Different global gene expression profiles in benzo[a]pyrene-and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice

Abstract

Benzo[a]pyrene (B[a]P) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are potent ligands for the aryl hydrocarbon receptor (AHR). High-density oligonucleotide microarrays were used to generate global gene expression profiles of wild-type and Ahr(-/-) vascular smooth muscle cells (SMCs) from mouse aorta. To determine whether there are signaling pathways other than the AHR involved in B[a]P metabolism, wild-type and AHR knockout (Ahr(-/-) SMCs were exposed to B[a]P. Two signaling pathways, represented by TGF-beta2 and IGF-1, were identified as potential candidates of an AHR alternate pathway for cells to respond to B[a]P. The wild-type SMCs responded similarly to B[a]P and TCDD in the regulation of a small set of common genes known to respond to the activated AHR (e.g., glutamine S-transferase). However, wild-type SMCs responded in a way that involves many additional genes, suggesting that a very divergent cellular response may be involved when SMCs are exposed to the two classic inducers of the AHR. In contrast, many more genes in the Ahr(-/-) cells responded similarly to B[a]P and TCDD, including Cyp1b1, than responded differently, which indicates that eliminating the AHR is effective for investigating potential alternate cellular mechanisms that respond to B[a]P and TCDD.

An osteopontin splice variant induces anchorage independence in human breast cancer cells

“…For each comparison, several hybridizations (four for OPNc versus OPNa and two each for OPNa versus vector and OPNc versus vector) were performed with RNA from distinct soft agar plates and dyeflip of the fluorescent labels. The microarray experiment was carried out as described (Hosack et al, 2003;Karyala et al, 2003;Guo et al, 2004) (see also http://microarray.uc.edu). The human 70-mer oligonucleotide library version 2.0 (21 329 optimized oligos) (Qiagen, Alameda, CA, USA) were printed on aminosilane-coated slides (Cel Associates Inc., Pearland, TX, USA).…”

MicroRNAs and regeneration: Let-7 members as potential regulators of dedifferentiation in lens and inner ear hair cell regeneration of the adult newt

“…Data normalization was performed in two steps for each microarray separately [15][16][17]. First, background adjusted intensities were log-transformed and the differences (R) and averages (A) of log-transformed values were calculated as R = log 2 (X1) − log 2 (X2) and A = [log 2 (X1) + log 2 (X2)]/2, where X1 and X2 denote the Cy5 and Cy3 intensities after subtracting local backgrounds, respectively.…”

Conditional Activation of RET/PTC3 and BRAFV600E in Thyroid Cells Is Associated with Gene Expression Profiles that Predict a Preferential Role of BRAF in Extracellular Matrix Remodeling

“…The Cy3 and Cy5 fluorescence signal intensities were normalized. Data normalization was done in two steps for each microarray separately (19)(20)(21). First, background-adjusted intensities were log transformed, and the differences (R) and averages (A) of logtransformed values were calculated as R = log 2 (X 1 ) À log 2 (X 2 ) and A = [log 2 (X 1 ) + log 2 (X 2 )] / 2, where X 1 and X 2 denote the Cy5 and Cy3 intensities after subtracting local backgrounds, respectively.…”