Prediction of the number of activated genes in multiple independent Cd(+2)- and As(+3)-induced malignant transformations of human urothelial cells (UROtsa).

Scott H Garrett,Donald A Sens,Ke K Zhang,Seema Somji

doi:10.1371/journal.pone.0085614

Abstract

BackgroundMany toxic environmental agents such as cadmium and arsenic are found to be epidemiologically linked to increasing rates of cancers. In vitro studies show that these toxic agents induced malignant transformation in human cells. It is not clear whether such malignant transformation induced by a single toxic agent is driven by a common set of genes. Although the advancement of high-throughput technology has facilitated the profiling of global gene expression, it remains a question whether the sample size is sufficient to identify this common driver gene set.ResultsWe have developed a statistical method, SOFLR, to predict the number of common activated genes using a limited number of microarray samples. We conducted two case studies, cadmium and arsenic transformed human urothelial cells. Our method is able to precisely predict the number of stably induced and repressed genes and the number of samples to identify the common activated genes. The number of independent transformed isolates required for identifying the common activated genes is also estimated. The simulation study further validated our method and identified the important parameters in this analysis.ConclusionsOur method predicts the degree of similarity and diversity during cell malignant transformation by a single toxic agent. The results of our case studies imply the existence of common driver and passenger gene sets in toxin-induced transformation. Using a pilot study with small sample size, this method also helps microarray experimental design by determining the number of samples required to identify the common activated gene set.

Highlights

Transcriptome studies and the sequencing of gene coding regions obtained from human tumors have revealed that the gene expression show both similarity and diversity for a given tumor type
If common driver mutations exist in transformed cells, a constant number of induced and repressed genes, as the product of pathways affected by driver mutations, would be found over a large number of independent isolates
Transformed isolates have carcinogen-specific gene expression patterns Global gene expression analysis was performed on the 6 Cd+2 transformed, 5 As3+ transformed cell lines and 3 non-transformed parental control cell lines using the Affymetrix 133 Plus 2.0 chip

Summary

Introduction

Transcriptome studies and the sequencing of gene coding regions obtained from human tumors have revealed that the gene expression show both similarity and diversity for a given tumor type. If common driver mutations exist in transformed cells, a constant number of induced and repressed genes, as the product of pathways affected by driver mutations, would be found over a large number of independent isolates. A large number of genomic studies have found common gene sets that were activated during toxin-induced in vivo or in vitro cell transformation [14,15,16,17,18,19]. It is a question whether the common gene sets are stabilized because it is usually difficult to obtain sufficient number of independent transformations in genomic studies. The advancement of high-throughput technology has facilitated the profiling of global gene expression, it remains a question whether the sample size is sufficient to identify this common driver gene set

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