Expression profiling of human tumors: the end of surgical pathology?

Presented by Marc Ladanyi Expression profiling is a new investigative and diagnostic modality made possible by recent scientific and technological advances (for recent reviews, see 1, 2 ). The key scientific advance is the Human Genome Project, in particular, its so-called “expressed sequence tag” (EST) component, which focused on collecting the sequences (in most cases only partial, i.e., “sequence tags”) of all of the genes (both known and unknown) expressed in a wide variety of human tissues. By now, the majority of named and anonymous human genes are represented respectively in the GenBank and the EST sequence databases. The key technological advance has been the miniaturization and automation of molecular biology, specifically the advent of DNA microarray technology. DNA microarrays can be made on either nylon membranes, glass slides, or synthetic “chips,” and can consist either of cDNA clones or cDNA clone-specific oligonucleotides. The numbers of DNA spots on microarrays can number from the hundreds to the tens of thousands. Expression profiling refers to the process of establishing the pattern of expression of thousands of individual genes simultaneously in a given cell or tissue sample by extracting its RNA, converting it to cDNA and hybridizing the labeled cDNA to a DNA microarray. In a sense, pathologists already use gene expression studies diagnostically on a daily basis in the form of immunohistochemistry. Expression profiling provides a supraexponential increase to the amount of gene expression data available on a given tumor, but lacks the topographical information of immunohistochemistry. Nonetheless, it is widely believed that the latter shortcoming will be more than compensated by the sheer multiplicity of the gene expression data. It is already apparent that expression profiling can be used to distinguish different human tumors. With fascinating exceptions, 3 some of the differential diagnoses achieved so far by this approach have been rather straigthforward by the standards of histopathology. 4, 5, 6, 7, 8 Thesetypes of microarray-based “assays” have not yet been subjected to a rigorous evaluation of sensitivity, specifity, and cost-effectiveness as a diagnostic modality. However, ongoing developments such as the rapid and continual scientific refinement of expression profiling, the possibility of mass production of smaller more narrowly targeted microarrays, and the potential for automated software-based recognition of specific gene expression patterns, promise to address many of these concerns and present limitations. Aside from its diagnostic applications, expression profiling can also provide important prognostic information. 6 It is evident that morphology alone, while quite useful for the diagnostic classification of tumors, does not reflect the entire biology of a given tumor. Tumors of similar appearance can behave differently and expression profiling is expected to predict tumor behavior and response to chemotherapy more reliably than tumor histopathology. In recent years, the impact of diagnostic molecular genetic markers, typically based on the detection of specific translocations, has been felt most acutely in hematopathology and sarcoma pathology, where the concept of morphological/genetic entities has become well accepted. Expression profiling promises to extend this process to all tumors, including carcinomas. A key difference is that, as a more “global” approach, expression profiling may require less prior expert histopathological “triage” that any prior ancillary diagnostic technique. Will expression profiling evolve into another “ancillary” technique or will it come to be seen as an alternative to expert surgical pathology? At present, expression profiling studies are highly dependent on histopathology for validation, 1, 9 but it is conceivable that expression profiles may eventually become “disconnected” from the underlying morphology, assuming the role of clinically relevant entities. The extent of involvement of the pathology community in the further development of microarray-based expression profiling as a diagnostic test may determine the nature of its ultimate relationship to conventional tissue-based diagnosis. 9