Microarray data meta-Analysis of several cancer cell lines grown under spheroids and adherent conditions

Introduction & Aim:Majority of Human body cells Interact with other cells and extracellular matrix (ECM) to form 3D tissues and organs. In 2D or monolayer culture these cell-cell and cell-matrix interactions are eliminated, and thus the physiology of the cells varies with its actual state in a three-dimensional environment. Over the past few years, cell-based assays have become increasingly important models in the study of diseases and medications. Tumors are growing in three-dimensional (3D) environment which provided by body tissues. Accordingly, in-vitro 3D models are essential for cancer research. As well as cells that cultured in 3D condition display the characteristics of solid tumors and metastatic cancers. Here we examined 12 cancerous cell lines including breast cancer cell line and other types of cancers which cultured in adherent and 3D culture in order to obtain most important genes which show differential expression from 2D to 3D culture in all or majority of studies. Methods: Microarray data were obtained from GEO dataset and preprocessed by Biobase, GEOquery and limma R packages. Meta-analysis was performed using MetaDE R package according to Fisher s combined probability test. Results were filtered based on adjusted p-value<0.05 and fold change> 2.Results:Finally, we found that ARRDC3, CREBRF, MXI1, PCMTD1 genes consistently up-regulated and PRSS23, TPM1 genes consistently down-regulated in the majority of studies.Conclusion: Based on our results these genes are crucial for cells in 3D condition, additionally, as 3D models of cancer show metastatic like features, these genes can be crucial targets for further researches.