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.
- Missiaglia E, Dalai I, Barbi S, Beghelli S, Falconi M, Della Peruta M, Piemonti L, Capurso G, Di Florio A, Delle Fave G, Pederzoli P, Croce CM, Scarpa A
Pancreatic Endocrine Tumors: Expression Profiling Evidences a Role for AKT-mTOR Pathway.
J Clin Oncol. 2009 Nov 16; [Epub ahead of print] - de Oliveira JE, Druyan S, Uni Z, Ashwell CM, Ferket PR
Prehatch intestinal maturation of turkey embryos demonstrated through gene expression patterns.
Poult Sci. 2009 Dec; 88(12):2600-9 - Gao C, Zhang Z, Liu W, Xiao S, Gu W, Lu H
Reduced microRNA-218 expression is associated with high nuclear factor kappa B activation in gastric cancer.
Cancer. 2009 Nov 4; [Epub ahead of print] - Edson MA, Lin YN, Matzuk MM
Deletion of the Novel Oocyte-Enriched Gene, Gpr149, Leads to Increased Fertility in Mice.
Endocrinology. 2009 Nov 3; [Epub ahead of print] - Shahzad-ul-Hussan S, Cai M, Bewley CA
Unprecedented glycosidase activity at a lectin carbohydrate-binding site exemplified by the cyanobacterial lectin MVL.
J Am Chem Soc. 2009 Nov 18; 131(45):16500-8
- Salk JJ, Salipante SJ, Risques RA, Crispin DA, Li L, Bronner MP, Brentnall TA, Rabinovitch PS, Horwitz MS, Loeb LA
Clonal expansions in ulcerative colitis identify patients with neoplasia.
Proc Natl Acad Sci U S A. 2009 Nov 19; [Epub ahead of print] - Hrushesky WJ, Grutsch JF, Wood P, Yang X, Oh EY, Ansell C, Kidder S, Ferrans C, Quiton DF, Reynolds J, Du-Quiton J, Levin R, Lis C, Braun D
Circadian Clock Manipulation for Cancer Prevention and Control and the Relief of Cancer Symptoms.
Integr Cancer Ther. 2009 Nov 18; [Epub ahead of print] - Nozawa H, Yamada Y, Muto Y, Endo J, Asakage M, Oka T, Furukawa Y, Arai M
Double primary adenocarcinomas of the jejunum and descending colon with lung metastases presenting rare immunohistochemical phenotypes: a case report.
Eur J Gastroenterol Hepatol. 2009 Nov 17; [Epub ahead of print] - Sarver AL, French AJ, Borralho PM, Thayanithy V, Oberg AL, Silverstein KA, Morlan BW, Riska SM, Boardman LA, Cunningham JM, Subramanian S, Wang L, Smyrk TC, Rodrigues CM, Thibodeau SN, Steer CJ
Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states.
BMC Cancer. 2009 Nov 18; 9(1):401 [Epub ahead of print]
- Koslowski M, Türeci O, Huber C, Sahin U
Selective activation of tumor growth-promoting Ca2+ channel MS4A12 in colon cancer by caudal type homeobox transcription factor CDX2.
Mol Cancer. 2009 Sep 25; 8:77 - Stecker K, Koschel A, Wiedenmann B, Anders M
Loss of Coxsackie and adenovirus receptor downregulates alpha-catenin expression.
Br J Cancer. 2009 Nov 3; 101(9):1574-9 [Epub 2009 Sep 22] - Dai Y, Qiao L, Chan KW, Yang M, Ye J, Zhang R, Ma J, Zou B, Lam CS, Wang J, Pang R, Tan VP, Lan HY, Wong BC
Adenovirus-mediated down-regulation of X-linked inhibitor of apoptosis protein inhibits colon cancer.
Mol Cancer Ther. 2009 Sep; 8(9):2762-70 [Epub 2009 Sep 8]
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.
