Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

This article is part of the supplement: Third Annual MCBIOS Conference. Bioinformatics: A Calculated Discovery

Open Access Proceedings

Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats

Tao Chen1*, Lei Guo2, Lu Zhang35, Leming Shi2, Hong Fang4, Yongming Sun3, James C Fuscoe2 and Nan Mei1

Author Affiliations

1 Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA

2 Division of Systems Toxicology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA

3 Molecular Biology SDS/Arrays Group, Applied BioSystems, Foster City, CA 94404, USA

4 Z-Tech Corporation, 3900 NCTR Road, Jefferson, Arkansas 72079 USA

5 Solexa, Inc., 25861 Industrial Boulevard Hayward, CA 94545, USA

For all author emails, please log on.

BMC Bioinformatics 2006, 7(Suppl 2):S20  doi:10.1186/1471-2105-7-S2-S20

Published: 26 September 2006



Aristolochic acid (AA) is the active component of herbal drugs derived from Aristolochia species that have been used for medicinal purposes since antiquity. AA, however, induced nephropathy and urothelial cancer in people and malignant tumors in the kidney and urinary tract of rodents. Although AA is bioactivated in both kidney and liver, it only induces tumors in kidney. To evaluate whether microarray analysis can be used for distinguishing the tissue-specific carcinogenicity of AA, we examined gene expression profiles in kidney and liver of rats treated with carcinogenic doses of AA.


Microarray analysis was performed using the Rat Genome Survey Microarray and data analysis was carried out within ArrayTrack software. Principal components analysis and hierarchical cluster analysis of the expression profiles showed that samples were grouped together according to the tissues and treatments. The gene expression profiles were significantly altered by AA treatment in both kidney and liver (p < 0.01; fold change > 1.5). Functional analysis with Ingenuity Pathways Analysis showed that there were many more significantly altered genes involved in cancer-related pathways in kidney than in liver. Also, analysis with Gene Ontology for Functional Analysis (GOFFA) software indicated that the biological processes related to defense response, apoptosis and immune response were significantly altered by AA exposure in kidney, but not in liver.


Our results suggest that microarray analysis is a useful tool for detecting AA exposure; that analysis of the gene expression profiles can define the differential responses to toxicity and carcinogenicity of AA from kidney and liver; and that significant alteration of genes associated with defense response, apoptosis and immune response in kidney, but not in liver, may be responsible for the tissue-specific toxicity and carcinogenicity of AA.