Basic Concepts of Molecular Pathology

Archives of Pathology & Laboratory Medicine, Oct 2008 by Allen, Timothy Craig, Cagle, Philip T, Popper, Helmut H

This month's issue of the Archives of Pathology & Laboratory Medicine includes a unique special section on "Molecular Signatures of Lung and Pleural Tumors" that represents the proceedings of a special Joint Symposium of the European Working Groups for Molecular Pathology and Pulmonary Pathology at the 21st European Congress of Pathology in Istanbul, Turkey, in September 2007. This symposium and the subsequent special section were organized by Dr Helmut Popper of the Institute of Pathology at the Medical University of Graz, Graz, Austria, president elect of the Austrian Society of Pathologists and immediate past president of the European Working Group for Pulmonary Pathology. In this brief review, we have provided some definitions of terms and concepts used in the proceedings of the "Molecular Signatures of Lung and Pleural Tumors" special section for those readers who are not already familiar with molecular pathology.

Molecular pathology may have once been a specialized component of the research laboratory or the clinical laboratory, but today molecular diagnostic and prognostic techniques are in common use within the anatomic pathology laboratory, especially in the realm of infectious organism diagnosis and cancer diagnosis. Molecular testing continues to expand as more easily obtainable archival paraffin-embedded tissue replaces fresh and frozen tissues as the source of DNA and RNA needed for molecular analysis, and as newer technologies allow for more streamlined methods of testing. This review addresses the increased application of molecular testing in lung pathology, specifically how the current state of molecular pathology may be applied to practical, everyday lung pathology diagnosis.

GENES

Genes, made up of nucleic acids, contain the information necessary for the construction of proteins from amino acids within a cell. Genes code for proteins required for metabolic reactions and cellular structure. DNA makes up genes, and RNA transcribes the genetic code held within the DNA into proteins. The genetic code within the genes is composed of nucleic acids, for which nucleotides are the building blocks. Nucleotides, made up of a sugar-phosphate backbone with a nitrogenous base, are either purines-adenine (A) and guanine (G) in DNA and RNA- or pyrimidines-thymine (T) and cytosine (C) in DNA (uracil [U] replaces T in RNA). The nucleotides that make up the genes are arranged in a double-stranded righthanded helix. Nucleotides in DNA are arranged sequentially so that a gene will code for a matching protein. Within a double helix pattern, A, a purine, always binds with T, a pyrimidine, and G always binds with C, giving a nucleotide sequence for which 1 strand is a "mirror image" of the other strand.1-6

There are 46 chromosomes (23 pairs) in a human diploid cell, on which all genes are located. Chromosomes are paired, and as such a gene is found on a locus on each of the 2 paired chromosomes, giving 2 copies, or alleles, of genes. Gametes are haploid rather than diploid and therefore contain only 1 allele for each gene. Diploid status is reestablished when the nuclear material from an egg and sperm combine during fertilization.1-6

Transcription, the synthesis of messenger RNA (mRNA) from a DNA strand, is a key step in the formation of protein coded by DNA. During transcription, enzymes called topoisomerases break a DNA strand and allow the DNA double-helix to uncoil, giving 2 DNA strands, 1 of which is the template for mRNA, called the DNA template. Base pairs are matched with the DNA template to produce a mirror image of the DNA template, except with the substitution of U for T, forming a strand of mRNA. A series of 3 base pairs in a gene, called a codon, code for a specific amino acid, so that a series of codons code for a particular sequence of amino acids resulting in the synthesis of a specific protein. Translation, the assembly of the protein molecule from the mRNA template, occurs with the addition of amino acids in a particular sequence based on the specificity of the mRNA. Transfer RNA assists in translation.1-6

After translation, modifications to the newly formed protein occur in order for it to function, to move within the cell, or to fold properly. Methylation, acetylation, phosphorylation, glycosylation, posttranslational cleavage, and the addition of lipid groups are examples of posttranslational modifications. End regions of chromosomes are made up of telomeres, hundreds of repeats of the nucleotide sequence TTAGGG. Some of these telomere sequences are lost each time a cell divides, until they are lost and the cell can no longer divide. This process is called senescence. A polymerase called telomerase is able to replace the DNA sequences at the end regions, allowing for continuing cell division-a significant feature in some cancers. 1-6

The polypeptide chain formed by the specific amino acid sequence causes the newly formed protein to fold into a tertiary arrangement giving it a 3-dimensional structure. Often, the newly formed protein is inert until made functional by a posttranslational modification such as phosphorylation or proteolytic cleavage. Phosphorylation, the addition to the protein of a phosphate group catalyzed by enzymes called kinases, may cause, for example, translocation of the protein from the cytosol into the nucleus. Dephosphorylation is the removal of a phosphate group catalyzed by enzymes called phosphatases. Phosphorylation and dephosphorylation of proteins are often important in the activation and deactivation of cell cycle proteins, signaling pathway proteins, and transcription factor proteins.1-6