A Review Article on Genes and Proteins

In medicine, a biomarker can be referred to anything that can be used as an indicator of a particular disease state or some other biological state of an organism. Biomarkers can be genes, proteins, small molecules, or hormones. Commonly, for the purposes of diagnostics, biomarkers are broadly divided in two groups – one group encompasses genetic markers such as DNA or RNA; and the other – proteins, hormones or small molecules. In essence, DNA testing examines DNA molecule itself, and protein testing examines changes in protein concentration or alterations in its structure. To understand the difference between these two groups, it is important to define genes, proteins and how proteins are synthesized based on the genetic code.
A gene is a unit of heredity in an organism. It is normally a strand of DNA that codes for a type of protein or for an RNA chain in the organism. All proteins and functional RNA chains are specified by genes. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring.
Proteins (also known as polypeptides) are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code (1).
In all organisms, there are two major steps separating a protein-coding gene from its protein: First, the DNA on which the gene resides must be transcribed from DNA to messenger RNA (mRNA); and, second, it must be translated from mRNA to protein. The process of producing a biologically functional molecule of either RNA or protein is called gene expression, and the resulting molecule itself is called a gene product.
Transcription is a genetic process that produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed. The DNA strand whose sequence matches that of the RNA is known as the coding strand and the strand from which the RNA was synthesized is the template strand.
Translation is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein. Translation is carried out by ribosomes, large complexes of RNA and protein responsible for carrying out the chemical reactions to add new amino acids to a growing polypeptide chain by the formation of peptide bonds.
As mentioned above, gene tests (also called DNA-based tests) involve direct examination of the DNA molecule itself. Genetic testing allows the genetic diagnosis of vulnerabilities to inherited diseases, and can also be used to determine a child's paternity (genetic father) or a person's ancestry. Normally, every person carries two copies of every gene, one inherited from their mother, one inherited from their father. In addition to studying chromosomes to the level of individual genes, genetic testing in a broader sense includes biochemical tests for the possible presence of genetic diseases, or mutant forms of genes associated with increased risk of developing genetic disorders. Most of the time, testing is used to find changes that are associated with inherited disorders. The results of a genetic test can confirm or rule out a suspected genetic condition or help determine a person's chance of developing or passing on a genetic disorder.
Diagnostic DNA testing is used to diagnose or rule out a specific genetic or chromosomal condition. In many cases, genetic testing is used to confirm a diagnosis when a particular condition is suspected based on physical mutations and symptoms. Diagnostic testing can be performed at any time during a person's life, but is not available for all genes or all genetic conditions. The results of a diagnostic test can influence a person's choices about health care and the management of the disease.
Predictive and presymptomatic types of DNA testing are used to detect gene mutations associated with disorders that appear after birth, often later in life. These tests can be helpful to people who have a family member with a genetic disorder, but who have no features of the disorder themselves at the time of testing. Predictive testing can identify mutations that increase a person's chances of developing disorders with a genetic basis.
The results of genetic tests are not always straightforward, which often makes them challenging to interpret and explain. When interpreting test results, healthcare professionals consider a person’s medical history, family history, and the type of genetic test that was done.
A positive test result means that the laboratory found a change in a particular gene, or chromosome of interest. Depending on the purpose of the test, this result may confirm a diagnosis, indicate that a person is a carrier of a particular genetic mutation, identify an increased risk of developing a disease in the future, or suggest a need for further testing. It is important to note that a positive result of a predictive or presymptomatic genetic test usually cannot establish the exact risk of developing a disorder. Also, health professionals typically cannot use a positive test result to predict the course or severity of a condition.
A negative test result means that the laboratory did not find a dangerous copy of the gene, chromosome, or protein under consideration. This result can indicate that a person is not affected by a particular disorder, is not a carrier of a specific genetic mutation, or does not have an increased risk of developing a certain disease. It is possible, however, that the test missed a disease-causing genetic alteration because many tests cannot detect all genetic changes that can cause a particular disorder. Further testing may be required to confirm a negative result.
In some cases, a negative result might not give any useful information. This type of result is called uninformative. Uninformative test results sometimes occur because everyone has common, natural variations in their DNA, called polymorphisms, that do not affect health. If a genetic test finds a change in DNA that has not been associated with a disorder in other people, it can be difficult to tell whether it is a natural polymorphism or a disease-causing mutation. An uninformative result cannot confirm or rule out a specific diagnosis, and it cannot indicate whether a person has an increased risk of developing a disorder. In some cases, testing other affected and unaffected family members can help clarify this type of result.
Testing for protein biomarkers is generally more straightforward – a change in the quantity of a certain biomarker normally signals of the presence of a disease or a pathological condition. For instance, it is widely known that C-reactive protein (CRP) is a marker for inflammation; or that matrix metalloproteases are markers for cancer (2,3).
Other examples include pregnancy tests or immunohistochemical tests performed by pathologists to diagnose cancer.
Modern pregnancy tests look for chemical markers associated with pregnancy. These markers are found in urine and blood, and pregnancy tests require sampling one of these substances. The most commonly used marker is human chorionic gonadotropin (hCG), that was discovered in 1930 to be produced by the trophoblast cells of the fertilised ovum (blastocyst). The presence of this marker normally indicates that a woman is pregnant.
Immunohistochemistry (IHC) is also a straightforward process of localizing antigens (proteins) in cells of a tissue section using the principle of antibodies binding specifically to antigens in biological tissues (4). It takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue. IHC is a very good detection technique and has the advantage of being able to show exactly where a given protein is located within the tissue examined. Immunohistochemical staining is widely used in diagnostic surgical pathology for typing tumors (e.g. immunostaining for e-cadherin to differentiate between DCIS (ductal carcinoma in situ: stains positive) and LCIS (lobular carcinoma in situ: does not stain positive) (5); or cytokeratins for identification of carcinomas (6).

References:
1. Ridley, M. (2006). Genome. New York, NY: Harper Perennial.
2. Eiji Sunami, Nelson Tsuno, Takuya Osada, Shinsuke Saito, Joji Kitayama, Shigeru Tomozawa, Takashi Tsuruo, Yoichi Shibata, Tetsuichiro Muto, Hirokazu Nagawa:”MMP-1 is a Prognostic Marker for Hematogenous Metastasis of Colorectal Cancer”, The Oncologist, Vol. 5, No. 2, 108-114, April 2000
3. Pia Vihinen, Veli-Matti Kähäri: “Matrix metalloproteinases in cancer: Prognostic markers and therapeutic targets”, International Journal of Cancer, Volume 99 Issue 2, Pages 157 – 166, 12 Mar 2002.
4. Ramos-Vara, JA (2005). "Technical Aspects of Immunohistochemistry". Vet Pathol 42 (4): 405–426
5. O'Malley F and Pinder S, Breast Pathology, 1st. Ed. Elsevier 2006.
6. Leader M, Patel J, Makin C, Henry K (December 1986). "An analysis of the sensitivity and specificity of the cytokeratin marker CAM 5.2 for epithelial tumours. Results of a study of 203 sarcomas, 50 carcinomas and 28 malignant melanomas". Histopathology 10 (12): 1315–24.