August 16, 2004 Cell
Culture Drug Resistance Testing (CCDRT) is the "Rosetta Stone" for
microarray gene expression patterns to clinical drug resistance
The August 5, 2004 edition of the New England Journal of Medicine contains a truly seminal article (New Engl J Med 351:533-542, 2004), relating microarray gene expression patterns to clinical drug resistance. The investigators used a 96 hour suspension culture drug resistance assay with a cell death (MTT) endpoint to define cut-offs for "sensitivity" and "resistance." They then used these data to define gene expression patterns associated with sensitivity and resistance to each of 4 drugs commonly used in the treatment of childhood leukemia. They were then able to show that these gene expression definitions of sensitivity and resistance were significantly and independently associated with treatment outcome on multivariate analysis.
Note that this work could not have been done without the prior work in more than a thousand CCDRT assays from children with leukemia to define sensitivity and resistance cuf-offs for each of the four drugs. The cell culture assays, therefore, are the "Rosetta Stone" which allows for identification of clinically relevant gene expression patterns which correlate with clinical drug resistance for different drugs in specific diseases. This further shows how short-sighted it has been for the academic and clinical oncology community not to support the development and clinical application of CCDRT.
In an accompanying editorial (N Engl J Med 351:601-603, 2004), Winick, et al review the study and note that the findings indicate that "the observed gene expression profiles represent fundamental biochemical features, not epiphenomena, and suggests that gene-expression profiles could be used to alter therapy instead of the more cumbersome method of in vitro sensitivity testing." Winick, et al go on to note the study findings that "the genes predictive of a response to individual agents did not overlap [which] suggests that critical defects in common or more terminal drug-induced apoptotic pathways are not crucial mediators of resistance; the problem may lie in more proximal pathways unique to each drug." They go on to state that "there is no single gene whose expression accurately predicts ...outcome...emphasizing what clinicians have always known -- cancer is a complex disease and needs to be attacked on many fronts."
Our laboratory currently has data from approximately 5,500 fresh human tumor specimens, representing virtually all types of human solid and hematologic neoplasms, in which we tested a median of 17 drugs and/or drug combinations under very similar conditions to that of the above acute lymphoblastic leukemia study (the above authors originally modeled their assay conditions on our methods). Cells were exposed to drugs and cultured in suspension for 96 hours (as in the above study) and tested simultaneously with two different cell death endpoints (one of these being the same MTT endpoint as used in the above study and the other being the DISC endpoint, which enables specific determination of death of tumor cells in a mixed population of tumor and normal cells; n.b. in acute lymphoblastic leukemia, even the presence of 10% non-A.L.L. blast cells can significantly skew the results). Thus, we have the "Rosetta Stone" database necessary to define sensitive/resistance cut-offs for virtually all of the currently available drugs in virtually all types of human solid and hematologic neoplasms.We are presently seeking collaborators to help us use these resources and data to make further progress in this field of inquiry.