Commentary Pattern Recognition and Arrays The Times Are A-Changing

Not so long ago, very little was known of the estimated three billion base pairs of the human genome. Little bits were painstakingly unraveled. With relatively few genes known, entire laboratories could be devoted to the discovery of a new gene or the characterization of a few genes. Even fewer genes could be considered relevant to cancer and deserving the label of oncogene or tumor suppressor gene. Most of these genes were pounced on quickly, often with rapid publication of the usual spectrum of studies—transfections, knockouts, mutation frequencies in various tumor types, mutational spectrum, molecular epidemiology, biomarker potential, and so on. Some of these genes faded into relative obscurity whereas others, like p53, became “workhorses” or “molecules of the year. ” As long as the pace of oncogene or tumor suppressor discovery was reasonable, sufficient manpower was available to populate the ever-growing number of pages in an ever-growing number of journals. However, the Human Genome Project threatens business as usual. Soon all of the estimated 80,000 human genes will be identified and sequenced. Indeed, one can now make or purchase filters or chips covered with probes representing ;25% (20,000 genes) of all human genes. With a single hybridization, one can potentially obtain more information than a thousand graduate students of yore. Moch et al present in this issue one of the first studies using such cDNA arrays to probe for differences between renal cell carcinoma (RCC) and normal kidney. From the ;5184 genes on their filters, they noted that vimentin RNA was overexpressed in a RCC cell line. Taking this hint, they examined vimentin protein expression in primary tumors by immunohistochemistry. However, in the spirit of the times, they did not examine just any set of tumors. Continuing their previous work, they examined a collection of 532 formalin-fixed, paraffin-embedded RCC specimens arranged in microarrays (0.6-mm circular cores with as many as 1000 tumors per block), greatly facilitating the immunohistochemistry. Vimentin was overexpressed in a subset of the tumors, confirming the authors’ cell line observations. Furthermore, clinical follow-up was available for 386 of the tumors. Therefore, the authors were able to retrospectively link vimentin overexpression in RCC with a significantly poorer prognosis. From hybridization to immunohistochemistry to a possibly clinically significant biomarker in perhaps weeks. Amazing! The genetic database is relatively well organized, with definite links between a cDNA and appropriate genomic annotations. The link is usually weaker between a mRNA and its protein, as specific and sensitive antibodies must typically be developed. The authors were fortunate (or, as we shall see, in some ways unfortunate) that vimentin antibodies suitable for fixed tissues have been available for years and that they were able to quickly employ their remarkable tumor block arrays. These arrays, linked to a clinical database, greatly facilitate correlation between expression and clinical significance, and are immensely important in an efficient system geared to high throughput. Perhaps as a tribute to the current industry of tumor analysis, at the end of this high-technology voyage the authors find that others had already preceded them. They note that one study published in 1989 also found vimentin overexpression in RCC to be associated with a less favorable prognosis, whereas another study from 1991 found no association between vimentin expression and outcome. Is vimentin overexpression a clinically useful biomarker for RCC? Only time will tell. However, the focus on a single biomarker is in many ways a relic of a past when only a limited number of markers was available. Given the ;80,000 genes soon to be available and their potential transcriptional and posttranslational modifications, it may not be rational to focus on a single marker. It may be possible and more powerful to consider the expression of all genes. Vimentin, for example, may be neither an oncogene nor a tumor suppressor gene, but rather overexpressed along with a number of other genes when certain critical pathways are altered. Because gene products