Welcome to the Digestive Disease Research Center Microarray Core webpage, spotlighting the latest information regarding genomic technologies as they relate to DDRC interests. Members of the DDRC are urged to contact the VMSR to find out how microarray, genotyping, and RNAi technologies may enhance their research. Three VMSR bioinformaticists are available to help members design and plan experiments, obtain high-quality data, and prepare the data for publication. New platforms, products, and analysis techniques allow exploration of genomics in ways never before possible.
Featured research
Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer.
Genome Biol. 2007; 8(7):R131
This manuscript is the result of collaboration between the Robert Coffey lab at Vanderbilt and the Bruce Aronow lab at the University of Cincinnati. Kaiser et al compared gene expression patterns of human colorectal cancers and mouse colon tumor models to those of mouse colon development embryonic days 13.5-18.5. All microarray experiments were performed by the VMSR. Mouse tumors were analyzed on VMSR-printed 20K mouse cDNA arrays composed of PCR products derived from three sources: the 15K National Institute of Aging mouse cDNA library; the Research Genetics mouse 5K set; and an additional set of cDNAs mapped to RefSeq transcripts. The mouse tumor sample array data were composed of Lowess-normalized Cy3:Cy5 labeling ratios of each individual tumor sample versus a universal E17.5 whole fetal mouse reference RNA. Also available was previously collected mouse expression data for normal E13.5-E18.5 colon samples from inbred C57BL/6J and outbred CD-1 mice run on the same 20K arrays. Human RNA colorectal cancer samples were analyzed on Affymetrix HG-U133 Plus 2.0 microarrays. Expression profiles of mouse tumor, mouse embryonic, and human tumor samples were obtained and analyzed for the occurrence of multiple genes involved in related gene function categories by comparing each list of coordinately regulated genes to categories within Gene Ontology, pathways, or literature-based gene associations. Mouse and human tumor data were compared using gene ortholog mapping and showed a striking recapitulation of embryonic colon gene expression.
- Tremblay E, Ferretti E, Babakissa C, Seidman EG, Levy E, Ménard D, Beaulieu JF, for the Canadian Institutes of Health Research Team on Digestive Epithelium
Gene-expression Profile Analysis in the Mid-gestation Human Intestine Discloses Greater Functional Immaturity of the Colon as Compared With the Ileum.
J Pediatr Gastroenterol Nutr. 2011 Apr 7; [Epub ahead of print] - Silver A, Sengupta N, Propper D, Wilson P, Hagemann T, Patel A, Parker A, Ghosh A, Feakins R, Dorudi S, Suraweera N
A distinct DNA methylation profile associated with microsatellite and chromosomal stable sporadic colorectal cancers.
Int J Cancer. 2011 Mar 31; [Epub ahead of print] - Poynton HC, Taylor NS, Hicks J, Colson K, Chan S, Clark C, Scanlan L, Loguinov AV, Vulpe C, Viant MR
Metabolomics of Microliter Hemolymph Samples Enables an Improved Understanding of the Combined Metabolic and Transcriptional Responses of Daphnia magna to Cadmium.
Environ Sci Technol. 2011 Apr 15; 45(8):3710-7 [Epub 2011 Mar 18] - Bao WB, Ye L, Pan ZY, Zhu J, DU ZD, Cai JJ, Huang XG, Zhu GQ, Wu SL
[cDNA microarray on differently expressed genes in duodenum in porcine sensitive or resistant to Escherichia coli F18].
Yi Chuan. 2011 Jan; 33(1):60-6 - Tuefferd M, de Bondt A, Van den Wyngaert I, Talloen W, Göhlmann H
Microarray profiling of DNA extracted from FFPE tissues using SNP 6.0 Affymetrix platform.
Methods Mol Biol. 2011; 724:147-60
- Steine EJ, Ehrich M, Bell GW, Raj A, Reddy S, van Oudenaarden A, Jaenisch R, Linhart HG
Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer.
J Clin Invest. 2011 Apr 1; [Epub ahead of print] - Savas S, Azorsa DO, Jarjanazi H, Ibrahim-Zada I, Gonzales IM, Arora S, Henderson MC, Choi YH, Briollais L, Ozcelik H, Tuzmen S
NCI60 Cancer Cell Line Panel Data and RNAi Analysis Help Identify EAF2 as a Modulator of Simvastatin and Lovastatin Response in HCT-116 Cells.
PLoS One. 2011 Apr 4; 6(4):e18306 - Baehner FL, Lee M, Demeure MJ, Bussey KJ, Kiefer JA, Barrett MT
Genomic signatures of cancer: Basis for individualized risk assessment, selective staging and therapy.
J Surg Oncol. 2011 May 1; 103(6):563-73 - He T, Wang Q, Feng G, Hu Y, Wang L, Wang Y
Computational Detection and Functional Analysis of Human Tissue-Specific A-to-I RNA Editing.
PLoS One. 2011 Mar 23; 6(3):e18129
- Savas S, Azorsa DO, Jarjanazi H, Ibrahim-Zada I, Gonzales IM, Arora S, Henderson MC, Choi YH, Briollais L, Ozcelik H, Tuzmen S
NCI60 Cancer Cell Line Panel Data and RNAi Analysis Help Identify EAF2 as a Modulator of Simvastatin and Lovastatin Response in HCT-116 Cells.
PLoS One. 2011 Apr 4; 6(4):e18306 - Shen Y, Herde R, Doxey BW, Xu C, Gray PD, Kuwada SK
Pharmacologic downregulation of c-FLIP(L) restores juxtacrine death receptor-mediated apoptosis in cancer cells in a peritoneal carcinomatosis model.
Int J Cancer. 2011 Apr 7; [Epub ahead of print] - He T, Wang Q, Feng G, Hu Y, Wang L, Wang Y
Computational Detection and Functional Analysis of Human Tissue-Specific A-to-I RNA Editing.
PLoS One. 2011 Mar 23; 6(3):e18129
News and Notes
- Previously analyzed data could benefit from a second look using new analysis techniques and software, which can uncover expression patterns, provide pathway analysis, or drug discovery information.
- Agilent arrays are now offered for CGH and gene expression analysis.
- Interested in miRNA detection? Exiqon miRCURY™ LNA microRNA Arrays offer high-quality miRNA data from total RNA - no fractionation required!
- Tiling arrays are a discovery tool for studying gene regulation, including mapping sites of protein/DNA interaction in ChIP experiments, discovering new RNA transcripts, and understanding DNA methylation or acetylation.
- VMSR functional genomics capabilities include RNAi and full-length cDNA libraries, with clones available to Vanderbilt researchers at a fraction of the cost of commercial websites. Synthetic RNAi libraries with specific focuses are also available, including Human Druggable Genome, Protein Kinase, Phosphatases, and GPCR screening libraries.
- The newest DNA Mapping arrays probe almost 1 million SNPs and an additional 1 million copy number analysis probes. High-throughput handling in the VMSR has yielded decreased costs, making genotyping affordable to any budget. Copy number analysis can be done on as little as one tumor or diseased sample, when compared to publicly available normal controls.
Selected papers of interest
Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array.
BMC Genomics. 2006 Dec 27; 7:325
This manuscript from Affymetrix largely serves to introduce the Exon arrays, and a great deal of space is committed to describing the design and analysis of the array itself. However, they were able to use this array to detect nine splice variants that are present in colon tumors but not in normal colon.
Targeting cyclooxygenase-2 and the epidermal growth factor receptor for the prevention and treatment of intestinal cancer.
Cancer Res. 2007 Oct 1; 67(19):9380-8
Buchanan et al used Affymetrix microarrays as a measure of verification, noting that "genes involved in cell cycle progression were negatively regulated" as tumors were reduced during treatment.