Case Study Conclusion: Pharmacogenomics
Arya asked their doctor about Pharmacogenomics. The doctor explains to Arya that Pharmacogenomics is the tailoring of drug treatments to people’s genetic makeup, a form of ‘personalized medicine’.
The picture above shows a beta cell of the pancreas. As the blood glucose rises, it enters into the cell via GLUT 2 channel. After entering into the cell, it causes the production of ATP that closes the potassium pump. As potassium stops exiting the cell, it causes calcium channel to open and, finally, that causes insulin release from the cells. This process is even more complicated as many enzymes and proteins are skipped in this brief description of the pathway. The sulfonylurea-based drugs force the closing of a potassium pump by attaching to it. This causes the release of insulin by skipping many steps. Because many enzymes and other proteins are involved in this complicated process, people respond differently to medicines. Most respond well and their health improves. Some do not gain any benefits from the treatment, and a minority suffer from side effects. After you take a drug, it is processed (metabolized) by your body. How the drug is processed and how you respond to it is determined, in part, by your genes. Understanding how different genetics affect and how a drug is processed can help doctors to more accurately determine which drug and which dose is best for individual patients. In this chapter, you learned what genome is and how to recognize genes in the genome. In pharmacogenomics, scientists look at the genome of an individual to identify the genetic factors that influence his or her response to a drug. By finding these genes, medical researchers hope to develop genetic tests that will predict how patients will respond to a drug. This is personalized medicine.
The reason people vary in their responses to drug treatments lies in the genetic differences, or variation, between them. Following the Human Genome Project, research has focused on comparing human genomes to understand genetic variation and work out which genetic variants are important in health and in the way we respond to drugs. We also learned in this chapter that two types of variation are common in the human genome: 1) Single nucleotide polymorphisms (SNPs): changes in single nucleotide bases (A, C, G, and T). This was the case in Arya’s physical response to the sulfonylurea. 2) Structural variation: changes affecting chunks of DNA that can consequently alter the structure of the entire chromosome. Structural variation can happen in a number of ways, for example, Copy number variation (CNV): when there is an increase or decrease in the amount of DNA. This can be due to: deletion, where an entire block of DNA is missing; insertion, where a block of DNA is added in duplication; or where there are additional copies of a section of DNA. Inversion: when chromosome breaks in two places and the resulting piece of DNA is reversed and reinserted back into the chromosome (the opposite way round). Translocation: when genetic material is exchanged between two different chromosomes. SNPs are like changing a single letter in the metaphorical 'recipe book of life', while structural variation is the equivalent of whole paragraphs or pages being lost or repeated. Scientists have been aware of SNPs for a long time, but the extent of structural variation was only revealed when it was possible to sequence and compare many genomes. The structural variation appears to be quite common, affecting around 12 percent of the genome. It has been found to cause a variety of genetic conditions.
Finding disease variants
Humans share around 99.5 percent of their genomes. The 0.5 percent that differs between each of us affects our susceptibility to disease and response to drugs. Although this doesn’t sound like a lot, it still means that there are millions of differences between the DNA of two individuals. For example, because SNPs are common in the genome, it is difficult to work out which single letter changes cause disease and which are passengers that have just come along for the ride and have no effect on health.
So how is it possible to know which genetic variants cause disease and which are passengers?
The way scientists look at disease variants is to compare the genetic makeup of a large number of people who have a specific disease with those who do not. This allows scientists to look for genetic variants that are more common in people with a disease compared to people without the disease. For example, if a particular genetic variant is present in 80 percent of patients with the disease but only 20 percent of the healthy population it suggests that this variant is increasing the risk of that disease. However, looking for a disease that is caused by variants in a single gene is the simplest example. There are many complex diseases where variants in many different genes might be involved. As well as the transcriptional and translational regulation of some enzyme production may vary due to the genetic variation in the enhancer and repressors of a gene. So, for this type of comparison to be effective very large groups of people need to be studied, usually in the tens of thousands, to find the variants that have subtle effects on disease risk. Researchers also try to pick individuals with similar phenotypes, in both the diseased and healthy groups, so that the disease genes are easier to identify and study.
Challenges of pharmacogenomics
Although pharmacogenomics is likely to be an important part of future medical care, there are many obstacles to overcome before it becomes routine. It is relatively rare for a particular drug response to be affected by a single genetic variant. A particular genetic variant may increase the likelihood of an adverse reaction but it will not guarantee it.
As a result, some people with the variant may not experience an adverse reaction to a drug. Similarly, if an individual doesn’t have the gene variant, it doesn’t guarantee they won’t experience an adverse reaction. Often, a large number of interacting genetic and environmental factors may influence the response to a drug.
Even when associations between a genetic variant and a drug response have been clearly demonstrated, suitable tests still have to be developed and proven to be effective in clinical trials. A test that has succeeded in a clinical trial still has to be shown to be useful and cost-effective in a healthcare setting. Regulatory agencies will have to consider how they assess and license pharmacogenetic products. Health services will have to adjust to new ways of deciding the best drug to give to an individual.
The behavior of individual doctors will need to change. A lot of side effects are due to patients not taking their drugs as prescribed or to doctors prescribing the wrong dose. Some examples of pharmacogenomics that work effectively, for example, abacavir for HIV, show that these challenges can be overcome. However, in most cases, implementing the findings from pharmacogenomics is likely to be a complicated process.
- Determining that DNA is the genetic material was an important milestone in biology.
- In the 1920s, Griffith showed that something in virulent bacteria could be transferred to nonvirulent bacteria and make them virulent as well.
- In the 1940s, Avery and colleagues showed that the "something" Griffith found was DNA and not protein. This result was confirmed by Hershey and Chase, who demonstrated that viruses insert DNA into bacterial cells.
- In the 1950s, Chargaff showed that in DNA, the concentration of adenine is always the same as the concentration of thymine, and the concentration of guanine is always the same as the concentration of cytosine. These observations came to be known as Chargaff's rules.
- In the 1950s, James Watson and Francis Crick, building on the prior X-ray research of Rosalind Franklin and others, discovered the double-helix structure of the DNA molecule.
- Knowledge of DNA's structure helped scientists understand how DNA replicates, which must occur before cell division. DNA replication is semi-conservative because each daughter molecule contains one strand from the parent molecule and one new strand that is complementary to it.
- Genes that are located on the same chromosome are called linked genes. Linkage explains why certain characteristics are frequently inherited together.
- The central dogma of molecular biology can be summed up as DNA → RNA → Protein. This means that the genetic instructions encoded in DNA are transcribed to RNA, and then from RNA, they are translated into a protein.
- RNA is a nucleic acid. Unlike DNA, RNA consists of just one polynucleotide chain instead of two, contains the base uracil instead of thymine, and contains the sugar ribose instead of deoxyribose.
- The main function of RNA is to help make proteins. There are three main types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
- According to the RNA world hypothesis, RNA was the first type of biochemical molecule to evolve, predating both DNA and proteins.
- The genetic code was cracked in the 1960s by Marshall Nirenberg. It consists of the sequence of nitrogen bases in a polynucleotide chain of DNA or RNA. The four bases make up the "letters" of the code. The letters are combined in groups of three to form code "words," or codons, each of which encodes for one amino acid or a start or stop signal.
- AUG is the start codon, and it establishes the reading frame of the code. After the start codon, the next three bases are read as the second codon, and so on until a stop codon is reached.
- The genetic code is universal, unambiguous, and redundant.
- Protein synthesis is the process in which cells make proteins. It occurs in two stages: transcription and translation
- Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It includes the steps of initiation, elongation, and termination. After the mRNA is processed, it carries the instructions to a ribosome in the cytoplasm.
- Translation occurs at the ribosome, which consists of rRNA and proteins. In translation, the instructions in mRNA are read, and tRNA brings the correct sequence of amino acids to the ribosome. Then rRNA helps bonds form between the amino acids, producing a polypeptide chain.
- After a polypeptide chain is synthesized, it may undergo additional processing to form the finished protein.
- Mutations are random changes in the sequence of bases in DNA. They are the ultimate source of all new genetic variation in any species
- Mutations may happen spontaneously during DNA replication or transcription. Other mutations are caused by environmental factors called mutagens.
- Germline mutations occur in gametes and may be passed on to offspring. Somatic mutations occur in other cells than gametes and cannot be passed on to offspring.
- Chromosomal alterations are mutations that change chromosome structure or number and usually affect the organism in multiple ways. Down syndrome (trisomy 21) is an example of a chromosomal alteration.
- Point mutations are changes in a single nucleotide. The effects of point mutations depend on how they change the genetic code and may range from no effects to very serious effects.
- Frameshift mutations change the reading frame of the genetic code and are likely to have a drastic effect on the encoded protein.
- Many mutations are neutral and have no effects on the organism in which they occur. Some mutations are beneficial and improve fitness, while others are harmful and decrease fitness.
- Using a gene to make a protein is called gene expression. Gene expression is regulated to ensure that the correct proteins are made when and where they are needed. Regulation may occur at any stage of protein synthesis or processing.
- The regulation of transcription is controlled by regulatory proteins that bind to regions of DNA called regulatory elements, which are usually located near promoters. Most regulatory proteins are either activators that promote transcription or repressors that impede transcription.
- The regulation of gene expression is extremely important during the early development of an organism. Homeobox genes, which encode for chains of amino acids called homeodomains, are important genes that regulate development.
- Some types of cancer occur because of mutations in genes that control the cell cycle. Cancer-causing mutations most often occur in two types of regulatory genes, called tumor-suppressor genes and proto-oncogenes.
- Biotechnology is the use of technology to change the genetic makeup of living things for human purposes.
- Biotechnology methods include gene cloning and the polymerase chain reaction. Gene cloning is the process of isolating and making copies of a DNA segment such as a gene. The polymerase chain reaction makes many copies of a gene or other DNA segment.
- Biotechnology can be used to transform bacteria so they are able to make human proteins, such as insulin. It can also be used to create transgenic crops, such as crops that yield more food or resist insect pests.
- Biotechnology has raised a number of ethical, legal, and social issues including health, environmental, and privacy concerns.
- The human genome refers to all of the DNA of the human species. It consists of more than 3.3 billion base pairs divided into 20,500 genes on 23 pairs of chromosomes.
- The Human Genome Project (HGP) was a multi-billion dollar international research project that began in 1990. By 2003, it had sequenced and mapped the location of all of the DNA base pairs in the human genome. It published the results as a human reference genome that is available to anyone on the Internet.
- The sequencing of the human genome is helping researchers better understand cancer and genetic diseases. It is also helping them tailor medications to individual patients, which is the focus of the new field of pharmacogenomics. In addition, it is helping researchers better understand human evolution.
- Put the following units in order from the smallest to the largest:
- nitrogen base
- Put the following processes in the correct order of how a protein is produced, from earliest to latest:
- tRNA binding to mRNA
- traveling of mRNA out of the nucleus
- folding of the polypeptide
- What are the differences between a sequence of DNA and the sequence of mature mRNA that it produces?
- Scientists sometimes sequence DNA that they “reverse transcribe” from the mRNA in an organism’s cells, which is called complementary DNA (cDNA). Why do you think this technique might be particularly useful for understanding an organism’s proteins versus sequencing the whole genome (i.e. nuclear DNA) of the organism?
- What are proteins are made in the cytoplasm on small organelles called?
- What might happen if codons encoded for more than one amino acid?
- Explain why a human gene can be inserted into bacteria and can still produce the correct human protein, despite being in a very different organism.
- True or False. All of your genes are expressed by all the cells of your body.
- What does The central dogma of molecular biology describe?
The following videos explain Pharmacogenomics in a very simple way.