Pharmacogenomics and its applications

Medical Laboratory Observer, March, 2005 by Robert M. White, Steven H.Y. Wong

The Great Paracelsus (Philipus Aureolus Theophrastus Bombastus von Hohenheim-Paracelsus, 1493-1541) is remembered by toxicologists for his famous quote: "All substances are poisons; there is none which is not a poison. The right dose differentiates a poison from a remedy." (1) Indeed, the basic principle from the quotation still applies today. The right dose of morphine that will produce a blood level of approximately 0.07 mg/L to 0.083 mg/L is essential for the relief of pain. An overdose that results in a markedly increased blood level (0.2 mg/L to 2.3 mg/L) can cause death due to central nervous system depression. (2) In general, the same applies to all chemical substances.

As an important exception to Paracelsus' statement, however, there are instances in which a drug should be avoided completely. An example is found in the administration of succinylcholine as a skeletal muscle relaxant in surgery patients. Most patients can convert succinylcholine into inert metabolites through an enzyme called pseudocholinesterase because most patients possess two alleles for the common gene that can produce active enzyme. A certain small percentage of patients, however, carries the genes that are aberrant or silent and, thus, either produce protein (enzyme) that is defective in its function or cannot produce the protein that is capable of inactivating administered succinylcholine at all. Thus, these patients expire or suffer severe sequelae from administration of the drug. (3)

Along the same line of thinking, the dose of a given drug for certain individuals may differ from that used for the majority of the population due to genetic differences between the individual and the general population (e.g., a reduced dose of 6-mercaptopurine in the presence of reduced thiopurine methyl transferase, or TPMT, activity due to a genetic deficiency in synthesis of the active enzyme). (4,5) Therefore, in the Third Millennium, an expansion of Paracelsus' statement might be that the "right dose" for one individual may not be the "right dose" or even the right drug for another, due to differences in each individual's genetic makeup. The determination of what is the "right dose" and, in some cases, what is even the right drug for a given individual constitutes the reason for the development of the sciences of pharmacogenetics and pharmacogenomics.

Although often used interchangeably, there are subtle differences between pharmacogenetics and pharmacogenomics. Pharmacogenetics focuses on individual traits with respect to one compound or drug. Thus, pharmacogenetics, which historically actually preceded pharmacogenomics, looks at the responses of different individuals to one drug, while pharmacogenomics studies the differences among several compounds with regard to a single genome. (6,7) Pharmacogenomics is concerned with the systematic assessment of how chemical compounds (e.g., drugs) modify the overall expression pattern in certain tissues. Pharmacogenomics is not focused on the differences between individuals. Rather, pharmacogenomics focuses on differences among several drugs or compounds with regard to a generic set of expressed or nonexpressed genes. The focus in pharmacogenomics is on compound variability. For the purposes of this brief introduction, the two terms will be used interchangeably unless stated otherwise.

[FIGURE 1 OMITTED]

Before embarking upon a cursory journey through pharmacogenomics, a very brief discussion of DNA (deoxyribonucleic acid) and its products is in order. DNA is the genetic code that determines all of an individual's characteristics, including the synthesis of the proper proteins essential for life. The so-called "central dogma" of molecular biology is outlined in Figure 1. (8) DNA is a long chain of chemically linked (phosphate bond), single nucleotides. Although there is a great deal more detail to the system due to phenomena such as splice variants, (9) basically DNA is transcribed in the cell nucleus by an enzyme called RNA polymerase to yield messenger RNA, or mRNA. DNA sequences called promoters and enhancers are also usually required to initiate RNA synthesis. Silencers balance the effects of promoters and enhancers when synthesis is not required. A stop codon (a series of the nucleotides that tell the polymerase to stop transcription) also is required so that only the required RNA, not an almost infinitely long RNA, is produced. Regions of the DNA that do not code for amino acids are called introns. The introns are spliced out before the completed mRNA is capped (vide infra) and exported from the nucleus for translation. The regions of the DNA that do code for protein are called exons. RNA that has had the introns removed is capped on the 5-prime end with a special nucleotide called 7-methylguanosine and has a poly-adenosine (poly-A) "tail" added to the 3-prime end. The capped mRNA with its poly-A "tail" is then translated into protein in a cellular apparatus called a ribosome. (9)

Also required before pharmacogenomics can be discussed is a basic knowledge of the proteins that are the end product of the transcription of DNA and the translation of RNA. Essentially, a protein is a long chain of chemically linked (amide or peptide bond) amino acids. The sequence in the chain of amino acids is called the primary structure. The chain may form loops and/or helices (secondary structure), and the loops and helices may fold to form the tertiary structure. Further, the protein may exist by itself, associate with other protein chains like itself (e.g., dimerize to form an aggregate of two like chains), or associate with dissimilar protein chains to form the final, active structure, which is known as the quarternary structure. Further, a protein may be chemically and functionally changed (post-translational modification) by the addition of phosphate groups (phosphorylation), glucuronic acid groups (glucuronidation), or other groups, or by the addition or removal of amino acids or short stretches of amino acids called polypeptides. The study of proteins, along with the analysis by 2D gel and mass spectrometry and data analysis by bioinformatics, constitute the emerging field of clinical proteomics. (10,11)