The sciences behind the rise of biotechnology
A collection of information and resources about some of the technologies helped build biotechnology into one of the most important tools in our lives today.
In 2016 the American Society of Clinical Oncology nominated immunotherapy as one of the most significant medical breakthroughs for cancer. How does cancer immunotherapy work? Cancer immunotherapy is designed to induce, enhance, or suppress the body’s immune system to combat tumours by using the body’s own properties, or cells grown in the laboratory. Such therapy takes two different forms. The first, known as active immunotherapy, aims to stimulate the immune system, and the second, known as passive immunotherapy, aims to strengthen the cancer patient's immune system. Immunotherapy is achieved through a number of different approaches. These range from re-activating a switch in immune cells that tumour cells turn off to prevent their own destruction, to tagging cancer cells for their elimination by immune cells, or genetically modifying a patient’s own T cells, the foot soldiers of the immune system, to directly destroy cancer cells. Immunotherapy developped on the back of knowledge accumulated from the early development of vaccines and serum therapies for infectious diseases.
CRISPR-Cas 9 is one of the newest tools for gene editing. Its development is paving the way to the insertion and removal of DNA within the genome on an unprecedented scale and at relatively small cost. The flexibility and efficiency of the technology promises to open up a new era in biotechnology and medicine.
DNA, or deoxyribonucleic acid, is a long stringy molecule that carries the genetic instructions necessary for all living organisms to grow, develop, function and reproduce. The discovery of its structure and function underpins many of the recent advances that have been made in understanding the molecular cause of disease and the formulation of new avenues of treatment.
DNA extraction is the process by which a cell is broken open to expose and extract its DNA. This is done by breaking down and emulsifying the fat and proteins that make up the cell's membrane through the addition of both salt and detergent solutions. Then the DNA is separated by by adding alcohol and centrifuging the resulting solution.
All living organisms have DNA polymerases. A single cell can contain several different polymerases. This includes complex ones which replicate DNA when the cell divides, and simpler ones which help in the day-to-day repair and maintenance of DNA. While each of the different kinds of polymerase differ in size and shape, they all share a common structural framework. The polymerase does not create a novel DNA strand from scratch. Instead it synthesizes a new strand of DNA based on the template of two existing DNA strands. This it does with the help of another enzyme, called helicase, which unwinds the double helix structure of the DNA molecule into two single DNA strands. In addition to a template strand, polymerases require a primer to function. This is a fragment of nucleic acid that serves as the starting point for DNA replication. The primer, often a short strand of RNA, needs to be complementary to the template. DNA polymerase works by sliding along the single strand template of DNA reading its nucleotide bases as it goes along and inserting new complementary nucleotides into the primer so as to make a sequence complementary to the template. DNA polymerase is thought to be able to replicate 749 nucleotides per second. By the end of the replication process two new DNA molecules will have been made, each identical to the other and to the original parent molecule. Such accurate replication is helped by the fact that DNA polymerase has an inbuilt capacity to detect and correct any mistakes it makes in the replication process.
DNA sequencing is a technique that is used to unravel the order of the four nucleotide bases that comprise a DNA strand. Several methods have been developed for this process. These consist of four key steps. In the first instance DNA is removed from the cell. This can be done either mechanically or chemically. The second phase involves breaking up the DNA and inserting its pieces into vectors, cells that indefinitely self-replicate, for cloning. In the third phase the DNA clones are placed with a dye-labelled primer (a short stretch of DNA that promotes replication) into a thermal cycler, a machine which automatically raises and lowers the temperature to catalyse replication. The final phase consists of electrophoresis, whereby the DNA segments are placed in a gel and subjected to an electrical current which moves them. Originally the gel was placed on a slab, but today it is inserted into a very thin glass tube known as a capillary. When subjected to an electrical current the smaller nucleotides in the DNA move faster than the larger ones. Electrophoresis therefore helps sort out the DNA fragments by their size. The different nucleotide bases in the DNA fragments are identified by their dyes which are activated when they pass through a laser beam. All the information is fed into a computer and the DNA sequence displayed on a screen for analysis.
Epigenetics is one of the hottest research topics in biomedical science today. It seeks to understand how genes are switched on and off. Controlled by different chemical tags that latch on to DNA and its associated proteins, this process helps explain how cells can interpret the genetic code in different ways. Such chemical modifications are key to regulating gene expression, the process that dictates the production of proteins, the workers of the cell. Epigenetic changes underpin normal cellular development and help differentiate one type of cell from another. Any disruption to this process can cause disease. For this reason epigenetics now lies at the heart of personalised medicine.
Immune checkpoint inhibitors
Checkpoint inhibitors are drugs that help release the brakes cancer cells put on the immune system to prevent their destruction. This is usually achieved with an antibody which is used to block certain proteins carried on the surface of cancer cells that prevent their recognition by the immune system and hence their destruction. In 2015 Jimmy Carter, the former president of the US, announced he was free of melanoma that had spread to his liver and brain. He had improved following treatment with an immune checkpoint inhibitor drug. How do checkpoint inhibitors work? Such therapy is designed to block the biological pathways cancer cells use to disguise themselves from the immune system and prevent their destruction. Immune checkpoint inhibitors are now considered one of the most promising avenues for the treatment of advanced cancer. Their development grew out of research to understand the regulation of immune responses.
Monoclonal antibodies are made from natural antibodies made by the body to fight foreign invaders. Their production involves several steps. In the first instance a laboratory animal is injected with a desired target to stimulate their immune system. Following this, antibody producing cells, B lymphocytes, are harvested from the animal's spleen and fused with an immortal myeloma cell line to create hybrid cells, or hybridomas. The hybrid cells are then screened to find those that secrete antibodies with the desired specificity for a particular target. Once identified the hybrid cell is cloned to establish a hybridoma colony. This colony is then maintained in a culture medium to provide a continual supply of monoclonal antibodies. Each of the antibodies secreted by the hybrid cell is identical (monoclonal) and has the capacity to bind to a specific receptor found on the surface of a cell.
The p53 gene codes for a protein that helps regulate cell division and growth and is vital to the suppression of tumours and cancer. More than half of all cancers are linked to a deficient p53, usually caused by a genetic mutation. Due to its importance in regulating the cell cycle and inhibition of tumours, p53 has become an important target in both the diagnosis and therapeutic management of cancer.
PCR (polymerase chain reaction) denotes a process that is used to replicate DNA. The first step in PCR, known as denaturing, involves heating a DNA sample to separate its two strands. Once separated the two strands are used as templates to synthesise two new DNA strands. This is done with the help of an enzyme called Taq polymerase. Once made, the newly synthesised molecules are used as templates to generate two more copies of DNA. The two basic steps involved in PCR, denaturing and synthesis, are repeated multiple times with the help of a thermocycler, a machine that automatically alters the temperature every few minutes. Each time the process of denaturing and synthesis occurs, the number of DNA molecules doubles. This makes it possible to generate one billion exact copies of an original target DNA within a couple of hours.
Phage display is a laboratory platform that facilitates the study of protein to protein, protein to peptide, and protein to DNA interactions. The technique relies on the generation of a library of millions of bacteriophages that have been genetically engineered to display different peptides or proteins on their surface. This is achieved by inserting a gene encoding a protein of interest into the phage's protein shell, which sets up a direct physical link between DNA sequences and their encoding proteins. The aim of the modification is to generate a molecule that can mimic a natural modulator within the cellular process. Several types of phages are used for the purpose of phage display. Filamentous bacteriophages are the most popular.
The genetically modified phages are assembled into a library for use as a platform to screen proteins, peptides and DNA sequences. Screening is performed by the addition of the phage-display library to the wells of a microtiter plate that contains immobilised target proteins or DNA sequences. The plate is then incubated for some time to allow the phages to bind with the target of interest and then washed so as to flush away any non-binding phages. Any phages that remain attached to the wells are then removed and inserted into other bacteria for replication. The cycle is repeated until only phage-displaying proteins highly specific for the target remain. Once the whole process is completed, the gene coding for the specific protein is isolated and purified from the phage so that it can be used for different applications.
A plasmid is a strand or loop of DNA that is typically found in bacteria as well as archae (single-cell organisms) and eukarya (organisms of complex cell structure). Plasmids carry only a few genes and exist independently of chromosomes, the primary structures that contain DNA in cells. Able to self-replicate, plasmids can be picked up from the environment and transferred between bacteria. Plasmids are used by their host organism to cope with stress-related conditions. Many plasmids, for example, carry genes that code for the production of enzymes to inactivate antibiotics or poisons. Others contain genes that help a host organism digest unusual substances or kill other types of bacteria. Several characteristics of plasmids make them easy to modify genetically. Firstly, they have relatively small DNA sequences, between 1,000 and 20,000 DNA base pairs. Secondly, they are easy to cut open, without falling apart, and snap back into shape. This makes it easy to insert new DNA into plasmids. Once a new DNA is inserted, the modified plasmid can be grown in bacteria for self-replication to make endless copies.
Recombinant DNA is an artificial form of DNA that cannot be found in natural organisms. It is made in the laboratory by joining together genes taken from different sources. This is done by selecting and cutting out a gene at a specific point on a strand of DNA using restriction enzymes which act as molecular scissors. The gene is chosen on the basis of its ability to code for or alter different traits in another organism. It is inserted into a circular piece of bacterial DNA, called a plasmid, or a bacterial virus, called a phage, and then put into a host organism, such as the bacteria Escherichia-Coli, for replication by its cell machinery.
Restriction enzymes, also called restriction endonucleases, are DNA cutting enzymes that bacteria produce as part of their defence mechanism to prevent their destruction by invading viruses, known as bacteriophages. Such enzymes splice DNA into small fragments at specific sites in a sequence. Since the early 1970s restriction enzymes have become one of the most important tools for cutting and pasting DNA segments for different biotechnology purposes. They are particularly important for making recombinant DNA.
Stem cells are some of the body's master cells which have the ability to grow into any one of the body's more than 200 cell types. Such cells contribute to the body's ability to renew and repair its tissues. There are different types of stem cells. The first, known as embryonic stem cells, are sourced from embryos formed during the blastocyst phase of embryonic development, which is four or five days after fertilisation. They are usually taken from human embryos left-over from in vitro fertilisation. The second, known as adult or mesenchymal stem cells, are found in different types of tissue, including bone marrow, blood, blood vessels, skeletal muscles, skin and the liver. Stem cells can also be sourced from umbilical cord blood.
Transgenic animals are animals (most commonly mice) that have had a foreign gene deliberately inserted into their genome. Such animals are most commonly created by the micro-injection of DNA into the pronuclei of a fertilised egg which is subsequently implanted into the oviduct of a pseudopregnant surrogate mother. This results in the recipient animal giving birth to genetically modified offspring. The progeny are then bred with other transgenic offspring to establish a transgenic line. Transgenic animals can also be created by inserting DNA into embryonic stem cells which are then micro-injected into an embryo which has developed for five or six days after fertilisation, or infecting an embryo with viruses that carry a DNA of interest. This final method is commonly used to manipulate a single gene, in most cases this involves removing or 'knocking out' a target gene. The end result is what is known as a ‘knockout’ animal.