Temporal changes in genomic expression patterns of mouse model for squamous cell carcinomas: genomic analysis guided by contrast-enhancing magnetic resonance imaging

Abstract

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Purpose: To obtain the gene expression profiles using oligonucleotide microarray on tissue samples from different stages of tumor growth guided by MRI; and to identify statistically significant changes in gene expression across stages. Materials and Method: A murine model with squamous cell carcinoma VII cells subcutaneously implanted was used. MRIs were performed every 3 to 4 days once the tumors reached at a diameter of ∼6 mm. Spin echo (T1-wt) and fast spin echo (T2-wt) sequences were used. Pre- and Post-contrast images were obtained pre- and post-injection of Gd-DTPA. The temporal tumor stages were characterized by T1- and T2-wt MR imaging features. Tissue samples from different stages were obtained for microarray analysis. A probe-level normalization package, Bioconductor, was used to minimize variability, followed by a modified t-test via Significance Analysis of Microarray (SAM) for identifying significant expression levels. Temporal expression profiles for similar tumor regions across different stages were compared. Results: Three distinct stages of tumor progression were defined based on the T1- and T2-wt MRI features. Stage 1 tumors show a homogeneous pattern in the T1- and T2-wt images. Stage 2 tumors show regions of contrast enhancement in the post-contrast T1-wt images. Stage 3 tumors show intensity changes in post-contrast T1- and T2-wt images. Microarray analysis was performed on the rim and center regions of Stage 1 tumors, and the contrast-enhancing (CE) and non-enhancing (NE) regions of Stages 2 and 3 tumors. Genes with statistically significant changes in rim/CE and center/NE regions across the 3 stages were obtained. Results from the comparisons in the rim/CE regions show genes related to 6 different functions, with >90% of them having a concave or convex temporal expression pattern. Results from the comparisons in the center/NE regions show much less activity as tumors progress, with the majority of the genes falling into the similar function categories, but with 50% of the gene expression levels increasing monotonically across the stages. Caspase 8, a protein involved in apoptosis pathway, was found to have increasing expression level as tumor progress from Stage 1 to 3. In addition, Notch 2 signaling has pleiotropic affects in cell differentiation and cell faith; keeping cells in an undifferentiated state. We found that Notch 2 expression level also increases with tumor progression. Conclusion: Probe-level normalization followed by SAM transformed the microarray data from different stages of tumor progression into a scale suitable for analysis. We found more genes showing significant temporal expression changes in the rim/CE region compared to the center/NE region. Among significant genes in both regions, we found differences in the temporal expression profile with less monotonic properties in the rim/CE region.