Biology-on-Array

Application Example

The Biology-on-Array can be used for understanding the transcriptional regulation of any known gene as well as the mode of action of any drug candidate. For example, 5-Fluoro Uracil (5FU) is a drug used for the treatment of cancer. Genome-wide microarray data using 5FU treated versus untreated MCF7 cells revealed that 5FU significantly increases the expression of 19 genes including CDKN1A, GADD45A, BTG2, SESN1, ACTA2, TP53INP1, TNFRSF10B, RNM14 and FAS genes and represses 14 genes in MCF7 cells. This information provides a gene signature for the effect of 5FU. However, microarray results are not sufficient for determining the molecular mechanism behind these changes in gene expression. Biology-on-Array provides an innovative tool to identify the transcription factors involved in the cells' response to 5FU. Since 5FU is used as a drug in the treatment of cancer, the Cancer Transcription Factors siRNA plate was selected for this study.

Cancer Transcription Factors siRNA plate was reverse transfected with MCF7 cells. siRNA transfected MCF7 cells were treated with 5FU and total RNA was extracted from the 96 samples. The HT First Strand Kit was used for parallel processing of the 96 RNA samples for reverse transcription. The synthesized cDNA samples were scored by real time PCR using a specific primer pair for CDKN1A (Fig. 2A) and FAS (Fig. 2B)

Figure 2. Cancer Transcription Factor siRNA plate identified TP53 as a main mediator of 5-FU mode of action. (A) CDKN1A specific qRT-PCR assay on 88 samples (84 samples obtained by knocking down 84 cancer-related transcription factors and 4 samples obtained from negative control siRNA treatment) showed that, under the influence of 5FU, knockdown of TP53 significantly down-regulated CDKN1A expression indicating that TP53 is a positive transcriptional regulator of CDKN1A. VDR and SMAD4 also shown to be involved in 5-FU mediated up-regulation of CDKN1A. (B) Likewise, FAS specific qRT-PCR assay on 88 samples indicate that TP53 is the main factor involved in up-regulating FAS gene expression, whereas, VDR and RXRa also play a role in regulating expression of FAS gene.

For more information about how to use the Biology-on-Array Systems:

Biology-on-Array Home Page

For a detailed description of the protocol and other technical tips:

User Manual
For more information about the data analysis software:

Data Analysis
Biology-on-Array protocols use a reverse transfection. For users that need to optimize a reverse transfection, please see the Optimization System for Biology-on-Array:
Optimization System

Optimization System