DNA technology, the clinical laboratory, and the future

Archives of Pathology & Laboratory Medicine, Jan 2001 by Kiechle, Frederick L

* Objective.-To review the advances in clinically useful molecular biological techniques and their applications in clinical practice as presented at the Ninth Annual William Beaumont Hospital DNA Symposium.

Data Sources.-The 10 manuscripts submitted were reviewed and their major findings were compared with literature on the same topic.

Study Selection.-One manuscript reviewed the development of pharmacogenetics, 3 described analytic approaches to detect aneuploidy or cancer, 1 described transcription factor E2F-1 increase during apoptosis, 2 reported on genetic and pharmacologic factors that influence platelet aggregation, 2 described molecular methods for detecting long QT syndrome or mycobacteria, and 1 reported a modification in collection of buccal DNA.

Data Synthesis.-Genomic and proteomic approaches to develop clinically useful assays have been successful. Aneuploidy can be easily detected by comparative genomic hybridization, which does not require cell culture like cy

togenetics. Mutations have been characterized for a variety of hereditary cancer syndromes, 2 inherited long QT syndromes, and thromboembolism. PI^sup A1^ and PI^sup A2^ polymorphisms in platelets are associated with a difference in aggregation inhibition by estrogen, another example of genotypic pharmacogenetics. Protein expression differences may define colorectal cancer stage and explain apoptotic signal transduction. Mycobacterial detection by nucleic acid amplification and simplified buccal DNA collection demonstrate cost-effective strategies.

Conclusion.-The working draft of the Human Genome Project is completed and the number of clinically useful molecular pathologic techniques and assays will expand as additional disease-associated mutations are defined. Expanded use of database software for genomic and proteomic screening should increase the efficiency of clinical useful assay development.

(Arch Pathol Lab Med. 2001;125:72-76)

This issue of the Archives of Pathology & Laboratory Medicine features 10 papers presented at the Ninth Annual William Beaumont Hospital DNA Symposium, entitled DNA Technology in the Clinical Laboratory, held on April 13 to 15, 2000, in Royal Oak, Mich. In June 2000, both Celera Genomics and the Human Genome Project jointly announced completion of the working draft of the human genome sequence.1 Before this development, the complete sequence of chromosome 22 was reported in December 19992 and chromosome 21 in May 2000.3 Of the 3 billion base pairs (bp) in the human genome, 97% have no known function and 80000 functional human genes are scattered throughout this genome.4 Work to sequence these genes is in progress. Also, single-nucleotide polymorphisms, insertions, deletions, and differences in the copy number of repeated sequences are being mapped. A single-nucleotide polymorphism may occur in 1 of every 300 to 500 bp of human DNA.4

The generation and assembly of these large amounts of nucleic acid sequence data are referred to as genomics. Gene functionality is emphasized when genes or gene products are assembled in microarrays on a gene chip. Transcriptomics refers to monitoring gene activity by measuring the quantity of messenger RNA present in a cell at a particular time.5,6 Using this method, the messenger RNA content in normal and tumor cell lines, for example, can be compared. This comparison may lead to the discovery of anticancer targets for potential therapeutic development using pharmacogenetic or pharmacoproteomic techniques.5,7-13 Genetic treatment strategies (pharmacogenetics) may include use of antisense oligonucleotides designed to bind to a region of a gene or messenger RNA to block transcription or translation or somatic gene therapy to transfer and express an exogenous normal gene into a patients somatic cells.7,10

Proteomics defines aspects of protein characterization, including rate of translation, rate of protein degradation, posttranslational modification, subcellular distribution, and physical interaction with other cellular elements.11,14 Heterogeneous proteins with diverse functions may be separated by charge and molecular weight using 2-dimensional electrophoresis and computer-assisted analysis.5 This electrophoretic technique has 2 disadvantages. First, the concentration of a specific protein may be too low to characterize. Second, insoluble proteins cannot be separated by this method.5 Pharmacoproteomics include treatment strategies using proteins such as specific marker proteins synthesized during disease, protein drug targets, metabolic suicide genes, or antibody genetic engineering.7-13 Metabolic suicide gene therapy is the introduction of bacterial genes into specific mammalian cells, either neoplastic or immunologically defective, that generate substances that inhibit the metabolic function of these cells.15 This modality holds promise for the treatment of cancer and human immunodeficiency virus infection.15 A variety of genetically engineered antibodies are licensed for reduction in renal graft rejection and anticancer, antiplatelet, or antiviral therapy.12,13 One example of antibody recombinant engineering is a chimeric antibody or a hybrid immunoglobulin composed of a murine variable region and human constant region.