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Gene expression profiling of processing glycosidase inhibitors: defining a common gene set produced by processing glycosidase inhibition in human cervical carcinoma HeLa cells

ABSTRACT: The objective of the present study is to investigate the role of processing glycosidase inhibition induced by processing glycosidase inhibitors, namely castanospermin as the processing glucosidases inhibitor, deoxymannojirimycin as the processing mannosidases inhibitor, and deoxyfuconojirimycin as the fucosidase inhibitor. Comparative gene expression analysis was performed in human cervical carcinoma HeLa cells, with non-inhibitor-treated cells as the negative control. Gene expression was analyzed using 3D-Gene® Human 25k oligonucleotide microarrays and computational gene expression analysis tools.

ORGANISM(S): Homo sapiens

PROVIDER: GSE40297 | GEO | 2014/09/01

SECONDARY ACCESSION(S): PRJNA173434

REPOSITORIES: GEO

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Project description:Analysis of various of up-regulated and down-regulated genes in Normal Cervical mucosa, Cervical intraepithelial neoplasia and Cervical squamous cell carcinoma. The report provides a data analysis methodology for identification of co-expressed gene patterns, as emerging clusters, in global transcriptome of cervical mucosal pre-malignant and malignant conditions in comparison to their normal counterparts. Microarray based study of global gene expression is often used to extract molecular signatures underlying cancer progression. Such endeavors endorse self organizing map, a type of artificial neural network to analyze high dimensional pre-processed transcriptome data to segregate hotspot genes in component plane for disease subtypes. This report provides a data analysis methodology for identification of coexpressed gene patterns, as emerging clusters, in global transcriptome of oral and cervical mucosal premalignant and malignant conditions in comparison to their normal counterparts. Four exclusive cluster patterns, each involving 100 − 300 genes, were identified from component planes for oral study groups. Gene expression associated with each pattern belonged to 32 biological processes. Analysis on cervical biopsies, where cancer was compared to cervical interepithelial neoplasia and normal counterpart, it revealed three non-overlapping patterns for each condition. In cervical interepithelial neoplasia an intermediate pattern with nine different dominant functional processes was identified, whereas, in cervical squamous cell carcinoma pattern showed dominance for seven different functions. This analysis demonstrated utility of self organizing map to capture dominant enriched patterns as visual plots and revealed six common biological processes like transcription and RNA processing, cytoskeleton reorganization, angiogenesis, immunity, neuron signalling, and connective tissue remodelling in the pathogenesis of oral and cervical cancers. In fact it could provide an intuitive understanding of molecular course in carcinogenesis and may contribute for combinatorial biomarker discovery.

Dataset Information

Gene expression profiling of processing glycosidase inhibitors: defining a common gene set produced by processing glycosidase inhibition in human cervical carcinoma HeLa cells

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