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publications by UHNMAC users: array services
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We are a Certified Agilent Service Provider and an Authorised Affymetrix
Service Provider. We offer services on the Affymetrix, Agilent, Illumina and in-house array platforms.
Our services include array-based services such as gene expression profiling, array CGH, ChIP-on-Chip,
data analysis, informatics and data mining; scanning services and integrity testing. In addition, we
also offer data validation, including Luminex Technology (using the Bio-Plex instrument from Bio-Rad),
Nanostring Technology. |
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- Affymetrix Services
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George SH, Greenaway J, Milea A et al.
Identification of abrogated pathways in fallopian tube epithelium from BRCA1 mutation carriers.
J Pathol. 2011 225(1):106-17
Navab R, Strumpf D, Bandarchi B et al. Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer.. Proc. Natl. Acad. Sci. USA, 2011, 108(17):7160-65
Tone AA, Virtanen C, Shaw PA et al. Decreased progesterone receptor isoform expression in luteal phase fallopian tube epithelium and high-grade serous carcinoma. Endocr Relat Cancer. 2011, 18(2):221-34
Alajez NM, Shi W, Hui AB, et al. Enhancer of Zeste homolog 2 (EZH2) is overexpressed in recurrent nasopharyngeal carcinoma and is regulated by miR-26a, miR-101, and miR-98. Cell Death Dis. 2010, 1(10):e85
May T, Virtanen C, Sharma M, et al. Low malignant potential tumors with micropapillary features are molecularly similar to low-grade serous carcinoma of the ovary. Gynecologic Oncology 2010, 117(1):9-17
Spagnuolo PA, Hu J, Hurren R, et al. The antihelmintic flubendazole inhibits microtubule function through a mechanism distinct from Vinca alkaloids and displays preclinical activity in leukemia and myeloma. Blood 2010, 115(23):4824
Jones RA, Campbell CI, Petrik JJ, Moorehead RA. Characterization of a Novel Primary Mammary Tumor Cell Line Reveals that Cyclin D1 Is Regulated by the Type I Insulin-Like Growth Factor Receptor. Mol Cancer Res, 2008, 6:819
This study used the Affymetrix GeneChip Mouse Genome 430 2.0 to characterise the first primary murine mammary tumour cell line with inducible insulin-like growth factor receptor (IGF-IR) expression. These cells provide a powerful model to examine the function of IGF-IR in mammary tumourigenesis.
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Tone AA, Begley H, Sharma M, Murphy J, Rosen B, Brown TJ, Shaw PA. Gene expression profiles of luteal phase fallopian tube epithelium from BRCA mutation carriers resemble high-grade serous carcinoma. Clin Cancer Res, 2008, 14(13):4067
Using the Affymetrix platform to profile the gene expression of histologically normal fallopian tube epithelial from BCRA1/2 mutation carriers, this study found that the increased expression of SKIL, combined with decreased expression of DAB2, could represent some of the earliest initiating or predisposing events of serous carcinoma.
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Lovegrove FE, Gharib SA, Patel SN, Hawkes CA, Kain KC, Liles WC. Expression Microarray Analysis Implicates Apoptosis and Interferon-Responsive Mechanisms in Susceptibility to Experimental Cerebral Malaria. Am J Pathol, 2007, 171(6):1
Using Affymetrix mouse whole genome expression arrays and computational biology tools, researchers assessed whole-brain transcriptional responses of cerebral malaria by comparing genetically resistant and susceptible inbred mouse strains infected with a strain of Plasmodium berghei. By examining the disease progression in cerebral malaria, novel therapeutic targets can be identified.
- Agilent Services
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Shimizu M, Cohen B, Goldvasser P et al.
Plasminogen activator uPA is a direct transcriptional target of the JAG1-notch receptor signaling pathway
in breast cancer. Cancer Res. 2011,
71(1):277-86
Kovalenko A, Kim J-C, Kang T-B, Rajput A, Bogdanov K, Dittrich-Breiholz O, Kracht M, Brenner O, Wallach D. Caspase-8 deficiency in epidermal keratinocytes triggers an inflammatory skin disease. J Exp Med 2009, 206(10):2161-2177
Using the Agilent gene expression platform, this study investigated mice with chronic skin inflammation triggered by caspase-8-deficient basal epidermal keratinocytes. This study found that the inflammatory response was not dependent on TNF, IL-1, dermal macrophage function, or expression of toll-like receptor adaptor proteins MyD88 or TRIF, and that alterations in gene expression resulting from caspase-8-deficiency are initiated before birth and around the same time as cornification.
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Xuan W, Li Y-J, Liu G, Ben-David Y, Archer MC. Interleukin-24 Induces Expression of β4 Integrin but Suppresses Anchorage-Independent Growth of Rat Mammary Tumor Cells by a Mechanism That Is Independent of β4. Mol Cancer Res 2009, 7(3): 433
Using the UHNMAC Agilent gene expression service, Xuan et al. found that the expression of IL-24 and β4 integrin was highly correlated with the inability for cells to grow in soft agar (anchorage-independent growth), and that IL-24 suppresses the growth of rat mammary carcinoma cells and may play a role in the resistance of Copenhagen rats to mammary carcinogenesis.
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Ponzielli R, Boutros PC, Katz S, Stojanova A, Hanley AP, Khosravi F, Bros C, Jurisica I, Penn LZ. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res 2008, 36(21):e144
This study is the first to provide a comprehensive evaluation of experimental ChIP-chip design parameters. Parameters specific to ChIP-chip, such as antibody purity, amplification method for enriched DNA, and the array hybridization control were evaluated, in addition to parameters previously evaluated for gene expression studies.
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Kanellis P, Gagliardi M, Banath JP, et al. A Screen for Suppressors of Gross Chromosomal Rearrangements Identifies a Conserved Role for PLP in Preventing DNA Lesions. PLoS Genet 2007, 3(8):e134 (hybridisation and scanning only)
This study identifies nine novel genes that increase the rate of genome instability in yeast when deleted. One of these genes, which encodes pyridoxal kinase, is shown to influence genome stability by promoting the conversion of vitamin B6 into its biologically active form, pyridoxal 5` phosphate.
Zippo A, De Robertis A, Serafini R, Oliviero S. PIM1-dependent phosphorylation of histone H3 at serine 10 is required for MYC-dependent transcriptional activation and oncogenic transformation. Nature Cell Biol, 2007, 9(8):932
Expression profiling in this study revealed that PIM1 contributes to the regulation of 20% of the c-MYC-regulated genes. This study also establishes serine/threonine kinase PIM1 as a MYC cofactor that phosphorylates the chromatin at MYC-target loci and suggests that nucleosome phosphorylation contributes to MYC-dependent transcriptional activation and cellular transformation.
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- Illumina Services
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Gandhi R, Takahashi M, Virtanen C et al.
Microarray analysis of the infrapatellar fat pad in knee osteoarthritis: relationship with joint inflammation.
J. Rheumatol. 2011 38(9):1966-1972
Navab R, Strumpf D, Bandarchi B et al. Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer.. Proc. Natl. Acad. Sci. USA, 2011, 108(17):7160-65
- In-house Array Services
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Bouchard L, Rabasa-Lhoret R, Faraj M, et al.
Differential epigenomic and transcriptomic responses in subcutaneous adipose tissue between low and high responders
to caloric restriction. Am J Clin Nutr 2010,
91(2):309
Nguyen A, Rauch TA, Pfeifer GP, et al. Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain. FASEB Journal 2010, 24(8):3036
van Straten EME, Bloks VW, Huijkman NCA, et al. The liver X-receptor gene promoter is hypermethylated in a mouse model of prenatal protein restriction. Am J Physiol Regul Integr Comp Physiol 2010, 298:R275
Vivekanandan P, Daniel HDJ, Kannangai R, et al. Hepatitis B Virus Replication Induces Methylation of both Host and Viral DNA. J Virology 2010 84(9):4321
Wong WW, Boutros PC, Wasvlishen AR, et al. Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. BMC Cancer 2010 10:351
Goranov AI, Cook M, Ricicova M, et al. The rate of cell growth is governed by cell cycle stage. Genes Dev 2009, 23(12):1408
Using custom printed yeast arrays and the UHNMAC gene expression service, this study uses budding yeast to show that cells grow differently during the various stages of the cell cycle. This study found that cell growth is faster in cells arrested in anaphase and G1, and the establishment of a polarised actin cytoskeleton attenuates protein synthesis and growth.
Morettin A, Ward A, Nantais J, Hudson JW. Gene expression patterns in heterozygous Plk4 murine embryonic fibroblasts. BMC Genomics 2009, 10:319
Using Mouse 22.4K cDNA arrays to examine the transcript profiles of Plk4 wild type and heterozygous mouse embryonic fibroblasts (MEF), this study found that 143 genes were significantly upregulated in the heterozygous MEFs. Of these 143 genes, some were identified to be involved in p53-dependent pathways and the majority were found to contain putative p53 responsive elements. This study determined that Plk4 haploinsufficiency leads to changes in RNA transcript levels for a number of key cellular genes as well as changes in protein levels for several important cell cycle/DNA damage proteins. A model in which reduced Plk4 levels invoke an increase in p53 levels is proposed.
Gowher H, Stuhlmann H, Felsenfeld G. Vezf1 regulates genomic DNA methylation through its effects on expression of DNA methyltransferase Dnmt3b. Genes Dev 2008, 22:2075-2084 [MeDIP using MCGI4.6k arrays]
Using Mouse CGI 4.6k arrays, Gowher et al. report that mouse embryonic stem cell line deletion of vascular endothelial zinc finger 1 (Vezf1) results in loss of DNA methylation throughout the genome due to a decrease in the abundance of the de novo DNA methyltransferase, Dnmt3b. This result suggests that Vezf1 mutations may have widespread effects on the epigenetic regulation of gene expression.
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Hauck TS, Ghazani AA, Chan WCW. Assessing the Effect of Surface Chemistry on Gold Nanorod Uptake, Toxicity, and Gene Expression in Mammalian Cells. Small, 2008, 4(1):153 [Use of Hum10k arrays]
UHNMAC Human10K cDNA arrays were used to examine the molecular changes of cells exposed to gold nanorods coated with polydiallyldimethylammonium chloride (PDADMAC). The finding that these nanorods have negligible impact on cell function suggests the nanorods are well suited for therapeutic applications, such as thermal cancer therapy, due to their tunable cell uptake and low toxicity.
Onken MD, Worley LA, Harbour JW. A Metastasis Modifier Locus on Human Chromosome 8p in Uveal Melanoma Identified by Integrative Genomic Analysis. Clin Cancer Res 2008, 14(12):3737 [Use of HCGI 12K arrays]
The purpose of this study was to identify genes that modify metastatic risk in uveal melanoma, a type of cancer that has a consistent metastatic pattern. Using integrative genomic methods, including gene expression profiling, aCGH, and DMH, this study found a candidate gene, leucine zipper tumor suppressor-1 (LZTS1), located in chromosome region 8p12- 22, strongly linked to rapid metastasis.
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