Molecular profiling using immunohistochemistry (IHC) and DNA microarray (DMA) as a tool to determine potential therapeutic targets in patients who have progressed on multiple prior therapies
Authors: Mitesh J. Borad, Robert Penny, Michael Bittner, Johanna Gardner, Sonsole Shack, Elizabeth Campbell, Darin Taverna, Richard Love, Jeffrey Trent, Daniel Von Hoff
Journal: Clinical Cancer Research (2006)

B82   This study was undertaken to address the question - if the tumors of patients being evaluated for Phase I trials were studied carefully could one find potential targets that would be amenable to treatment with therapeutic agents given their known mechanisms of action. Inherently it may seem that employing this approach may have a higher chance of success than utilizing a random agent in Phase I clinical trials. To address this issue we have performed IHC assays for up to 14 targets (e.g. HER-2/neu, ER, c-kit, etc.) on 171 patients where a recent formalin fixed paraffin embedded tumor sample was available and have carried out expression profiling using a two color Agilent oligonucleotide microarray with 17,085 unique probes, on tumors from 112 patients with advanced cancer who have exhausted conventional therapy and who were undergoing a procedure for a cancer related matter (e.g. obstruction, ascites, etc.). One-hundred twelve patients had excess tissue submitted from their procedure, immediately frozen and subjected to microarray analysis. One hundred seventy one patients had IHC performed on sections obtained from the paraffin blocks prepared as part of their standard surgical workup. IHC was considered positive if ≥ 30% of tumor cells were scored as 2+ or greater staining. For DNA microarray (DMA) studies the gene expression ratios were called significantly increased or decreased if the fold change in expression relative to the normal tissue of origin reference was significant at p≤0.001. For the 112 patients where frozen tumor was assayed (100%) of them had RNA that was of excellent quality. The findings were a surprise in that IHC identified an average of 1.6 targets (for which a conventional therapeutic agent is available) per patient (range 0-5 targets) and 74% of those patients had at least one target. The DMA identified an average of 11.1 targets per patient (range 0-26 targets). Overall, a target was found for 111 (99%) of the patients. In the 214 instances (in 65 patients) where an IHC was positive and where a DMA was also available there was a positive correlation in 25 cases (11.7%), no correlation in 158 cases (73.8%) and negative correlation in 31 cases (14.5%). Of course these correlations have to be evaluated in the context that these methodologies are measuring the same parameter in different ways and as such are exploratory. This data indicates that using IHC and DMA one can consistently find a potential target for which we have a therapeutic agent in patients9 tumors even though they have progressed on prior therapies. This has implications for patients planning on participating in phase I clinical trials. It is important to conduct a prospective clinical trial to determine whether the targets discovered using IHC and DMA can be used to select therapy which will further benefit the patient who would otherwise be participating in a phase I clinical trial.