2, GPX1 (putative glutathione peroxidase), LCB4 (putative sphingosine kinase), RTA3 (putative phospholipid flippase), and orf19.1887 (putative lipase), as well as IFU5 and orf19.4898 of unknown function. Our results show that Tac1p binds under nonactivating conditions to the promoters of its targets, including to its own promoter. They also suggest roles for Tac1p in regulating lipid metabolism (mobilization and trafficking) and oxidative stress response in C. albicans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17668868,

title = {Lack of response to exogenous interferon-alpha in the liver of chimpanzees chronically infected with hepatitis C virus},

author = {Robert E Lanford and Bernadette Guerra and Catherine B Bigger and Helen Lee and Deborah Chavez and Kathleen M Brasky},

doi = {10.1002/hep.21776},

issn = {0270-9139},

year  = {2007},

date = {2007-10-01},

journal = {Hepatology},

volume = {46},

number = {4},

pages = {999--1008},

abstract = {The mechanism of the interferon-alpha (IFNalpha)-induced antiviral response is not completely understood. We recently examined the transcriptional response to IFNalpha in uninfected chimpanzees. The transcriptional response to IFNalpha in the liver and peripheral blood mononuclear cells (PBMCs) was rapidly induced but was also rapidly down-regulated, with most interferon-alpha-stimulated genes (ISGs) returning to the baseline within 24 hours. We have extended these observations to include chimpanzees chronically infected with hepatitis C virus (HCV). Remarkably, using total genome microarray analysis, we observed almost no induction of ISG transcripts in the livers of chronically infected animals following IFNalpha dosing, whereas the response in PBMCs was similar to that in uninfected animals. In agreement with this finding, no decrease in the viral load occurred with up to 12 weeks of pegylated IFNalpha therapy. The block in the response to exogenous IFNalpha appeared to be HCV-specific because the response in a hepatitis B virus-infected animal was similar to that of uninfected animals. The lack of a response to exogenous IFNalpha may be due to an already maximally induced ISG response because chronically HCV-infected chimpanzees already have a highly up-regulated hepatic ISG response. Alternatively, negative regulation may block the response to exogenous IFNalpha, yet it does not prevent the continued response to endogenous ISG stimuli. The IFNalpha response in chronically HCV-infected chimpanzees may be mechanistically similar to the null response in the human population.



CONCLUSION: In chimpanzees infected with HCV, the highly elevated hepatic ISG expression may prevent the further induction of ISGs and antiviral efficacy following an IFNalpha treatment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17935615,

title = {The histone deacetylase inhibitor belinostat (PXD101) suppresses bladder cancer cell growth in vitro and in vivo},

author = {Michael T Buckley and Joanne Yoon and Herman Yee and Luis Chiriboga and Leonard Liebes and Gulshan Ara and Xiaozhong Qian and Dean F Bajorin and Tung-Tien Sun and Xue-Ru Wu and Iman Osman},

doi = {10.1186/1479-5876-5-49},

issn = {1479-5876},

year  = {2007},

date = {2007-10-01},

journal = {J Transl Med},

volume = {5},

pages = {49},

abstract = {BACKGROUND: Treatment options for patients with recurrent superficial bladder cancer are limited, necessitating aggressive exploration of new treatment strategies that effectively prevent recurrence and progression to invasive disease. We assessed the effects of belinostat (previously PXD101), a novel histone deacetylase inhibitor, on a panel of human bladder cancer cell lines representing superficial and invasive disease, and on a transgenic mouse model of superficial bladder cancer.



METHODS: Growth inhibition and cell cycle distribution effect of belinostat on 5637, T24, J82, and RT4 urothelial lines were assessed. Ha-ras transgenic mice with established superficial bladder cancer were randomized to receive either belinostat or vehicle alone, and assessed for bladder weight, hematuria, gene expression profiling, and immunohistochemistry (IHC).



RESULTS: Belinostat had a significant linear dose-dependent growth inhibition on all cell lines (IC50 range of 1.0-10.0 microM). The 5637 cell line, which was derived from a superficial papillary tumor, was the most sensitive to treatment. Belinostat (100 mg/kg, intraperitoneal, 5 days each week for 3 weeks) treated mice had less bladder weight (p < 0.05), and no hematuria compared with 6/10 control mice that developed at least one episode. IHC of bladder tumors showed less cell proliferation and a higher expression of p21WAF1 in the belinostat-treated mice. Gene expression profile analysis revealed 56 genes significantly different in the treated group; these included the upregulation of p21WAF1, induction of core histone deacetylase (HDAC), and cell communication genes.



CONCLUSION: Our data demonstrate that belinostat inhibits bladder cancer and supports the clinical evaluation of belinostat for the treatment of patients with superficial bladder cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bowen2007,

title = {Differential Gene Expression Induced by Exposure of Captive Mink to Fuel Oil: A Model for the Sea Otter},

author = {Lizabeth Bowen and Federica Riva and Chuck Mohr and Brian Aldridge and Julie Schwartz and A. Keith Miles and Jeffrey L. Stott},

url = {https://doi.org/10.1007/s10393-007-0113-5},

doi = {10.1007/s10393-007-0113-5},

issn = {1612-9210},

year  = {2007},

date = {2007-09-01},

journal = {EcoHealth},

volume = {4},

number = {3},

pages = {298-309},

abstract = {Free-ranging sea otters are subject to hydrocarbon exposure from a variety of sources, both natural and anthropogenic. Effects of direct exposure to unrefined crude oil, such as that associated with the Exxon Valdez oil spill, are readily apparent. However, the impact of subtle but pathophysiologically relevant concentrations of crude oil on sea otters is difficult to assess. The present study was directed at developing a model for assessing the impact of low concentrations of fuel oil on sea otters. Quantitative PCR was used to identify differential gene expression in American mink that were exposed to low concentrations of bunker C fuel oil. A total of 23 genes, representing 10 different physiological systems, were analyzed for perturbation. Six genes with immunological relevance were differentially expressed in oil-fed mink. Interleukin-18 (IL-18), IL-10, inducible nitric oxide synthase (iNOS), cyclooxygenase 2 (COX-2), and complement cytolysis inhibitor (CLI) were down-regulated while IL-2 was up-regulated. Expression of two additional genes was affected; heat shock protein 70 (HSP70) was up-regulated and thyroid hormone receptor (THR) was down-regulated. While the significance of each perturbation is not immediately evident, we identified differential expression of genes that would be consistent with the presence of immune system-modifying and endocrine-disrupting compounds in fuel oil. Application of this approach to identify effects of petroleum contamination on sea otters should be possible following expansion of this mink model to identify a greater number of affected genes in peripheral blood leukocytes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17334389,

title = {Opposing roles of netrin-1 and the dependence receptor DCC in cancer cell invasion, tumor growth and metastasis},

author = {S Rodrigues and O De Wever and E Bruyneel and R J Rooney and C Gespach},

doi = {10.1038/sj.onc.1210347},

issn = {0950-9232},

year  = {2007},

date = {2007-08-01},

journal = {Oncogene},

volume = {26},

number = {38},

pages = {5615--5625},

abstract = {Deleted in colon cancer (DCC) and UNC5 function as netrin dependence receptors by inducing apoptosis in the absence of their ligand and accordingly were recently designated as putative conditional tumor suppressors. Herein, we determined whether netrin-1 and its receptors are implicated in cancer cell invasion and tumor progression. Expression of DCC, UNC5 and adenosine A2B-receptors (A2B-Rs) was investigated by reverse transcription polymerase chain reaction in human colon cancer cells. The impact of DCC restitution and netrin-1 was evaluated on collagen type I invasion, tumor growth and metastasis in nude mice, cancer cell survival and gene expression profiling. Flow cytometry, poly(ADP-ribose)polymerase-1 and caspase-8 activation were used to evaluate the impact of DCC on cell death. Both netrin-1 and A2B-R activation induced the invasive phenotype through the Rho-Rho kinase axis in DCC-deficient human colorectal cancer cells. Restitution of wild-type DCC blocked invasion induced by netrin-1, A2B-R agonist and other agents. Ectopic expression of netrin-1 led to increased growth of human colon tumor xenografts in athymic mice. Conversely, introduction of wt-DCC in kidney MDCKts.src-ggl cells strongly inhibited metastasis in lymph nodes and lungs and increased sensitivity to apoptosis in hypoxia. DNA microarrays revealed that netrin and DCC had common and divergent impacts on gene expression linked to cell cycle, survival, surface signaling and adhesion. Our findings underscore that netrin is a potent invasion and tumor growth-promoting agent and that DCC is a metastasis suppressor gene targeting both proinvasive and survival pathways in a cumulative manner.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17463181,

title = {Leptin regulates gallbladder genes related to absorption and secretion},

author = {Deborah A Swartz-Basile and Debao Lu and David P Basile and Shannon J Graewin and Hayder Al-Azzawi and James M Kiely and Abhishek Mathur and Kyle Yancey and Henry A Pitt},

doi = {10.1152/ajpgi.00389.2006},

issn = {0193-1857},

year  = {2007},

date = {2007-07-01},

journal = {Am J Physiol Gastrointest Liver Physiol},

volume = {293},

number = {1},

pages = {G84--G90},

abstract = {Dysregulation of gallbladder ion and water absorption and/or secretion has been linked to cholesterol crystal and gallstone formation. We have recently demonstrated that obese, leptin-deficient (Lep(ob)) mice have enlarged gallbladder volumes and decreased gallbladder contractility and that leptin administration to these mice normalizes gallbladder function. However, the effect of leptin on gallbladder absorption/secretion is not known. Therefore, we sought to determine whether leptin would alter the expression of genes involved in water and ion transport across the gallbladder epithelium. Affymetrix oligonucleotide microarrays representing 39,000 transcripts were used to compare gallbladder gene-expression profiles from 12-wk-old control saline-treated Lep(ob) and from leptin-treated Lep(ob) female mice. Leptin administration to Lep(ob) mice decreased gallbladder volume, bile sodium concentration, and pH. Leptin repletion upregulated the expression of aquaporin 1 water channel by 1.3-fold and downregulated aquaporin 4 by 2.3-fold. A number of genes involved in sodium transport were also influenced by leptin replacement. Epithelial sodium channel-alpha and sodium hydrogen exchangers 1 and 3 were moderately downregulated by 2.0-, 1.6-, and 1.3-fold, respectively. Carbonic anhydrase-IV, which plays a role in the acidification of bile, was upregulated 3.7-fold. In addition, a number of inflammatory cytokines that are known to influence gallbladder epithelial cell absorption and secretion were upregulated. Thus leptin, an adipocyte-derived cytokine involved with satiety and energy balance, influences gallbladder bile volume, sodium, and pH as well as multiple inflammatory cytokine genes and genes related to water, sodium, chloride, and bicarbonate transport.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17611618,

title = {Genetic diversity among Enterococcus faecalis},

author = {Shonna M McBride and Vincent A Fischetti and Donald J Leblanc and Robert C Moellering and Michael S Gilmore},

doi = {10.1371/journal.pone.0000582},

issn = {1932-6203},

year  = {2007},

date = {2007-07-01},

journal = {PLoS One},

volume = {2},

number = {7},

pages = {e582},

abstract = {Enterococcus faecalis, a ubiquitous member of mammalian gastrointestinal flora, is a leading cause of nosocomial infections and a growing public health concern. The enterococci responsible for these infections are often resistant to multiple antibiotics and have become notorious for their ability to acquire and disseminate antibiotic resistances. In the current study, we examined genetic relationships among 106 strains of E. faecalis isolated over the past 100 years, including strains identified for their diversity and used historically for serotyping, strains that have been adapted for laboratory use, and isolates from previously described E. faecalis infection outbreaks. This collection also includes isolates first characterized as having novel plasmids, virulence traits, antibiotic resistances, and pathogenicity island (PAI) components. We evaluated variation in factors contributing to pathogenicity, including toxin production, antibiotic resistance, polymorphism in the capsule (cps) operon, pathogenicity island (PAI) gene content, and other accessory factors. This information was correlated with multi-locus sequence typing (MLST) data, which was used to define genetic lineages. Our findings show that virulence and antibiotic resistance traits can be found within many diverse lineages of E. faecalis. However, lineages have emerged that have caused infection outbreaks globally, in which several new antibiotic resistances have entered the species, and in which virulence traits have converged. Comparing genomic hybridization profiles, using a microarray, of strains identified by MLST as spanning the diversity of the species, allowed us to identify the core E. faecalis genome as consisting of an estimated 2057 unique genes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17557114,

title = {The role of LANP and ataxin 1 in E4F-mediated transcriptional repression},

author = {Marija Cvetanovic and Robert J Rooney and Jesus J Garcia and Nataliya Toporovskaya and Huda Y Zoghbi and Puneet Opal},

doi = {10.1038/sj.embor.7400983},

issn = {1469-221X},

year  = {2007},

date = {2007-07-01},

journal = {EMBO Rep},

volume = {8},

number = {7},

pages = {671--677},

abstract = {The leucine-rich acidic nuclear protein (LANP) belongs to the INHAT family of corepressors that inhibits histone acetyltransferases. The mechanism by which LANP restricts its repression to specific genes is unknown. Here, we report that LANP forms a complex with transcriptional repressor E4F and modulates its activity. As LANP interacts with ataxin 1--a protein mutated in the neurodegenerative disease spinocerebellar ataxia type 1 (SCA1)--we tested whether ataxin 1 can alter the E4F-LANP interaction. We show that ataxin 1 relieves the transcriptional repression induced by the LANP-E4F complex by competing with E4F for LANP. These results provide the first functional link, to our knowledge, between LANP and ataxin 1, and indicate a potential mechanism for the transcriptional aberrations observed in SCA1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17426818,

title = {Differential cerebral cortex transcriptomes of baboon neonates consuming moderate and high docosahexaenoic acid formulas},

author = {Kumar S D Kothapalli and Joshua C Anthony and Bruce S Pan and Andrea T Hsieh and Peter W Nathanielsz and J Thomas Brenna},

doi = {10.1371/journal.pone.0000370},

issn = {1932-6203},

year  = {2007},

date = {2007-04-01},

journal = {PLoS One},

volume = {2},

number = {4},

pages = {e370},

abstract = {BACKGROUND: Docosahexaenoic acid (DHA, 22:6n-3) and arachidonic acid (ARA, 20:4n-6) are the major long chain polyunsaturated fatty acids (LCPUFA) of the central nervous system (CNS). These nutrients are present in most infant formulas at modest levels, intended to support visual and neural development. There are no investigations in primates of the biological consequences of dietary DHA at levels above those present in formulas but within normal breastmilk levels.



METHODS AND FINDINGS: Twelve baboons were divided into three formula groups: Control, with no DHA-ARA; "L", LCPUFA, with 0.33%DHA-0.67%ARA; "L3", LCPUFA, with 1.00%DHA-0.67%ARA. All the samples are from the precentral gyrus of cerebral cortex brain regions. At 12 weeks of age, changes in gene expression were detected in 1,108 of 54,000 probe sets (2.05%), with most showing <2-fold change. Gene ontology analysis assigns them to diverse biological functions, notably lipid metabolism and transport, G-protein and signal transduction, development, visual perception, cytoskeleton, peptidases, stress response, transcription regulation, and 400 transcripts having no defined function. PLA2G6, a phospholipase recently associated with infantile neuroaxonal dystrophy, was downregulated in both LCPUFA groups. ELOVL5, a PUFA elongase, was the only LCPUFA biosynthetic enzyme that was differentially expressed. Mitochondrial fatty acid carrier, CPT2, was among several genes associated with mitochondrial fatty acid oxidation to be downregulated by high DHA, while the mitochondrial proton carrier, UCP2, was upregulated. TIMM8A, also known as deafness/dystonia peptide 1, was among several differentially expressed neural development genes. LUM and TIMP3, associated with corneal structure and age-related macular degeneration, respectively, were among visual perception genes influenced by LCPUFA. TIA1, a silencer of COX2 gene translation, is upregulated by high DHA. Ingenuity pathway analysis identified a highly significant nervous system network, with epidermal growth factor receptor (EGFR) as the outstanding interaction partner.



CONCLUSIONS: These data indicate that LCPUFA concentrations within the normal range of human breastmilk induce global changes in gene expression across a wide array of processes, in addition to changes in visual and neural function normally associated with formula LCPUFA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17185341,

title = {Non-human primate fetal kidney transcriptome analysis indicates mammalian target of rapamycin (mTOR) is a central nutrient-responsive pathway},

author = {Mark J Nijland and Natalia E Schlabritz-Loutsevitch and Gene B Hubbard and Peter W Nathanielsz and Laura A Cox},

doi = {10.1113/jphysiol.2006.122101},

issn = {0022-3751},

year  = {2007},

date = {2007-03-01},

journal = {J Physiol},

volume = {579},

number = {Pt 3},

pages = {643--656},

abstract = {Developmental programming is defined as the process by which gene-environment interaction in the developing organism leads to permanent changes in phenotype and function. Numerous reports of maternal nutrient restriction during pregnancy demonstrate altered renal development. Typically this alteration manifests as a reduction in the total number of glomeruli in the mature kidney of the offspring, and suggests that predisposition to develop chronic renal disease may include an in utero origin. In a previous study, we defined the transcriptome in the kidney from fetuses of control (CON, fed ad libitum) and nutrient-restricted (NR, fed 70% of CON starting at 0.16 gestation (G)) pregnancies at half-way through gestation (0.5G), and established transcriptome and morphological changes in NR kidneys compared to CON. One goal of the present study was to use transcriptome data from fetal kidneys of CON and NR mothers at 0.5G with histological data to identify the molecular mechanisms that may regulate renal development. A second goal was to identify mechanisms by which NR elicits its affect on fetal baboon kidney. We have used an end-of-pathway gene expression analysis to prioritize and identify key pathways regulating the 0.5G kidney phenotype in response NR. From these data we have determined that the mammalian target of rapamycin (mTOR) signalling pathway is central to this phenotype.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17256055,

title = {Hyperactivation of Ha-ras oncogene, but not Ink4a/Arf deficiency, triggers bladder tumorigenesis},

author = {Lan Mo and Xiaoyong Zheng and Hong-Ying Huang and Ellen Shapiro and Herbert Lepor and Carlos Cordon-Cardo and Tung-Tien Sun and Xue-Ru Wu},

doi = {10.1172/JCI30062},

issn = {0021-9738},

year  = {2007},

date = {2007-02-01},

journal = {J Clin Invest},

volume = {117},

number = {2},

pages = {314--325},

abstract = {Although ras is a potent mitogenic oncogene, its tumorigenicity depends on cellular context and cooperative events. Here we show that low-level expression of a constitutively active Ha-ras in mouse urothelium induces simple urothelial hyperplasia that is resistant to progression to full-fledged bladder tumors even in the absence of Ink4a/Arf. In stark contrast, doubling of the gene dosage of the activated Ha-ras triggered early-onset, rapidly growing, and 100% penetrant tumors throughout the urinary tract. Tumor initiation required superseding a rate-limiting step between simple and nodular hyperplasia, the latter of which is marked by the emergence of mesenchymal components and the coactivation of AKT and STAT pathways as well as PTEN inactivation. These results indicate that overactivation of Ha-ras is both necessary and sufficient to induce bladder tumors along a low-grade, noninvasive papillary pathway, and they shed light on the recent findings that ras activation, via point mutation, overexpression, or intensified signaling from FGF receptor 3, occurs in 70%-90% of these tumors in humans. Our results highlight the critical importance of the dosage/strength of Ha-ras activation in dictating its tumorigenicity--a mechanism of oncogene activation not fully appreciated to date. Finally, our results have clinical implications, as inhibiting ras and/or its downstream effectors, such as AKT and STAT3/5, could provide alternative means to treat low-grade, superficial papillary bladder tumors, the most common tumor in the urinary system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17110341,

title = {The fly CAMTA transcription factor potentiates deactivation of rhodopsin, a G protein-coupled light receptor},

author = {Junhai Han and Ping Gong and Keith Reddig and Mirna Mitra and Peiyi Guo and Hong-Sheng Li},

doi = {10.1016/j.cell.2006.09.030},

issn = {0092-8674},

year  = {2006},

date = {2006-11-01},

journal = {Cell},

volume = {127},

number = {4},

pages = {847--858},

abstract = {Control of membrane-receptor activity is required not only for the accuracy of sensory responses, but also to protect cells from excitotoxicity. Here we report the isolation of two noncomplementary fly mutants with slow termination of photoresponses. Genetic and electrophysiological analyses of the mutants revealed a defect in the deactivation of rhodopsin, a visual G protein-coupled receptor (GPCR). The mutant gene was identified as the calmodulin-binding transcription activator (dCAMTA). The known rhodopsin regulator Arr2 does not mediate this visual function of dCAMTA. A genome-wide screen identified five dCAMTA target genes. Of these, overexpression of the F box gene dFbxl4 rescued the mutant phenotypes. We further showed that dCAMTA is stimulated in vivo through interaction with the Ca(2+) sensor calmodulin. Our data suggest that calmodulin/CAMTA/Fbxl4 may mediate a long-term feedback regulation of the activity of Ca(2+)-stimulating GPCRs, which could prevent cell damage due to extra Ca(2+) influx.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17112382,

title = {Gene expression profiling following constitutive activation of MEK1 and transformation of rat intestinal epithelial cells},

author = {Koga Komatsu and F Gregory Buchanan and Michiro Otaka and Mario Jin and Masaru Odashima and Yohei Horikawa and Sumio Watanabe and Raymond N Dubois},

doi = {10.1186/1476-4598-5-63},

issn = {1476-4598},

year  = {2006},

date = {2006-11-01},

journal = {Mol Cancer},

volume = {5},

pages = {63},

abstract = {BACKGROUND: Constitutive activation of MEK1 (caMEK) can induce the oncogenic transformation of normal intestinal epithelial cells. To define the genetic changes that occur during this process, we used oligonucleotide microarrays to determine which genes are regulated following the constitutive activation of MEK in normal intestinal epithelial cells.



RESULTS: Microarray analysis was performed using Affymetrix GeneChip and total RNA from doxycycline inducible RIEtiCAMEK cells in the presence or absence of doxycycline. MEK-activation induced at least a three-fold difference in 115 gene transcripts (75 transcripts were up-regulated, and 40 transcripts were down-regulated). To verify whether these mRNAs are indeed regulated by the constitutive activation of MEK, RT-PCR analysis was performed using the samples from caMEK expressing RIE cells (RIEcCAMEK cells) as well as RIEtiCAMEK cells. The altered expression level of 69 gene transcripts was confirmed. Sixty-one of the differentially expressed genes have previously been implicated in cellular transformation or tumorogenesis. For the remaining 8 genes (or their human homolog), RT-PCR analysis was performed on RNA from human colon cancer cell lines and matched normal and tumor colon cancer tissues from human patients, revealing three novel targets (rat brain serine protease2, AMP deaminase 3, and cartilage link protein 1).



CONCLUSION: Following MEK-activation, many tumor-associated genes were found to have significantly altered expression levels. However, we identified three genes that were differentially expressed in caMEK cells and human colorectal cancers, which have not been previously linked to cellular transformation or tumorogenesis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16870260,

title = {Cultured lymphocytes from autistic children and non-autistic siblings up-regulate heat shock protein RNA in response to thimerosal challenge},

author = {Stephen J Walker and Jeffrey Segal and Michael Aschner},

doi = {10.1016/j.neuro.2006.06.003},

issn = {0161-813X},

year  = {2006},

date = {2006-09-01},

journal = {Neurotoxicology},

volume = {27},

number = {5},

pages = {685--692},

abstract = {There are reports suggesting that some autistic children are unable to mount an adequate response following exposure to environmental toxins. This potential deficit, coupled with the similarity in clinical presentations of autism and some heavy metal toxicities, has led to the suggestion that heavy metal poisoning might play a role in the etiology of autism in uniquely susceptible individuals. Thimerosal, an anti-microbial preservative previously added routinely to childhood multi-dose vaccines, is composed of 49.6% ethyl mercury. Based on the levels of this toxin that children receive through routine immunization schedules in the first years of life, it has been postulated that thimerosal may be a potential triggering mechanism contributing to autism in susceptible individuals. One potential risk factor in these individuals may be an inability to adequately up-regulate metallothionein (MT) biosynthesis in response to presentation of a heavy metal challenge. To investigate this hypothesis, cultured lymphocytes (obtained from the Autism Genetic Resource Exchange, AGRE) from autistic children and non-autistic siblings were challenged with either 10 microM ethyl mercury, 150 microM zinc, or fresh media (control). Following the challenge, total RNA was extracted and used to query "whole genome" DNA microarrays. Cultured lymphocytes challenged with zinc responded with an impressive up-regulation of MT transcripts (at least nine different MTs were over-expressed) while cells challenged with thimerosal responded by up-regulating numerous heat shock protein transcripts, but not MTs. Although there were no apparent differences between autistic and non-autistic sibling responses in this very small sampling group, the differences in expression profiles between those cells treated with zinc versus thimerosal were dramatic. Determining cellular response, at the level of gene expression, has important implications for the understanding and treatment of conditions that result from exposure to neurotoxic compounds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16696860,

title = {Gene expression profiling of microglia infected by a highly neurovirulent murine leukemia virus: implications for neuropathogenesis},

author = {Derek E Dimcheff and L Gwenn Volkert and Ying Li and Angelo L DeLucia and William P Lynch},

doi = {10.1186/1742-4690-3-26},

issn = {1742-4690},

year  = {2006},

date = {2006-05-01},

journal = {Retrovirology},

volume = {3},

pages = {26},

abstract = {BACKGROUND: Certain murine leukemia viruses (MLVs) are capable of inducing progressive spongiform motor neuron disease in susceptible mice upon infection of the central nervous system (CNS). The major CNS parenchymal target of these neurovirulent retroviruses (NVs) are the microglia, whose infection is largely coincident with neuropathological changes. Despite this close association, the role of microglial infection in disease induction is still unknown. In this paper, we investigate the interaction of the highly virulent MLV, FrCasE, with microglia ex vivo to evaluate whether infection induces specific changes that could account for neurodegeneration. Specifically, we compared microglia infected with FrCasE, a related non-neurovirulent virus (NN) F43/Fr57E, or mock-infected, both at a basic virological level, and at the level of cellular gene expression using quantitative real time RT-PCR (qRT-PCR) and Afffymetrix 430A mouse gene chips.



RESULTS: Basic virological comparison of NN, NV, and mock-infected microglia in culture did not reveal differences in virus expression that provided insight into neuropathogenesis. Therefore, microglial analysis was extended to ER stress gene induction based on previous experiments demonstrating ER stress induction in NV-infected mouse brains and cultured fibroblasts. Analysis of message levels for the ER stress genes BiP (grp78), CHOP (Gadd153), calreticulin, and grp58 in cultured microglia, and BiP and CHOP in microglia enriched fractions from infected mouse brains, indicated that FrCasE infection did not induce these ER stress genes either in vitro or in vivo. To broadly identify physiological changes resulting from NV infection of microglia in vitro, we undertook a gene array screen of more than 14,000 well-characterized murine genes and expressed sequence tags (ESTs). This analysis revealed only a small set of gene expression changes between infected and uninfected cells (<18). Remarkably, gene array comparison of NN- and NV-infected microglia revealed only 3 apparent gene expression differences. Validation experiments for these genes by Taqman real-time RT-PCR indicated that only single Ig IL-1 receptor related protein (SIGIRR) transcript was consistently altered in culture; however, SIGIRR changes were not observed in enriched microglial fractions from infected brains.



CONCLUSION: The results from this study indicate that infection of microglia by the highly neurovirulent virus, FrCasE, does not induce overt physiological changes in this cell type when assessed ex vivo. In particular, NV does not induce microglial ER stress and thus, FrCasE-associated CNS ER stress likely results from NV interactions with another cell type or from neurodegeneration directly. The lack of NV-induced microglial gene expression changes suggests that FrCasE either affects properties unique to microglia in situ, alters the expression of microglial genes not represented in this survey, or affects microglial cellular processes at a post-transcriptional level. Alternatively, NV-infected microglia may simply serve as an unaffected conduit for persistent dissemination of virus to other neural cells where they produce acute neuropathogenic effects.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16484296,

title = {Gene expression profile differences in left and right liver lobes from mid-gestation fetal baboons: a cautionary tale},

author = {Laura A Cox and Natalia Schlabritz-Loutsevitch and Gene B Hubbard and Mark J Nijland and Thomas J McDonald and Peter W Nathanielsz},

doi = {10.1113/jphysiol.2006.105726},

issn = {0022-3751},

year  = {2006},

date = {2006-04-01},

journal = {J Physiol},

volume = {572},

number = {Pt 1},

pages = {59--66},

abstract = {Interpretation of gene array data presents many potential pitfalls in adult tissues. Gene array techniques applied to fetal tissues present additional confounding pitfalls. The left lobe of the fetal liver is supplied with blood containing more oxygen than the right lobe. Since synthetic activity and cell function are oxygen dependent, we hypothesized major differences in mRNA expression between the fetal right and left liver lobes. Our aim was to demonstrate the need to evaluate RNA samples from both lobes. We performed whole genome expression profiling on left and right liver lobe RNA from six 90-day gestation baboon fetuses (term 180 days). Comparing right with left, we found 875 differentially expressed genes - 312 genes were up-regulated and 563 down-regulated. Pathways for damaged DNA binding, endonuclease activity, interleukin binding and receptor activity were up-regulated in right lobe; ontological pathways related to cell signalling, cell organization, cell biogenesis, development, intracellular transport, phospholipid metabolism, protein biosynthesis, protein localization, protein metabolism, translational regulation and vesicle mediated transport were down-regulated in right lobe. Molecular pathway analysis showed down-regulation of pathways related to heat shock protein binding, ion channel and transporter activities, oxygen binding and transporter activities, translation initiation and translation regulator activities. Genes involved in amino acid biosynthesis, lipid biosynthesis and oxygen transport were also differentially expressed. This is the first demonstration of RNA differences between the two lobes of the fetal liver. The data support the argument that a complete interpretation of gene expression in the developing liver requires data from both lobes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16513668,

title = {Effect of 30 per cent maternal nutrient restriction from 0.16 to 0.5 gestation on fetal baboon kidney gene expression},

author = {L A Cox and M J Nijland and J S Gilbert and N E Schlabritz-Loutsevitch and G B Hubbard and T J McDonald and R E Shade and P W Nathanielsz},

doi = {10.1113/jphysiol.2006.106872},

issn = {0022-3751},

year  = {2006},

date = {2006-04-01},

journal = {J Physiol},

volume = {572},

number = {Pt 1},

pages = {67--85},

abstract = {Previous studies in rodents and sheep show that maternal nutrient restriction during pregnancy alters fetal renal development. To date, no studies using fetal baboon RNA with human Affymetrix gene chips have been published. In the present study we have (1) evaluated the specificity of the Affymetrix human gene array 'Laboratory on a Chip' system for use with fetal baboon mRNA and (2) investigated the effects of moderate maternal global nutrient restriction (NR; 70% of ad libitum animals) from early (30 days gestation (dG)) to mid-gestation (90 dG; term = 184 dG) on the fetal baboon kidney. Morphometric and blood measurements were made on 12 non-pregnant baboons before they were bred. All baboons were fed ad libitum until 30 days pregnant, at which time six control baboons continued to feed ad libitum (control - C) while six received 70% of the C diet on a weight adjusted basis. Fetal kidneys were collected following caesarean section at 90 dG, with samples flash frozen and fixed for histological assessment. Fetal hip circumference was decreased in the NR group (68 +/- 2 versus 75 +/- 2 mm), while fetal body weight and all other measurements of fetal size were not different between C and NR at 90 dG. Maternal body weight was decreased in the NR group (12.16 +/- 0.34 versus 13.73 +/- 0.55 kg). Having established the specificity of the Affymetrix system for fetal baboon mRNA, gene expression profiling of fetal kidneys in the context of our maternal nutrient restriction protocol shows that NR resulted in a down-regulation of genes in pathways related to RNA, DNA and protein biosynthesis, metabolism and catabolism. In contrast, genes in cell signal transduction, communication and transport pathways were up-regulated in the NR group. These changes indicate that even a moderate level of maternal global NR impacts fetal renal gene pathways. Our histological assessment of renal structure indicates decreased tubule density within the cortex of NR kidneys compared with controls. The number of glomerular cross-sections per unit area were unaffected by NR, suggesting that tubule tortuosity and/or tubule length was decreased in the NR kidney. Taken together the changes indicate that NR results in accelerated fetal renal differentiation. The negative impact of poor maternal nutrition on the fetal kidney may therefore be in part due to shortening of critical phases of renal growth resulting in decreased functional capacity in later life. These findings may have important implications for postnatal renal function, thereby contributing to the observed increased predisposition to hypertension and renal disease in the offspring of nutrient restricted mothers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16517601,

title = {NFkappaB negatively regulates interferon-induced gene expression and anti-influenza activity},

author = {Lai Wei and Matthew R Sandbulte and Paul G Thomas and Richard J Webby and Ramin Homayouni and Lawrence M Pfeffer},

doi = {10.1074/jbc.M513286200},

issn = {0021-9258},

year  = {2006},

date = {2006-04-01},

journal = {J Biol Chem},

volume = {281},

number = {17},

pages = {11678--11684},

abstract = {Interferons (IFNs) are antiviral cytokines that selectively regulate gene expression through several signaling pathways including nuclear factor kappaB(NFkappaB). To investigate the specific role of NFkappaB in IFN signaling, we performed gene expression profiling after IFN treatment of embryonic fibroblasts derived from normal mice or mice with targeted deletion of NFkappaB p50 and p65 genes. Interestingly, several antiviral and immunomodulatory genes were induced higher by IFN in NFkappaB knock-out cells. Chromatin immunoprecipitation experiments demonstrated that NFkappaB was basally bound to the promoters of these genes, while IFN treatment resulted in the recruitment of STAT1 and STAT2 to these promoters. However, in NFkappaB knock-out cells IFN induced STAT binding as well as the binding of the IFN regulatory factor-1 (IRF1) to the IFN-stimulated gene (ISG) promoters. IRF1 binding closely correlated with enhanced gene induction. Moreover, NFkappaB suppressed both antiviral and immunomodulatory actions of IFN against influenza virus. Our results identify a novel negative regulatory role of NFkappaB in IFN-induced gene expression and biological activities and suggest that modulating NFkappaB activity may provide a new avenue for enhancing the therapeutic effectiveness of IFN.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16249385,

title = {Differential gene expression, GATA1 target genes, and the chemotherapy sensitivity of Down syndrome megakaryocytic leukemia},

author = {Yubin Ge and Alan A Dombkowski and Katherine M LaFiura and Dana Tatman and Ravikiran S Yedidi and Mark L Stout and Steven A Buck and Gita Massey and David L Becton and Howard J Weinstein and Yaddanapudi Ravindranath and Larry H Matherly and Jeffrey W Taub},

doi = {10.1182/blood-2005-06-2219},

issn = {0006-4971},

year  = {2006},

date = {2006-02-01},

journal = {Blood},

volume = {107},

number = {4},

pages = {1570--1581},

abstract = {Children with Down syndrome (DS) with acute megakaryocytic leukemia (AMkL) have very high survival rates compared with non-DS AMkL patients. Somatic mutations identified in the X-linked transcription factor gene, GATA1, in essentially all DS AMkL cases result in the synthesis of a shorter (40 kDa) protein (GATA1s) with altered transactivation activity and may lead to altered expression of GATA1 target genes. Using the Affymetrix U133A microarray chip, we identified 551 differentially expressed genes between DS and non-DS AMkL samples. Transcripts for the bone marrow stromal-cell antigen 2 (BST2) gene, encoding a transmembrane glycoprotein potentially involved in interactions between leukemia cells and bone marrow stromal cells, were 7.3-fold higher (validated by real-time polymerase chain reaction) in the non-DS compared with the DS group. Additional studies confirmed GATA1 protein binding and transactivation of the BST2 promoter; however, stimulation of BST2 promoter activity by GATA1s was substantially reduced compared with the full-length GATA1. CMK sublines, transfected with the BST2 cDNA and incubated with HS-5 bone marrow stromal cells, exhibited up to 1.7-fold reduced cytosine arabinoside (ara-C)-induced apoptosis, compared with mock-transfected cells. Our results demonstrate that genes that account for differences in survival between DS and non-DS AMkL cases may be identified by microarray analysis and that differential gene expression may reflect relative transactivation capacities of the GATA1s and full-length GATA1 proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16262907,

title = {A functional profile of gene expression in ARPE-19 cells},

author = {Rajesh K Sharma and William E Orr and Allyson D Schmitt and Dianna A Johnson},

doi = {10.1186/1471-2415-5-25},

issn = {1471-2415},

year  = {2005},

date = {2005-11-01},

journal = {BMC Ophthalmol},

volume = {5},

pages = {25},

abstract = {BACKGROUND: Retinal pigment epithelium cells play an important role in the pathogenesis of age related macular degeneration. Their morphological, molecular and functional phenotype changes in response to various stresses. Functional profiling of genes can provide useful information about the physiological state of cells and how this state changes in response to disease or treatment. In this study, we have constructed a functional profile of the genes expressed by the ARPE-19 cell line of retinal pigment epithelium.



METHODS: Using Affymetrix MAS 5.0 microarray analysis, genes expressed by ARPE-19 cells were identified. Using GeneChip annotations, these genes were classified according to their known functions to generate a functional gene expression profile.



RESULTS: We have determined that of approximately 19,044 unique gene sequences represented on the HG-U133A GeneChip, 6,438 were expressed in ARPE-19 cells irrespective of the substrate on which they were grown (plastic, fibronectin, collagen, or Matrigel). Rather than focus our subsequent analysis on the identity or level of expression of each individual gene in this large data set, we examined the number of genes expressed within 130 functional categories. These categories were selected from a library of HG-U133A GeneChip annotations linked to the Affymetrix MAS 5.0 data sets. Using this functional classification scheme, we were able to categorize about 70% of the expressed genes and condense the original data set of over 6,000 data points into a format with 130 data points. The resulting ARPE-19 Functional Gene Expression Profile is displayed as a percentage of ARPE-19-expressed genes.



CONCLUSION: The Profile can readily be compared with equivalent microarray data from other appropriate samples in order to highlight cell-specific attributes or treatment-induced changes in gene expression. The usefulness of these analyses is based on the assumption that the numbers of genes expressed within a functional category provide an indicator of the overall level of activity within that particular functional pathway.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16177293,

title = {Transcriptional profiling of target of RNAIII-activating protein, a master regulator of staphylococcal virulence},

author = {Moshe Korem and Yael Gov and Madanahally D Kiran and Naomi Balaban},

doi = {10.1128/IAI.73.10.6220-6228.2005},

issn = {0019-9567},

year  = {2005},

date = {2005-10-01},

journal = {Infect Immun},

volume = {73},

number = {10},

pages = {6220--6228},

abstract = {Staphylococcus aureus is a gram-positive bacterium that is part of the normal healthy flora but that can become virulent and cause infections by producing biofilms and toxins. The production of virulence factors is regulated by cell-cell communication (quorum sensing) through the histidine phosphorylation of target of RNAIII-activating protein (TRAP), which is a 21-kDa protein that is highly conserved among staphylococci. Using microarray analysis, we show here that the expression and phosphorylation of TRAP upregulate the expression of most, if not all, toxins known to date, as well as their global regulator agr. In addition, we show here that the expression and phosphorylation of TRAP are also necessary for the expression of genes known to be necessary for the survival of the bacteria in a biofilm, like arc, pyr, and ure. TRAP is thus demonstrated to be a master regulator of staphylococcal pathogenesis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15994225,

title = {The ErbB3-binding protein Ebp1 suppresses androgen receptor-mediated gene transcription and tumorigenesis of prostate cancer cells},

author = {Yuexing Zhang and Xin-Wei Wang and Danijela Jelovac and Takeo Nakanishi and Myoung-Hee Yu and Damilola Akinmade and Olga Goloubeva and Douglas D Ross and Angela Brodie and Anne W Hamburger},

doi = {10.1073/pnas.0503829102},

issn = {0027-8424},

year  = {2005},

date = {2005-07-01},

journal = {Proc Natl Acad Sci U S A},

volume = {102},

number = {28},

pages = {9890--9895},

abstract = {Down-regulation of the androgen receptor (AR) is being evaluated as an effective therapy for the advanced stages of prostate cancer. We report that Ebp1, a protein identified by its interactions with the ErbB3 receptor, down-regulates expression of AR and AR-regulated genes in the LNCaP prostate cancer cell line. Using microarray analysis, we identified six endogenous AR target genes, including the AR itself, that are down-regulated by ebp1 overexpression. Chromatin immunoprecipitation assays revealed that Ebp1 was recruited to the prostate-specific antigen gene promoter in response to the androgen antagonist bicalutamide, suggesting that Ebp1 directly affected the expression of AR-regulated genes in response to androgen antagonists. Ebp1 expression was reduced in cells that had become androgen-independent. Androgens failed to stimulate either the growth of ebp1 transfectants or transcription of AR-regulated reporter genes in these cells. The agonist activity of the antiandrogen cyproterone acetate was abolished in ebp1 transfectants. In severe combined immunodeficient mice, Ebp1 overexpression resulted in a reduced incidence of LNCaP tumors and slower tumor growth. These findings suggest that Ebp1 is a previously unrecognized therapeutic target for treatment of hormone refractory prostate cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15824099,

title = {Detoxification and transcriptome response in Arabidopsis seedlings exposed to the allelochemical benzoxazolin-2(3H)-one},

author = {Scott R Baerson and Adela Sánchez-Moreiras and Nuria Pedrol-Bonjoch and Margot Schulz and Isabelle A Kagan and Ameeta K Agarwal and Manuel J Reigosa and Stephen O Duke},

doi = {10.1074/jbc.M500694200},

issn = {0021-9258},

year  = {2005},

date = {2005-06-01},

journal = {J Biol Chem},

volume = {280},

number = {23},

pages = {21867--21881},

abstract = {Benzoxazolin-2(3H)-one (BOA) is an allelochemical most commonly associated with monocot species, formed from the O-glucoside of 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one by a two-step degradation process. The capacity of Arabidopsis to detoxify exogenously supplied BOA was analyzed by quantification of the major known metabolites BOA-6-OH, BOA-6-O-glucoside, and glucoside carbamate, revealing that detoxification occurs predominantly through O-glucosylation of the intermediate BOA-6-OH, most likely requiring the sequential action of as-yet-unidentified cytochrome P450 and UDP-glucosyltransferase activities. Transcriptional profiling experiments were also performed with Arabidopsis seedlings exposed to BOA concentrations, representing I(50) and I(80) levels based on root elongation inhibition assays. One of the largest functional categories observed for BOA-responsive genes corresponded to protein families known to participate in cell rescue and defense, with the majority of these genes potentially associated with chemical detoxification pathways. Further experiments using a subset of these genes revealed that many are also transcriptionally induced by a variety of structurally diverse xenobiotic compounds, suggesting they comprise components of a coordinately regulated, broad specificity xenobiotic defense response. The data significantly expand upon previous studies examining plant transcriptional responses to allelochemicals and other environmental toxins and provide novel insights into xenobiotic detoxification mechanisms in plants.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15851978,

title = {Identification of global gene expression differences between human lens epithelial and cortical fiber cells reveals specific genes and their associated pathways important for specialized lens cell functions},

author = {John R Hawse and Candida DeAmicis-Tress and Tracy L Cowell and Marc Kantorow},

issn = {1090-0535},

year  = {2005},

date = {2005-04-01},

journal = {Mol Vis},

volume = {11},

pages = {274--283},

abstract = {PURPOSE: In order to identify specific genes that may play important roles in maintaining the specialized functions of lens epithelial and fiber cells, we have analyzed the global gene expression profiles of these two cell types in the human lens. This analysis will also reveal those genes that are exclusively expressed in the epithelial and cortical fiber cells and those genes that may play important roles in the differentiation of epithelial cells to mature fiber cells.



METHODS: Oligonucleotide microarray hybridization was used to analyze the expression profiles of 22,215 genes between adult (average age greater than 56 years) human lens epithelial and cortical fiber cells. The expression levels of selected genes were further compared by semi-quantitative RT-PCR and selected genes were functionally clustered into common categories using the EASE bioinformatics software package.



RESULTS: Analysis of three separate microarray hybridizations revealed 1,196 transcripts that exhibit increased expression and 1,278 transcripts that exhibit decreased expression at the 2 fold or greater level between lens epithelial cells and cortical fiber cells on all three of the arrays analyzed. Of these, 222 transcripts exhibited increased expression and 135 transcripts exhibited decreased expression by an average of 5 fold or greater levels on all three arrays. Semi-quantitative RT-PCR analysis of 21 randomly selected genes revealed identical expression patterns as those detected by microarray hybridization indicating that the microarray data are accurate. Functional clustering of the identified gene expression patterns using the EASE program revealed a wide variety of biological pathways that exhibited altered expression patterns between the two cell types including mRNA processing, cell adhesion, cell proliferation, translation, protein folding, oxidative phosphorylation, and apoptosis, among others.



CONCLUSIONS: These data reveal novel and previously identified gene expression differences between lens epithelial and cortical fiber cells. The gene expression differences indicate distinct pathways and functions important for the specialization of lens epithelial and fiber cells and provide insight into potential mechanisms important for lens cell differentiation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15711545,

title = {Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function},

author = {Elissa J Chesler and Lu Lu and Siming Shou and Yanhua Qu and Jing Gu and Jintao Wang and Hui Chen Hsu and John D Mountz and Nicole E Baldwin and Michael A Langston and David W Threadgill and Kenneth F Manly and Robert W Williams},

doi = {10.1038/ng1518},

issn = {1061-4036},

year  = {2005},

date = {2005-03-01},

journal = {Nat Genet},

volume = {37},

number = {3},

pages = {233--242},

abstract = {Patterns of gene expression in the central nervous system are highly variable and heritable. This genetic variation among normal individuals leads to considerable structural, functional and behavioral differences. We devised a general approach to dissect genetic networks systematically across biological scale, from base pairs to behavior, using a reference population of recombinant inbred strains. We profiled gene expression using Affymetrix oligonucleotide arrays in the BXD recombinant inbred strains, for which we have extensive SNP and haplotype data. We integrated a complementary database comprising 25 years of legacy phenotypic data on these strains. Covariance among gene expression and pharmacological and behavioral traits is often highly significant, corroborates known functional relations and is often generated by common quantitative trait loci. We found that a small number of major-effect quantitative trait loci jointly modulated large sets of transcripts and classical neural phenotypes in patterns specific to each tissue. We developed new analytic and graph theoretical approaches to study shared genetic modulation of networks of traits using gene sets involved in neural synapse function as an example. We built these tools into an open web resource called WebQTL that can be used to test a broad array of hypotheses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15331573,

title = {Dietary olive oil and menhaden oil mitigate induction of lipogenesis in hyperinsulinemic corpulent JCR:LA-cp rats: microarray analysis of lipid-related gene expression},

author = {Xiong Deng and Marshall B Elam and Henry G Wilcox and Lauren M Cagen and Edwards A Park and Rajendra Raghow and Divyen Patel and Poonam Kumar and Ali Sheybani and James C Russell},

doi = {10.1210/en.2004-0371},

issn = {0013-7227},

year  = {2004},

date = {2004-12-01},

journal = {Endocrinology},

volume = {145},

number = {12},

pages = {5847--5861},

abstract = {In the corpulent James C. Russell corpulent (JCR:LA-cp) rat, hyperinsulinemia leads to induction of lipogenic enzymes via enhanced expression of sterol-regulatory-binding protein (SREBP)-1c. This results in increased hepatic lipid production and hypertriglyceridemia. Information regarding down-regulation of SREBP-1c and lipogenic enzymes by dietary fatty acids in this model is limited. We therefore assessed de novo hepatic lipogenesis and hepatic and plasma lipids in corpulent JCR rats fed diets enriched in olive oil or menhaden oil. Using microarray and Northern analysis, we determined the effect of these diets on expression of mRNA for lipogenic enzymes and other proteins related to lipid metabolism. In corpulent JCR:LA-cp rats, both the olive oil and menhaden oil diets reduced expression of SREBP-1c, with concomitant reductions in hepatic triglyceride content, lipogenesis, and expression of enzymes related to lipid synthesis. Unexpectedly, expression of many peroxisomal proliferator-activated receptor-dependent enzymes mediating fatty acid oxidation was increased in livers of corpulent JCR rats. The menhaden oil diet further increased expression of these enzymes. Induction of SREBP-1c by insulin is dependent on liver x receptor (LXR)alpha. Although hepatic expression of mRNA for LXR itself was not increased in corpulent rats, expression of Cyp7a1, an LXR-responsive gene, was increased, suggesting increased LXR activity. Expression of mRNA encoding fatty acid translocase and ATP-binding cassette subfamily DALD member 3 was also increased in livers of corpulent JCR rats, indicating a potential role for these fatty acid transporters in the pathogenesis of disordered lipid metabolism in obesity. This study clearly demonstrates that substitution of dietary polyunsaturated fatty acid for carbohydrate in the corpulent JCR:LA-cp rat reduces de novo lipogenesis, at least in part, by reducing hepatic expression of SREBP-1c and that strategies directed toward reducing SREBP-1c expression in the liver may mitigate the adverse effects of hyperinsulinemia on hepatic lipid production.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15277499,

title = {Temporal changes in gene expression after injury in the rat retina},

author = {Félix Vázquez-Chona and Bong K Song and Eldon E Geisert},

doi = {10.1167/iovs.03-1047},

issn = {0146-0404},

year  = {2004},

date = {2004-08-01},

journal = {Invest Ophthalmol Vis Sci},

volume = {45},

number = {8},

pages = {2737--2746},

abstract = {PURPOSE: The goal of this study was to define the temporal changes in gene expression after retinal injury and to relate these changes to the inflammatory and reactive response. A specific emphasis was placed on the tetraspanin family of proteins and their relationship with markers of reactive gliosis.



METHODS: Retinal tears were induced in adult rats by scraping the retina with a needle. After different survival times (4 hours, and 1, 3, 7, and 30 days), the retinas were removed, and mRNA was isolated, prepared, and hybridized to the Affymatrix RG-U34A microarray (Santa Clara, CA). Microarray results were confirmed by using RT-PCR and correlation to protein levels was determined.



RESULTS: Of the 8750 genes analyzed, approximately 393 (4.5%) were differentially expressed. Clustering analysis revealed three major profiles: (1) The early response was characterized by the upregulation of transcription factors; (2) the delayed response included a high percentage of genes related to cell cycle and cell death; and (3) the late, sustained profile clustered a significant number of genes involved in retinal gliosis. The late, sustained cluster also contained the upregulated crystallin genes. The tetraspanins Cd9, Cd81, and Cd82 were also associated with the late, sustained response.



CONCLUSIONS: The use of microarray technology enables definition of complex genetic changes underlying distinct phases of the cellular response to retinal injury. The early response clusters genes associate with the transcriptional regulation of the wound-healing process and cell death. Most of the genes in the late, sustained response appear to be associated with reactive gliosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15343150,

title = {The ldis1 lens mutation in RIIIS/J mice maps to chromosome 8 near cadherin 1},

author = {Monica M Jablonski and Lu Lu and XiaoFei Wang and Elissa J Chesler and Emily Carps and Shuhua Qi and Jing Gu and Robert W Williams},

issn = {1090-0535},

year  = {2004},

date = {2004-08-01},

journal = {Mol Vis},

volume = {10},

pages = {577--587},

abstract = {PURPOSE: We have discovered a spontaneous and severe mutation that leads to partial or complete disruption of the lens and cataract in the RIIIS/J inbred strain of mice. The purpose of this study was to determine the mode of inheritance, specificity, and range of phenotypes using histological, ophthalmic, quantitative electron microscopic, and microarray-based methods. We also have fine-mapped the mutation, ldis1 (lens disrupter 1), and have evaluated positional candidate genes.



METHODS: Eyes from mutant RIIIS/J animals and from an F2 intercross between RIIIS/J and DBA/2J were examined and scored to map the ldis1 mutation. Axons in the optic nerve were counted. Messenger RNA from mutant eyes was hybridized to Affymetrix short oligomer microarrays and compared to five control strains. Expression differences were used to evaluate molecular sequellae of the mutation.



RESULTS: Mice that are homozygous for ldis1 have small eyes. Lenses are without exception opaque, deformed, dislocated, fragmented, and small. In contrast, retinal architecture and ganglion cell numbers are within normal range. We have not detected any other ldis1-associated ocular or systemic abnormalities. ldis1 is recessive and maps to chromosome 8 at about 106.5 Mb between D8Mit242 and D8Mit199 with a peak LOD score near cadherin 1. The homologous human chromosomal interval is 16q22.1. The expression of several downstream crystallin transcripts are severely affected in the mutant, as are the expression levels of multiple members of the transforming growth factor superfamily and the glutathione S-transferases.



CONCLUSIONS: We have discovered and mapped a recessive mutation to mouse chromosome 8 between 105 and 109 Mb. Homozygous mutant mice have a selective and severe effect on lens integrity. On the basis of the phenotype and the locus position, several candidate genes have been identified.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15255935,

title = {Molecular genetic responses to lysergic acid diethylamide include transcriptional activation of MAP kinase phosphatase-1, C/EBP-beta and ILAD-1, a novel gene with homology to arrestins},

author = {Charles D Nichols and Elaine Sanders-Bush},

doi = {10.1111/j.1471-4159.2004.02515.x},

issn = {0022-3042},

year  = {2004},

date = {2004-08-01},

journal = {J Neurochem},

volume = {90},

number = {3},

pages = {576--584},

abstract = {We recently demonstrated that the potent hallucinogenic drug lysergic acid diethylamide (LSD) dynamically influences the expression of a small collection of genes within the mammalian prefrontal cortex. Towards generating a greater understanding of the molecular genetic effects of hallucinogens and how they may relate to alterations in behavior, we have identified and characterized expression patterns of a new collection of three genes increased in expression by acute LSD administration. These genes were identified through additional screens of Affymetrix DNA microarrays and examined in experiments to assess dose-response, time course and the receptor mediating the expression changes. The first induced gene, C/EBP-beta, is a transcription factor. The second gene, MKP-1, suggests that LSD activates the MAP (mitogen activated protein) kinase pathway. The third gene, ILAD-1, demonstrates sequence similarity to the arrestins. The increase in expression of each gene was partially mediated through LSD interactions at 5-HT2A (serotonin) receptors. There is evidence of alternative splicing at the ILAD-1 locus. Furthermore, data suggests that various splice isoforms of ILAD-1 respond differently at the transcriptional level to LSD. The genes thus far found to be responsive to LSD are beginning to give a more complete picture of the complex intracellular events initiated by hallucinogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15131130,

title = {Role of nuclear factor-kappaB in the antiviral action of interferon and interferon-regulated gene expression},

author = {Lawrence M Pfeffer and Jong-Gwan Kim and Susan R Pfeffer and Dennis J Carrigan and Darren P Baker and Lai Wei and Ramin Homayouni},

doi = {10.1074/jbc.M308975200},

issn = {0021-9258},

year  = {2004},

date = {2004-07-01},

journal = {J Biol Chem},

volume = {279},

number = {30},

pages = {31304--31311},

abstract = {Interferons (IFNs) play critical roles in host defense by modulating the expression of various genes via tyrosine phosphorylation of STAT transcription factors. IFN-alpha/beta activates another important transcription factor, nuclear factor-kappaB (NF-kappaB), but its role in IFN-mediated activity is poorly understood. Sensitivity to the antiviral and gene-inducing effects of IFN was examined in normal fibroblasts and in NF-kappaB knockout fibroblasts from p50- and p65-null mice. Antiviral assays demonstrated that NF-kappaB knockout fibroblasts were sensitized to the antiviral action of IFN. Moreover, analysis of IFN-stimulated gene expression by real-time PCR demonstrated selective effects of NF-kappaB on gene expression. Our results demonstrate that a subset of IFN-stimulated genes is regulated through an NF-kappaB-dependent pathway and that NF-kappaB may regulate the sensitivity of cells to IFN-mediated antiviral activity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14711822,

title = {Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling},

author = {Xueqiao Liu and Peter De Wulf},

doi = {10.1074/jbc.M313454200},

issn = {0021-9258},

year  = {2004},

date = {2004-03-01},

journal = {J Biol Chem},

volume = {279},

number = {13},

pages = {12588--12597},

abstract = {The ArcB/ArcA two-component signal transduction system of Escherichia coli regulates gene expression in response to the redox conditions of growth. Over the years, genetic screens have lead to the identification of about 30 ArcA-P-controlled operons that are involved in redox metabolism. However, the discovery of 3 targets that are not implicated in respiratory metabolism (the tra operon for plasmid conjugation, psi site for Xer-based recombination, and oriC site for chromosome replication) suggests that the Arc modulon may comprise additional operons that are involved in a myriad of functions. To identify these operons, we derived the ArcA-P-dependent transcription profile of E. coli using oligonucleotide-based microarray analysis. The findings indicated that 9% of all open reading frames in E. coli are affected either directly or indirectly by ArcA-P. To identify which operons are under the direct control of ArcA-P, we developed the ArcA-P recognition weight matrix from footprinting data and used it to scan the genome, yielding an ArcA-P sequence affinity map. By overlaying both methods, we identified 55 new Arc-regulated operons that are implicated in energy metabolism, transport, survival, catabolism, and transcriptional regulation. The data also suggest that the Arc response pathway, which translates into a net global downscaling of gene expression, overlaps partly with the FNR regulatory network. A conservative but reasonable assessment is that the Arc pathway recruits 100-150 operons to mediate a role in cellular adaptation that is more extensive than hitherto anticipated.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14551534,

title = {Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines},

author = {Anna T Rogojina and William E Orr and Bong K Song and Eldon E Geisert},

issn = {1090-0535},

year  = {2003},

date = {2003-10-01},

journal = {Mol Vis},

volume = {9},

pages = {482--496},

abstract = {PURPOSE: The present study was designed to compare the results obtained from two different microarray platforms: spotted cDNAs using a two-color system (Clontech, Atlas Glass Human 3.8) and the Affymetrix platform. We evaluated the internal consistency within each of the platforms, and compared the results across the two platforms.



METHODS: RNA was isolated from two retinal pigment epithelial (RPE) cell lines, D407 cells and ARPE19 cells. Each microarray system requires a specific RNA isolation and target preparation procedure. To compare the results between the two platforms, the intensity values for each platform were standardized and scaled. This allowed for a direct comparison of the data between two very different microarray platforms. Real-time RT-PCR was used as an independent conformation of expression levels for selected transcripts. The protein levels for some of these genes were determined using a quantitative immunoblot method.



RESULTS: First, we compared the transcriptome of the D407 cell line to itself. Within each of the platforms there was a high degree of consistency. However, when the data from the Atlas Glass Human 3.8 microarray platform was compared to that of the Affymetrix platform there was a dramatic lack of agreement. The second step was to compare the mRNA profile of the ARPE19 cell line to the D407 cell line. Again there was good agreement within each platform. When the results of the Atlas Glass Human 3.8 platform were compared to the Affymetrix platform, there was a surprising lack of agreement between the two data sets. Real-time RT-PCR was used as independent means of defining RNA levels in the two cell lines. In general, the real-time RT-PCR results were in better agreement with the Affymetrix platform (85%) than the Atlas Glass platform (33%). In addition, we also examined the levels of 11 proteins in these two cell lines using a quantitative immunoblot method. The results from this protein analysis had a higher degree of concordance with the results from Affymetrix platform.



CONCLUSIONS: In both the Atlas Glass Human 3.8 system and the Affymetrix platform, there is a high degree of internal consistency. However, comparisons between the two platforms show a lack of agreement. In general, the real-time RT-PCR confirmed the results on the Affymetrix system more often than those from Atlas Glass arrays. However, in both cases, conformation by an independent method proves to be of considerable value.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14551530,

title = {Identification and functional clustering of global gene expression differences between human age-related cataract and clear lenses},

author = {John R Hawse and James F Hejtmancik and Quingling Huang and Nancy L Sheets and Douglas A Hosack and Richard A Lempicki and Joseph Horwitz and Marc Kantorow},

issn = {1090-0535},

year  = {2003},

date = {2003-10-01},

journal = {Mol Vis},

volume = {9},

pages = {515--537},

abstract = {PURPOSE: Age-related cataract is a multi-factorial disease with a poorly understood etiology. Numerous studies provide evidence that the human eye lens has evolved specific regulatory and protective systems to ameliorate lens damage associated with cataract. Other studies suggest that the presence of cataract is associated with the altered expression of specific genes including metallothionein IIa, osteonectin, transglutaminase 2, betaig-h3, multiple ribosomal proteins, ADAM9, and protein phosphatase 2A. Here, we sought to identify further gene expression changes that are associated with cataract and to cluster the identified genes into specific biological pathways.



METHODS: Oligonucleotide microarray hybridization was used to analyze the full complement of gene expression differences between lens epithelia isolated from human age-related cataract relative to clear lenses. The expression levels of a subset of the identified genes were further evaluated by semi-quantitative RT-PCR. The identified genes were functionally clustered into specific categories and the probability of over-representation of each category was determined using the computer program EASE.



RESULTS: 412 transcripts were observed to be increased and 919 transcripts were observed to be decreased by 2 fold or more in lens epithelia isolated from age-related cataract relative to clear lenses. Of these, 74 were increased and 241 were decreased at the 5 fold level or greater. Seventeen genes selected for further confirmation exhibited similar trends in expression when examined by RT-PCR using both the original and separately prepared clear and cataract RNA populations. Functional clustering of the identified genes using the EASE bioinformatics software package revealed that, among others, transcripts increased in cataract are associated with transcriptional control, chromosomal organization, ionic and cytoplasmic transport, and extracellular matrix components while transcripts decreased in cataract are associated with protein synthesis, defense against oxidative stress, heat-shock/chaperone activity, structural components of the lens, and cell cycle control.



CONCLUSIONS: These data suggest that cataract is associated with multiple previously identified and novel changes in lens epithelial gene expression and they point to numerous pathways likely to play important roles in lens protection, maintenance, and age-related cataract.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12824174,

title = {Genome-wide expression profiling of the response to polyene, pyrimidine, azole, and echinocandin antifungal agents in Saccharomyces cerevisiae},

author = {Ameeta K Agarwal and P David Rogers and Scott R Baerson and Melissa R Jacob and Katherine S Barker and John D Cleary and Larry A Walker and Dale G Nagle and Alice M Clark},

doi = {10.1074/jbc.M306291200},

issn = {0021-9258},

year  = {2003},

date = {2003-09-01},

journal = {J Biol Chem},

volume = {278},

number = {37},

pages = {34998--35015},

abstract = {Antifungal compounds exert their activity through a variety of mechanisms, some of which are poorly understood. Novel approaches to characterize the mechanism of action of antifungal agents will be of great use in the antifungal drug development process. The aim of the present study was to investigate the changes in the gene expression profile of Saccharomyces cerevisiae following exposure to representatives of the four currently available classes of antifungal agents used in the management of systemic fungal infections. Microarray analysis indicated differential expression of 0.8, 4.1, 3.0, and 2.6% of the genes represented on the Affymetrix S98 yeast gene array in response to ketoconazole, amphotericin B, caspofungin, and 5-fluorocytosine (5-FC), respectively. Quantitative real time reverse transcriptase-PCR was used to confirm the microarray analyses. Genes responsive to ketoconazole, caspofungin, and 5-FC were indicative of the drug-specific effects. Ketoconazole exposure primarily affected genes involved in ergosterol biosynthesis and sterol uptake; caspofungin exposure affected genes involved in cell wall integrity; and 5-FC affected genes involved in DNA and protein synthesis, DNA damage repair, and cell cycle control. In contrast, amphotericin B elicited changes in gene expression reflecting cell stress, membrane reconstruction, transport, phosphate uptake, and cell wall integrity. Genes with the greatest specificity for a particular drug were grouped together as drug-specific genes, whereas genes with a lack of drug specificity were also identified. Taken together, these data shed new light on the mechanisms of action of these classes of antifungal agents and demonstrate the potential utility of gene expression profiling in antifungal drug development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12860567,

title = {Aldosteronism: an immunostimulatory state precedes proinflammatory/fibrogenic cardiac phenotype},

author = {Ivan C Gerling and Yao Sun and Robert A Ahokas and Linus A Wodi and Syamal K Bhattacharya and Kenneth J Warrington and Arnold E Postlethwaite and Karl T Weber},

doi = {10.1152/ajpheart.00113.2003},

issn = {0363-6135},

year  = {2003},

date = {2003-08-01},

journal = {Am J Physiol Heart Circ Physiol},

volume = {285},

number = {2},

pages = {H813--H821},

abstract = {Chronic inappropriate (relative to dietary Na+ intake) elevations in circulating aldosterone (ALDO), termed aldosteronism, are associated with remodeling of intramural arteries of the right and left heart. Lesions appear at week 4 of treatment with ALDO and 1% dietary NaCl in uninephrectomized rats (ALDOST) and include invading monocytes, macrophages and lymphocytes with intracellular evidence of oxidative and nitrosative stress, myofibroblasts, and perivascular fibrosis. In this study, we tested the hypothesis that an immunostimulatory state with activated circulating peripheral blood mononuclear cells (PBMCs) precedes this proinflammatory and profibrogenic cardiac phenotype and is initiated by reduction in the cytosolic free Mg2+ concentration ([Mg2+]i). At 1 and 4 wk of ALDOST (preclinical and clinical stages, respectively), we monitored serum Mg2+, PBMC [Mg2+]i and cytosolic free [Ca2+] (via fluorimetry), and expressed genes (via microchip array) as well as markers of oxidative and nitrosative stress in plasma [alpha1-antiproteinase activity (alpha1-AP)] and cardiac tissue (immunohistochemical detection of gp91phox subunit of NADPH oxidase and 3-nitrotyrosine). Age- and gender-matched unoperated and untreated (UO) rats and uninephrectomized salt-treated (UN) rats served as controls. Serum [Mg2+] was unchanged by ALDOST. In contrast with UO and UN, [Mg2+]i and plasma alpha1-AP were each reduced (P < 0.05) at weeks 1 and 4. The decline in PBMC [Mg2+]i was accompanied by Ca2+ loading. Differential (twofold and higher) expression (up- and downregulation) in PBMC transcriptomes was present at week 1 and progressed at week 4. Involved were genes for the alpha1-isoform of Na+-K+-ATPase, the ATP-dependent Ca2+ pump, antioxidant reserves, inducible nitric oxide synthase, and PBMC activation with autoimmune responses. Expression of 3-nitrotyrosine and activation of gp91phox were seen in inflammatory cells that invaded intramural arteries. Thus early in aldosteronism (preclinical stage), an immunostimulatory state featuring activated circulating PBMCs with reduced ionized [Mg2+]i and oxidative and nitrosative stress precedes and may even predispose to coronary vascular lesions that first appear at week 4.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Towards A Genetic Signature of Lymph Node Positive Breast Cancer},

author = {Paul Hergenroeder, David Peters, Dan Handley, David Dabbs, James Lyones-Weiler, Soumyaroop Bhattacharya, Adam Brufsky},

url = {https://genome-explorations.com/wp-content/uploads/2022/05/91-Towards-a-Genetic-Signature-of-Lymph-Nodes.pdf},

year  = {2003},

date = {2003-05-04},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12697649,

title = {Identification of genes differentially expressed in association with reduced azole susceptibility in Saccharomyces cerevisiae},

author = {Katherine S Barker and Margaret M Pearson and P David Rogers},

doi = {10.1093/jac/dkg217},

issn = {0305-7453},

year  = {2003},

date = {2003-05-01},

journal = {J Antimicrob Chemother},

volume = {51},

number = {5},

pages = {1131--1140},

abstract = {OBJECTIVE: An isolate of S. cerevisiae with reduced susceptibility to fluconazole and itraconazole was developed in the laboratory and used to identify genes that are differentially expressed in association with this phenotype.



METHODS: S. cerevisiae strain ATCC 9763 was passaged in increasing concentrations of itraconazole. Itraconazole and fluconazole MICs for the initial isolate (9763S) were 2 and 16 mg/L and for the final isolate (9763I) were 16 and > or =64 mg/L, respectively. Duplicate sets of total RNA from 9763S and 9763I were isolated and hybridized to Affymetrix S98 yeast arrays. To validate results, six differentially expressed genes were further examined by RT-PCR.



RESULTS: Of the nearly 6400 open reading frames represented on the array, a total of 116 genes (1.8%) were found to be differentially expressed. Cell wall maintenance genes TIR4 and CCW12, sterol metabolism gene UPC2, small molecule transport genes AUS1 and YHK8, and stress response gene CUP1-1 were expressed at a level at least 2.5-fold higher than the expression level found in 9763S. Eleven energy generation genes, ionic homeostasis genes FRE1, FRE2 and FRE4, and sterol metabolism genes ERG8 and ERG13 were expressed at least 2.5-fold lower than the expression level found in 9763S.



CONCLUSIONS: Several genes found to be differentially expressed in this study have been shown previously to be differentially expressed in the fungal response to azole treatment. In addition, the potential role of AUS1 and/or YHK8 as mediators of drug efflux is intriguing and warrants further study.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}