The Progressing Clinical Utility of DNA Microarrays

摘要

During the past 25 years, technical advances in nucleic acid analysis and methods have allowed scientists to identify several qualitative and quantitative changes in DNA and RNA sequences, and ultimately, in proteins that can result in the development of cancer. Microarray technology yields far more data, much more rapidly than previously known methods. Microarrays are hundreds, thousands, or even tens of thousands of miniature assays for biomolecules such as DNA, RNA, and proteins. This review considers the main types of DNA microarrays, the kinds of information they provide, how that information is changing the way we think about cancer and carcinogenesis, and the expanding role of this technology in clinical oncology. Protein microarrays and tissue microarrays are not discussed in detail here, but the interested reader is referred to recent reviews.1–6 The successful clinical management of human malignancies requires an ever-evolving arsenal of both diagnostic and prognostic methods, and microarray analysis may be able to serve as a new tool that provides useful information for both. Currently, histopathologic evaluation of tumor type and grade, and pathologic and clinical assessment of a cancer's stage are the mainstays for guiding therapeutic interventions and predicting outcomes. These data are usually supplemented with information from the patient's history, the physical exam, imaging tests, and clinical laboratory assays of tumor markers. However, even the combined use of all available clinical and laboratory information remains suboptimal for diagnosis, for predicting prognosis, and for predicting patient response to specific therapies. Tumors with identical histopathologies may progress differently, may respond differently to therapy, and may be associated with widely divergent clinical outcomes, suggesting that additional factors may be directing disease outcomes. DNA microarray technology may be a more comprehensive determinant for guiding therapeutic interventions in the future. Recent efforts to define factors or variables that guide tumor progression have focused on the molecular genetic definition of cancer. Early efforts focused at the DNA level endeavored to “allelotype” human tumors and attempted to identify DNA-base sequence deletions, insertions, or mutations associated with disease progression and clinical outcomes. For example, variation in nucleotides in specific positions of a sequence may or may not alter the functional activity of the protein encoded by that gene. Some of these variations may involve single nucleotides, and are called single nucleotide polymorphisms —abbreviated SNPs and pronounced “snips.” Some SNPs result in protein variants, while others do not directly alter a protein, but are linked to, and therefore act as, markers for another sequence change that is functionally significant. The discovery and cataloguing of these single nucleotide variations, has been enormously facilitated by the human genome project. Use of DNA microarrays is now revealing associations of specific SNPs with cancer risk, development, and progression at a substantially accelerated pace. Other efforts are focused at the transcriptional or RNA level. These attempt to “profile” the gene transcription pattern of normal and malignant tissues using cDNA microarrays—a new high-throughput technology. There are two basic varieties of DNA microarrays: spotted or cDNA microarrays and oligonucleotide microarrays. The first, cDNA or spotted arrays, are created by the deposition of concentrated solutions of double-stranded DNA on a grid. A variety of automated devices are available that can precisely control the amount and position of the DNA spots. The DNA sequences, usually somewhat longer than 100 nucleotide-base pairs, are typically polymerase chain reaction (PCR) products from the amplification of recombinant cDNA library clones.7,8 Oligonucleotides are shorter sequences—usually 16 to 20 base pairs. Sometimes the oligo