Cell Cycle, Chromosome, Cystic Fibrosis, CFTR gene, Deletion, DNA, Epigenetics, Frameshift Mutation, Gene, Gene Therapy, Genetic Testing, Genotype, Inversion, mRNA, Mutation, Personalized Medicine, Phenotype, Precision Medicine, Protein, Translocation, Tumour Heterogeneity, Tumor Suppressor Gene
Currently, the majority of healthcare systems around the world employ a ‘one-size-fits-all’ approach when treating patients that have been diagnosed with the same disease, meaning that people with the same diagnosis will most likely be prescribed the same treatment . However, through the use of sophisticated molecular techniques that have been developed in recent decades, we now know that not only does each individual have their own unique set of genetic information (DNA), but that epigenetic factors can also affect the expression of the genes encoded by our DNA. Epigenetic factors can include a variety of different environmental conditions and behaviours such as diet, pollutants, and physical activity, which can impact our physical health and lead to differences in how diseases present as well as their progression. Furthermore, the unique genetics of each individual in combination with these environmental factors can mean that not every person that is diagnosed with the same condition should receive the same treatment.
A person’s DNA or genetic information (‘genes’) provides the instructions to the cells of their body for how to build the majority of the proteins that are required for our cells to survive, to carry out all of the essential functions of the body, and to maintain good health. The human genome is packaged into 23 pairs of long DNA molecules, which are called ‘chromosomes’ which corresponds to a total of 46 chromosomes. These chromosomes include 22 pairs of numbered autosomes and one pair of sex chromosomes. The sex chromosomes are involved in sex determination (determining the sex of an embryo). Within chromosomes, DNA is packaged into a double-stranded helix (‘double helix’), in which each strand consists of a string of individual building blocks called nucleotides. There are four types of nucleotides which are as follows: Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). A and C pair and bond with T and G respectively, to form the double-helix shape of DNA (Fig. 1). Gene expression and protein production are dependent on the processes of transcription and translation. During transcription, the instructions that are encoded by the DNA are transcribed into an mRNA molecule, using one of the DNA strands as a template. The mRNA molecule is a single-stranded molecule which is also built from the nucleotide bases G, C and A. However, in RNA, the Thymine (T) base is replaced by the base Uracil (U). Subsequently, during translation, the mRNA molecule is read in a triplet nature in order to synthesize proteins. Each set of three nucleotides (‘a codon’) corresponds to one of the twenty different building blocks of proteins, which are called amino acids. These amino acids are then arranged into polypeptides through the formation of peptide bonds between them. The polypeptides are then further modified by the cell to form mature proteins.
A) A single chromosome
B) Zoomed-in image of a segment of a chromosome, showing the DNA double-helix structure
C) Close-up of the DNA molecule, which is made up of two strands which form a double helix, with each strands consisting of a string of nucleotides. The nucleotide C pairs with G, while A pairs with T. This is known as ‘Chargaff’s Rule’. The base pairs are held together by weak hydrogen bonds.
D) An mRNA molecule is produced during transcription, a process in which the top strand of the DNA molecule is used as a template.
E) Transcription of the mRNA molecule is followed by translation of the nucleotide sequence to form a string of amino acids (polypeptide) which subsequently further modifications (post-translational modifications) to produce the final mature protein.
Occasionally, genes can be mistakenly altered due to a ‘gene mutation’, and this can result in an alteration of the instructions that are provided to cells for producing particular proteins. The term ‘wildtype’ is used to refer to individuals who carry the normal gene and the resulting protein in a population, whereas ‘mutant’ is used to describe cells or organisms that carry a particular mutation within their DNA sequence. Mutations can be induced by a wide range of environmental agents (mutagens), which can include ultraviolet (UV) radiation, chemicals such as benzene, metal ions, or reactive oxygen species, smoke, and other types of radiation.
There are several different types of genetic mutations that can occur. The first type involves a change in a single nucleotide in the DNA (‘point mutation’), which can be due to the substitution, insertion, or deletion of a single nucleotide. As DNA encodes proteins in a triplet nature, an insertion or deletion mutation may alter the reading frame of the codons. The reading frame refers to the three individual ways in which a mRNA sequence can be read as triplets (Fig. 2). A change in the reading frame can result in a frameshift, resulting in an incorrect or non-functional amino acid being incorporated into a protein. .
The above diagram shows how frameshift mutations occur. The deletion of nucleotides causes an alteration in reading frame. This changes the triplet of nucleotides that are translated and this can alter the amino acids that are incorporated into the forming protein.
Three different reading frames can arise from a single mRNA sequence, depending on the point at which translation begins. Adapting a different reading frame will change the triplet of bases that are read, and subsequently translate a different corresponding amino acid and protein. Alternatively, larger segments of chromosomes can be altered (‘chromosomal mutations’) through inversion, deletion, duplication, or translocation (Fig. 3). These mutations can result in changed amino acid sequences, loss of a gene or altered gene dosage . Gene dosage refers to the number of copies of a particular gene present in an individual and may also correspond to the total amount of protein that is expressed. With the exception of the sex chromosomes, each person normally carries two copies of a gene. However, altered gene dosage can result in both under- and over-expression of a particular gene.
Single chromosomes are represented in either blue or green, with particular regions of interest shown in yellow and orange. (A) In a deletion type of mutation, a region of the chromosome (here shown in yellow and orange) is lost from the chromosome, leading to the loss of all genes that are contained within that region. (B) An inversion type results when a region of the chromosome becomes inverted in its orientation, and is then reinserted into the chromosome. This results in the presence of an inverted DNA sequence at this particular site within the chromosome. (C) In a duplication type of mutation, a region of the chromosome and all genes contained within it, are duplicated. As a result, two copies of each of these genes are present on the chromosome instead of just one copy. (D) In a translocation mutation, a region of the chromosome (shown in yellow and orange) is lost from one chromosome (from the chromosome shown in blue) and becomes inserted into another chromosome (here shown in green).
In other words, both point and chromosomal mutations may create proteins that are non-functional, are completely absent, or that behave differently to the wildtype, which can often lead to disease. For example, all cancers are caused by DNA mutations, many of which occur within the DNA sequence of genes that normally regulate the cell cycle. The cell cycle controls the rate at which a cell grows and divides to produce two identical daughter cells. The most commonly mutated genes involved in cancers are ‘tumour suppressor genes’ such as p53 or TP53, whose role is to limit cell growth, . In fact, in approximately 50% of all cancers, the p53 gene is mutated, resulting in a non-functional or absent protein . Other diseases that can be caused by gene mutations include sickle cell anaemia, Huntington’s Disease, cystic fibrosis and Marfan Syndrome. Such mutations can either be inherited (passed down from parents to their children) or can occur randomly during a person´s lifetime (‘acquired mutations’). Healthcare is constantly changing due to the rapid pace of advances in medical research and the development of novel medical innovations and technologies. As a result, a greater emphasis is beginning to be placed on personalized medicine and a more personalized approach to healthcare as a whole. ‘Personalized Medicine’ and ‘Precision Medicine’ are two terms whose meanings overlap and are often used interchangeably (Fig. 4) . However, these two terms have different meanings, and it is important to understand how they differ. ‘Personalized Medicine’ often refers to a medical strategy for diagnosing and treating each patient according to their individual clinical characteristics . On the other hand, ‘Precision Medicine’ has been defined by the National Institute of Health (NIH) as “An approach to disease treatment and prevention that seeks to maximize effectiveness by taking into account individual variability in genes, environment, and lifestyle” . Precision Medicine is centered around creating treatments and therapeutics that are precise and based on the patient’s characteristics including age, gender, and medical history, as well as genetic factors and environmental exposure to mutagens.
Personalized medicine is a holistic approach to medicine attitude in which the treatment of a disease is based on the sum of a patients’ individual characteristics. Personalized medicine is a broad term, which encompasses precision medicine. Precision medicine involves taking into account a patient´s individual genetics when prescribing therapeutics and drugs and not solely basing this on their diseases diagnosis.
Precision medicine in Cystic Fibrosis
An example of the use of a personalized medicine approach to treating disease, is the development of drugs to treat cystic fibrosis (CF). Cystic fibrosis is an inherited monogenic (regulated by a single gene), recessive condition that is caused by mutations within the gene that encodes a protein known as the cystic fibrosis transmembrane conductance regulator (CFTR). The most prevalent CF-causing mutation, that is present in 85% of CF patients globally, is a deletion of the amino acid Phenylalanine at position 508 (F508del) . This results in an abnormally folded protein that is quickly degraded by cells. The CFTR gene is located on chromosome 7, between base pair 117,287,120 and base pair 117,715,971 (Fig. 5) . The mutation prevents the movement of chloride ions (Cl–) out of the cell through channels formed by the CFTR protein [4, 6 – 10]. The transfer of Cl– occurs through a tube in the centre of the protein and is important in regulating appropriate fluid levels within airways. The CFTR gene is widely expressed across tissues of the body and this means that cystic fibrosis can impact many different organs of the body including the lungs and pancreas . The most common symptom of CF involves the build-up of mucus in the airways, which leaves patients prone to acquiring repeated bacterial infections and developing pulmonary disease [4, 7 – 10]. Cystic fibrosis can also affect the gastrointestinal system, sweat glands, and the male reproductive tract . The build-up of mucus also occurs in the pancreas of cystic fibrosis patients, and this build up can prevent the release of digestive enzymes. The impaired release of pancreatic enzymes can result in malnutrition, the malabsorption of fat, and diabetes mellitus . Malabsorption involves difficulties in absorption of nutrients, such as fat, within the intestines. Therefore, reduced levels of digestive enzymes can prevent food being broken down sufficiently in order to be absorbed into the blood.
Chromosome 7 has a long (q) arm and a short (p) arm. The CFTR gene is located on the long arm, at position 31.2, and is therefore said to be located on Chromosome 7 position q31. 
Over 2000 different mutations have been identified in the CFTR gene. Different mutations can lead to different degrees of severity and a variety of symptoms and disease . It has been hypothesized that the high number of different mutations that can occur within this gene may be due to people who are heterozygous for CFTR mutations carrying a survival advantage, as they are resistant to Salmonella typhi infections (typhoid fever) . In other words, because patients with CFTR mutations carry a survival advantage with improved protection against typhoid fever, this has prevented the gene from dying out. Instead, the gene has remained in the gene pool of the human population, having time to acquire a great number of mutations. All CF-inducing mutations are classified into classes depending on their downstream effects on the CFTR protein (Table 1). The class of mutation can reflect the severity of disease that a patient might experience. In general, Class I – III mutations lead to a lack of CFTR protein function and severe phenotypes, whereas Class IV – VI mutations are associated with milder disease symptoms due to retaining a protein which has some, albeit reduced function. However, epigenetic factors, as well as social and economic class may additionally affect the severity of disease symptoms .
The respective modulator treatments for each class, with examples of modulators that have been developed, assessed in clinical trials, and FDA-approved are also shown.
Cystic fibrosis is a prime example of a genetic condition for which a precision medicine approach has been taken towards the development of novel treatments. Patients with different types of mutations in their CFTR gene will not all respond in the same way to a particular treatment, even if their mutations may belong to the same class. Therefore, several new therapeutic strategies are currently being developed to target a patient’s individual DNA mutation. These include gene therapy, protein therapy, and genome editing [4, 7 – 10]. Gene therapy and genome editing are molecular methods that both aim to alter an individual’s DNA as a treatment strategy for a disease. Alternatively, protein therapy is a technique that administers functioning proteins to replace non-functioning ones.
With regards to protein therapies, CFTR modulators are compounds that are able to restore CFTR gene expression and function . The five types of CFTR modulators, include potentiators, correctors, stabilizers, amplifiers and read-through agents. Each of these induces different types of effects on the CFTR protein . Potentiators are compounds that increase the probability of CFTR channels opening and of allowing chloride ions to translocate successfully [11, 14]. Activators increase CFTR protein activity by inducing an increase in the levels of molecules such as cAMP/cGMP, which in turn stimulate CFTR activity . Correctors increase the amount of CFTR protein that is directed to the cell surface [11, 14]. Some CFTR mutations can still allow the formation of proteins that are functional, albeit with reduced stability that leads to their premature degradation by the cell [11, 14]. Stabilizers can prevent this degradation by securing the protein at the cell surface . Read-through agents are compounds that avoid incomplete CFTR proteins from being translated by overriding premature stop codons [11, 14]. Lastly, amplifiers increase gene expression to increase production of the CFTR protein [11, 14].
Currently there are four CFTR modulators that have been approved by the US Food and Drug Administration (FDA) . Ivacaftor (Kalydeco), was the first of these drugs to become available on the market. Ivacaftor is a potentiator, with a role to improve channel gating and resultantly enhance chloride transport out of cells . However, Ivacaftor is specific for only particular Class III or IV CFTR mutations . For example, it is only approved for one Class IV mutation that involves an Arginine-to-Histidine amino acid substitution at position 117 (R117H) . The high specificity of Ivacaftor means that this drug is only appropriate for approximately 8% of CF patients .
Personalized medicine approaches can be informed by genetic testing, which is used to identify whether a patient may carry a gene mutation that makes them more susceptible to a particular disease. As genetic testing becomes faster, cheaper, and more accurate, scientists and researchers are able to collect vast amounts of data to determine how successful a therapy is likely to be against a particular mutation in patients. Personalized and precision medicine approaches both focus on providing a more specific treatment strategy for individuals for whom standard treatments are ineffective, by designing treatments based on an improved understanding of the disease mechanism. These approaches have many advantages over traditional medicine.
Advantages of Precision Medicine
Personalized and precision medicine can provide a wide range of advantages to traditional medicine. Benefits can include the following:
- Target the cause, rather than symptoms of diseases 
- Improve disease diagnosis techniques: Genetic testing allows certain diseases to be categorized based on their genetic basis rather than on the symptoms experienced . This allows for a more specific diagnosis.
- Identify high-risk individuals and prevent disease progression: An understanding of family history can indicate a person´s risk of being affected by a genetic disease . Genetic testing can also be used to identify mutations that increase susceptibility to particular diseases for an early diagnosis or to introduce preventative measures and treatments .
- More effective treatment: Some diseases, (as in the case of CF), can be caused by a range of different types of gene mutations. Therefore, not all patients with the same diagnosis respond to treatments in the same way. Understanding the genetic basis of a disease can aid doctors in identifying treatments that are more likely to be effective in specific patients, while also potentially helping to avoid deleterious side-effects .
- May lower costs: Selecting treatment options that are more likely to be effective can reduce healthcare costs as patients can potentially avoid being started on treatments that are likely to be ineffective .
While the revolutionary approach of personalized medicine provides us with the possibility of offering individualized healthcare to patients, there are many challenges that must be overcome before this approach can become more widespread in medical practice. These obstacles include the following:
- Intra-tumour heterogeneity: This describes a concept in which tumour cells are not genetically and epigenetically identical, creating various different cell population can within a tumour. This diversity of cells within tumours resultantly poses difficulties for precision medicine in treating cancers.
- High costs: Very few effective drugs currently exist for the vast majority of rare diseases and developing drugs that are specific to a patients’ genome and individual genetics is currently very costly. Furthermore, sequencing vast amounts of DNA routinely for all patients will require large financial investments in order to become widely accessible [16, 17].
- Developing technologies: With the growing implementation of precision medicine in therapeutics, healthcare systems require the availability of digital platforms that are able to efficiently and quickly analyse large amounts of medical data . While artificial intelligence is transforming precision medicine with the development of computer algorithms and pattern-recognition software, obstacles relating to “data storage, processing, exchange, and curation” remain .
- Social and moral: Issues such as maintaining patient confidentiality and privacy can arise due to the possibility of security breaches and databases being compromised . It is essential that researchers ensure that they have been given informed consent by patients and that patients are properly informed ahead of taking part in genetic testing for particular conditions. Furthermore, the moral and ethical issues associated with identifying disease susceptibility and for diseases for which there is no treatment currently available, and the mental burden of providing patients with this information must be given proper consideration by doctors and healthcare workers. [20, 21].
How does Personalize My Medicine´s work involve personalized and precision medicine?
Personalize My Medicine (PMM) is an organization that strives to provide personalized research for patients and doctors on all types of medical conditions, while giving a particular emphasis to rare diseases and cancer. PMM´s personalized research service identifies the latest information related to your condition on your behalf. This can include information about both existing treatments and therapies and those currently in development. We can also look into new innovations in medical research, ongoing clinical trials that you may be eligible for, other organizations or charities that provide support, and non-drug interventions and innovations for the management of your condition. These can include apps, wearables, devices and other types of innovation. In addition, we can search for information related to your condition, which can be in a wide range of formats including literature, video, and audio. With the deluge of advancements currently being made in the fields of Biology and Medicine, it is becoming increasingly difficult for healthcare workers and doctors to be aware of, and therefore to apply, new technologies and innovations. We aim to support doctors by keeping them informed of these innovations and to support patients by helping them to become more proactive and better informed about their own health and health conditions.
Please note that Personalize My Medicine (PMM) does not offer any medical advice. For more information about PMM´s services, please visit: personalizemymedicine.com.
- What is Personalized Medicine?
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- What are some of the challenges facing precision medicine and the Precision Medicine Initiative?
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