Welcome to the Vanderbilt-Ingram Cancer Center Microarray Core webpage, spotlighting the latest information regarding genomic technologies as they relate to VICC interests. Members of the VICC 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
Analysis of host- and tumor-derived proteinases using a custom dual species microarray reveals a protective role for stromal matrix metalloproteinase-12 in non-small cell lung cancer.
Cancer Res. 2006 Aug 15; 66(16):7968-75
This manuscript is a result of collaboration between many colleagues at Vanderbilt (including the Matrisian, Sinnamon, Fingleton, and Carbone labs as well as VMSR faculty and staff) and investigators at Wayne State University. Acuff et al designed a customized Affymetrix protease microarray (Hu/Mu ProtIn chip) designed to distinguish human and mouse genes to analyze the expression of proteases and protease inhibitors in lung cancer. Traditional microarrays using RNA from whole tumors cannot distinguish if genes are expressed from tumor cells or surrounding host cells, such as fibroblasts, endothelial cells, or inflammatory cells. The Hu/Mu ProtIn chip was designed to distinguish mouse and human proteases and protease inhibitors by generating oligonucleotides specific for either mouse or human genes. By using a xenograft approach, in which human tumor cells were injected into a mouse, the Hu/Mu ProtIn chip allowed the identification of genes transcribed by the tumor (human) and the host (mouse), allowing a better understanding of the cross-talk between proteases in the tumor and the surrounding microenvironment. Many candidate stromal proteases were detected using this model system. These results were compared to a data set of human lung adenocarcinoma specimens from the Carbone lab run on Affymetrix U133 Plus 2.0 arrays by the VMSR. MMP-12, MMP-13, and cathepsin K showed an increase in expression in human tumors compared with normal lung similar to that seen in the orthotopic model
- Thomassen M, Tan Q, Kruse TA
Gene expression meta-analysis identifies chromosomal regions and candidate genes involved in breast cancer metastasis.
Breast Cancer Res Treat. 2009 Jan; 113(2):251-252 - Ruckhäberle E, Karn T, Rody A, Hanker L, Gätje R, Metzler D, Holtrich U, Kaufmann M
Gene expression of ceramide kinase, galactosyl ceramide synthase and ganglioside GD3 synthase is associated with prognosis in breast cancer.
J Cancer Res Clin Oncol. 2009 Jan 6; [Epub ahead of print] - Good KL, Avery DT, Tangye SG
Resting human memory B cells are intrinsically programmed for enhanced survival and responsiveness to diverse stimuli compared to naive B cells.
J Immunol. 2009 Jan 15; 182(2):890-901 - Gilcrease MZ, Kilpatrick SK, Woodward WA, Zhou X, Nicolas MM, Corley LJ, Fuller GN, Tucker SL, Diaz LK, Buchholz TA, Frost JA
Coexpression of {alpha}6{beta}4 Integrin and Guanine Nucleotide Exchange Factor Net1 Identifies Node-Positive Breast Cancer Patients at High Risk for Distant Metastasis.
Cancer Epidemiol Biomarkers Prev. 2009 Jan; 18(1):80-6 - Quinn MC, Filali-Mouhim A, Provencher DM, Mes-Masson AM, Tonin PN
Reprogramming of the transcriptome in a novel chromosome 3 transfer tumor suppressor ovarian cancer cell line model affected molecular networks that are characteristic of ovarian cancer.
Mol Carcinog. 2009 Jan 2; [Epub ahead of print]
- Michalik L, Wahli W
PPARs Mediate Lipid Signaling in Inflammation and Cancer.
PPAR Res. 2008; 2008:134059 [Epub 2008 Dec 21] - Palomaki GE, Bradley LA, Douglas MP, Dotson WD, Kolor K
Can UGT1A1 genotyping reduce morbidity and mortality in patients with metastatic colorectal cancer treated with irinotecan? An evidence-based review.
Genet Med. 2008 Dec 31; [Epub ahead of print] - Palomaki GE, McClain MR, Melillo S, Hampel HL, Thibodeau SN
EGAPP supplementary evidence review: DNA testing strategies aimed at reducing morbidity and mortality from Lynch syndrome.
Genet Med. 2008 Dec 31; [Epub ahead of print] - Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG
Predicting cellular growth from gene expression signatures.
PLoS Comput Biol. 2009 Jan; 5(1):e1000257 [Epub 2009 Jan 2]
- Gold K, Cotton JA, Stollewerk A
The role of Notch signalling and numb function in mechanosensory organ formation in the spider Cupiennius salei.
Dev Biol. 2008 Dec 16; [Epub ahead of print] - Bulk E, Sargin B, Krug U, Hascher A, Jun Y, Knop M, Kerkhoff C, Gerke V, Liersch R, Mesters RM, Hotfilder M, Marra A, Koschmieder S, Dugas M, Berdel WE, Serve H, Müller-Tidow C
S100A2 Induces Metastasis in Non-Small Cell Lung Cancer.
Clin Cancer Res. 2009 Jan 1; 15(1):22-29 - He S, Zhang D, Cheng F, Gong F, Guo Y
Applications of RNA interference in cancer therapeutics as a powerful tool for suppressing gene expression.
Mol Biol Rep. 2009 Jan 1; [Epub ahead of print]
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
Characterizing the cancer genome in lung adenocarcinoma.
Nature. 2007 Dec 6; 450(7171):893-8 [Epub 2007 Nov 4]
Weir et al present the results of a systematic copy number analysis of 371 lung adenocarcinoma tumors. Using the Affymetrix 250K SNP Mapping (Sty) array, they identify 57 significantly recurrent amplifications and deletions and present several candidate oncogenes.
Increased COX2 expression enhances tumor-induced osteoclastic lesions in breast cancer bone metastasis.
Clin Exp Metastasis. 2008; 25(4):389-400 [Epub 2007 Oct 27]
Li et al used Affymetrix expression arrays to identify genes involved in metastasis of breast cancer tumors to the bone. From the array data, they identified and then functionally verified the importance of COX2 to tumor metastasis.
RNAi screening of the tyrosine kinome identifies therapeutic targets in acute myeloid leukemia.
Blood. 2008 Feb 15; 111(4):2238-45 [Epub 2007 Nov 19]
Tyner et al report on the development of an RNAi screen to identify tyrosine kinase targets in specific cancer samples
