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Correlation analysis of genome-wide gene expression profiles by DNA microarray

ABSTRACT: We previously isolated a new angiogenesis inhibitor, terpestacin, from natural products. To investigate molecular mechanism of terpestacin for its anti-angiogenic activity, we identified a cellular binding protein of terpestacin using phage display biopanning analysis. Terpestacin specifically bound to the small molecular ubiquinone binding protein (QP-C), a 13.4 kD subunit of the mitochondrial Complex III. To explore the functional specificity of terpestacin at QP-C, we performed cDNA microarray analysis. The genome-wide gene expression profiling showed a significant phenotype correlation between terpestacin and QP-C genetic knock-down. These results demonstrate that QP-C is a biologically relevant target of terpestacin. Keywords: Sample comparison

ORGANISM(S): Homo sapiens

PROVIDER: GSE7953 | GEO | 2007/06/29

SECONDARY ACCESSION(S): PRJNA100695

REPOSITORIES: GEO

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Project description:Interaction of nanomaterials with the mammalian cells remains to be poorly understood at the molecular level. Here we report the first synthesis of hybrid nanomaterial termed phage mimetic nanorods (PMN’s) inspired from filamentous bacteriophage present in nature. We emulate filamentous bacteriophage structure by combining two separate nanoscale entities, one functionalized gold nanorods and the other is coat proteins isolated from filamentous bacteriophage obtained through landscape phage screening. Utilizing biochemical interactions between a phage-derived protein and functionalized gold nanorods, we synthesized novel phage mimetic nanorods. The resulting nanovectors showed excellent multi functional properties including target specificity, imaging and photo destruction ability in a model SKBR-3 breast cancer cells. In addition, to gain insight into the molecular interactions involved during internalization of PMNs by SKBR-3 cells, we performed gene expression profiling of cells exposed to PMNs as compared with naive cells. We identified 70 upregulated and 26 downregulated genes responding to PMNs. Heparin binding internalization was identified as most plausible mechanisms of PMNs entry. Members of Major Histocompatibility complex I (MHC class I) were activated by PMNs, leading to enhanced lysosome and proteasome activity. Seven members of poorly annotated G antigen family (GAGE) of genes were upregulated, and may represent novel mechanism of PMNs entry recognition by cells. In summary, we present a versatile technique of PMNs production as any protein isolated from phage libraries selected against any in vitro and in vivo cells can be used as a source to synthesize PMN’s. This study also opens new avenues to understand the role of nanomaterials at the molecular level. Investigate the effect of phage mimetic nanorods onto SKBT-3 cells Two groups were compared, three biological replicates each. One group was control cells and the other was test.

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Correlation analysis of genome-wide gene expression profiles by DNA microarray

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