Molecular dissection of a medicinal herb with anti-tumor activity by oligonucleotide microarray

It is difficult to understand precisely the physiological actions of herbs because they contain a complex array of constituent molecules. In the present study we used DNA microarray data for 12600 genes to examine the anti-proliferative activity of the herb Coptidis rhizoma and eight constituent molecules against eight human pancreatic cancer cell lines. We identified 27 genes showing strong correlation with the 50% inhibitory dose (ID50) of C rhizoma after 72-h exposure. Hierarchical cluster analysis with correlation coefficients between expression levels of these 27 C rhizoma-related genes and the ID50 of each constituent molecule classified these test molecules into two clusters, one consisting of C rhizoma and berberine and the other consisting of the remaining seven molecules. Our results suggest that one molecule, berberine, can account for the majority of the anti-proliferative activity of C rhizoma and that DNA microarray analyses can be used to improve our understanding of the actions of an intact herb. (c) 2005 Elsevier Inc. All rights reserved.