Cystic fibrosis: how could gene and cell therapy help?
Cystic fibrosis is one of the most common genetic diseases. It is associated with chronic lung disease, as well as damage to other organs. It arises from mutations in a single gene: the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Some forms of CF can be treated using modulator therapies; however, because the disease can be caused by different mutations, these therapies are not suitable for all forms of the disease. Can gene and cell therapy techniques help us to understand and treat CF more effectively?
What do we know?
Cystic fibrosis is one of the most common genetic diseases, with a frequency of between 1 in 3000 to 6000 in European populations. It arises from mutations in a single gene: the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Researchers have identified more than 2,000 CF-causing mutations in this CFTR gene. The CFTR gene makes a protein that functions as a channel in the cell membrane, allowing the movement of salt and water into and out of the cell. The inability to regulate this transport of salt and water into and out of the cells lining our airways results in chronic lung disease and reduced survival in people with CF. Importantly, different mutations impact on the severity of disease. This also means that therapies exist that benefit some patients but not others based on the mutation type. Modulator therapies, which target the faulty membrane channel, have had a significant impact on the majority of CF patients. However, approximately 15% have mutation types that means they are unable to benefit from these and require new treatments.
What are researchers working on?
Researchers are working on a range of therapeutic approaches that address the underlying cause of the disease and could potentially treat patients with any type of mutation. This includes gene therapy and gene editing options that seek to either:
- deliver a working copy of the gene that can generate functional CFTR protein or
- change the existing gene with a mutation back to the correct sequence through editing.
A number of these approaches have already been tested in clinical trials, and others are currently being evaluated in ongoing clinical trials.
What are the challenges?
One of the biggest challenges is developing vectors that can deliver the therapy to enough of the affected cells in the lungs. A number of approaches currently in development use modified viruses or types of nanoparticles that can carry genetic material such as DNA or mRNA into the cells. The cells that require therapy have a limited lifespan and many of the proposed approaches have limited duration. Depending on the vector, the effect can last from weeks to months. As a result, the therapy would need to be applied repeatedly. This presents another challenge: the immune system may develop antibodies to the viral vector following the first treatment. If the therapy is readministered, the immune response to the viral vector may render it ineffective. Safety is also a challenge in the context of vectors that integrate into host DNA and have the potential to cause mutations (insertional mutagenesis).
Introduction to Cystic Fibrosis
The lining of the airways in the lungs is made up of different types of epithelial cells. Many of these cells contribute to maintaining the composition of the thin layer of sticky fluid (mucus) that covers the airways. This mucus helps protect the lung from potentially infectious micro-organisms in the inhaled air, such as bacteria and viruses. It also lubricates the lungs, protecting the tissue from damage.
Cystic fibrosis (CF) is characterised by abnormal functioning of these epithelial secretory cells. At a cellular level, the mechanism for transporting water and salts into and out of the cells does not work. This affects the thickness of the mucus produced by the pulmonary (lung) epithelium. This abnormal mucus cannot adequately keep bacteria under control, leading to persistent infection. The most serious symptom, that has the biggest impact on quality of life, is the thick mucus secretions that build up in the lungs leading to infections and lung damage and result in a progressive decrease in lung function leading to breathing difficulties and periods of acute lung infection that often require hospitalisation.
The lungs are not the only organ system affected by CF. At a cellular level, CF is characterised by abnormal transport of ions such as salts in the epithelial secretory cells of many organs. This means that the cells cannot move water in and out the way healthy cells do. One consequence of this is that people with CF have unusually high amounts of salt within their sweat; this has been used as a diagnostic tool for many years. Additionally, the thickness of the mucus secretions in the gastrointestinal tract, reproductive tract, liver, and pancreas are all affected.
- Mutations in CFTR affect the production and availability of digestive enzymes. The thick mucus in the digestive tract may prevent digestive enzymes (produced in the pancreas) from reaching the gut. The build-up of these enzymes in the pancreas can cause inflammation, which damages the pancreas. People with CF may have to take supplements at mealtimes to replace these enzymes and aid digestion. The damage to the pancreas may also cause CF-related diabetes (CFRD), seen in approximately one-third of people with CF.
- 10-15% of newborns with CF suffer from severe intestinal blockage, termed Meconium ileus (MI). These infants cannot have normal bowel movements until the blockage is resolved. This causes issues with feeding, swelling (distension) of the abdomen, and may cause inflammation of the surrounding tissues. MI may require surgery to remove the blockage.
The Cystic Fibrosis Trust provides more detail about the effects of CF on the body at the link below. (This information is available in English only.)
CF frequency varies with ethnicity and is significantly more common in Caucasian populations. In the USA for example, CF occurs in 1 in 2,500 to 3,500 white newborns, similar to that observed in European populations. It is less common in other ethnic groups, estimated to affect about 1 in 4,000 – 10,000 Latin Americans, 1 in 17,000 African Americans and 1 in 31,000 Asian Americans.
Current treatments
There have been significant improvements in therapy for CF over the years. Historically, treatment has focused on controlling symptoms, rather than on treating the underlying cause of the disease. This changed with the recent development of modulator therapies – therapies which target the fault membrane channel. With these therapeutic advances, the majority of people with CF have a greatly improved quality of life and are living longer than ever before.
Current treatments include the following:
- Physiotherapy: This helps loosen and clear the thick mucus in the lungs.
- High-calorie diets and other nutritional interventions: These help to maintain a healthy weight. This can be challenging for people with CF due to the lack of the digestive enzymes that break down fats, proteins and carbohydrates and release the nutrients that the body needs.
- Pancreatic Enzyme Supplements: These replace the missing enzymes that are not being supplied to the gut, due to obstruction in the pancreatic ducts.
- Inhaled/IV antibiotics: These are used primarily to prevent or control respiratory infections. Advances in antibiotic therapy for people with CF has been the main reason for the significant improvements in quality of life and survival over the last few decades. These can be administered either by inhalation or intravenously, depending on the individual circumstances.
- Inhaled recombinant DNAse. These help break down the thick sticky mucus in the lungs. The unusual stickiness of mucus in people with CF is partly due to a high concentration of DNA, which is released from certain immune cells (neutrophils) as they disintegrate. Using DNAse to break down these DNA molecules decreases the stickiness and viscosity of the mucus.
- Modulator therapies: All of the treatments listed above can only treat symptoms of CF. CFTR modulator drugs, in contrast, tackle the underlying cause of the disease by helping the faulty CFTR protein work effectively. These drugs have been transformative for 80-90% of patients, leading to long term improvement in lung function, exacerbation frequency, weight and quality of life. However, it is estimated that 10-15% of people with CF worldwide are not able to benefit from these ground-breaking therapies due to the type of mutation they carry. These drugs are also very costly, meaning that access through centralised healthcare systems is highly variable.
You can find more detailed information about the treatments currently available for CF at the link below. (This page is available in English only.)
How might gene and cell therapies help?
Gene therapies
Genetic therapies have the potential to help people with CF by:
- adding a working copy of the gene to cells to make up for the faulty gene through conventional gene therapy
- delivering mRNA that can act as a CFTR-protein making template
- directly changing the error in the faulty gene back to the correct sequence, through gene editing.
The advantage of gene therapy is that it can benefit all people with CF no matter what their mutation type might be. If the correct gene can be delivered in enough cells then this can restore the correct movement of salt and water and prevent the accumulation of the thick sticky mucus. The main focus of this type of research has been the cells lining the lung. This is where the effects of the disease have the biggest impact of quality of life and survival.
Most gene therapy approaches to treat CF involve delivering a healthy copy of the CFTR gene directly to the affected cells. There are a number of different approaches. All of them require a way of getting the DNA into a sufficient number of cells.
To do this requires something to carry the DNA into the cell (a vector). Some vectors are made from inactivated viruses; and some of them are a form of non-viral nanoparticles (often made of lipid/protein components, which bind to DNA and target cells).
You can find more information on different kinds of vector here.
You can find more detail on genetic therapies for CF at the link below. (This page is available in English only).
At time of writing (2024), two gene therapy approaches are currently in clinical trials.
The first of these (from 4D Molecular Therapeutics), uses a modified adeno associated virus (AAV) (Details of this Phase 1/2 trial are available here.)
The second (from Krystal Biotech) uses a vector based on a Herpes Simplex Virus-1 (HSV-1) (Details of this Phase 1 trial are available here and here).
Importantly, these viruses have been inactivated so that they are not able to replicate in the target cells and cause cell damage or loss. Both these vectors carry a healthy copy of the CFTR gene into the cells but do not insert into the host cell DNA. Instead the DNA remains in the cell nucleus, separate from the host chromosomes. This means the patient’s own DNA remains unaltered. However, it also means the effects of the therapy do not persist in the long term. This therapy would therefore need to be repeated, rather than being a ‘one-off- solution.
At time of writing (July 2024), these trials are ongoing and do not have conclusive findings.
Several additional approaches are being investigated in the laboratory, and are progressing towards clinical trial. One of these, (from Spirovant) uses an AAV vector; one (from Carbon Biosciences) uses a hybrid AAV; and two (from Boehringer Ingelheim and Spirovant) use lentiviral vectors. The significant difference with the lentiviral vectors is that the DNA is inserted into the host cell DNA. This means that the effect is expected to be longer-lasting.
Since lentiviral vectors integrate into the host chromosomes, this has raised some safety concerns. Scientists must consider the possibility of adverse effects on other genes close to the integration site. The design of these lentiviral vectors has evolved over the years to greatly reduce this risk. These are termed self-inactivating (SIN) vectors. This type of lentiviral vector has been extensively used in therapies for other disease indications, in particular in the generation of CAR-T cells for blood cancers. To date, there have been no reported serious adverse events. However, as these are new therapies, researchers are required to continue conducting long-term follow-up in treated patients to monitor for adverse events.
Several organisations have therapies in the advanced stages of preclinical development. These include Boehring Ingelheim and the UK Respiratory Gene Therapy Consortium (BI 3720931, a lentiviral vector), Spirovant (SP-101, an AAV vector, and SP-102, a lentiviral vector), and Carbon Biosciences (a hybrid viral vector).
You can read more about viral vectors here.
mRNA therapies
Another approach is to deliver ‘messenger RNA’ (mRNA) instead of DNA. mRNA is the rather short-lived ‘template’ produced from DNA; the cell then uses this template to produce the protein coded by the gene. In mRNA-based therapy, this genetic material does not need to get to the nucleus and therefore never integrates into the host’s own genetic material. This also means that the delivered mRNA will only persist for a short time in the cell and would require regular re-administration. However, it has the potential advantage of not containing any components that may induce an immune response. Researchers are currently (in July 2024) recruiting participants for a Phase 1 clinical trial, to confirm the safety of this approach. (This trial is being conducted by Vertex/Moderna, examining the safety of the product VX-522.)
Another promising therapeutic approach for CF is full-length CFTR mRNA replacement: that is, inserting a complete mRNA template of a healthy CFTR gene. This should work regardless of the particular mutation carried by the patient.
Clinical trials for mRNA therapies
Three early-phase clinical trials of inhaled mRNA therapy for CF (CFTR mRNA encapsulated in a lipid nanoparticle) are in progress currently (2024). The three products being tested are:
1) RCT2100, in healthy volunteers
2) ARCT-032, in healthy volunteers and adults with CF
3) VX-522 in adults with CF who are ineligible for CFTR modulator therapy.
Gene editing
Gene editing is a very precise technology. Rather than inserting a new gene, it involves correcting the mutation in the patient’s own faulty gene. A Strategic Research Centre, co-funded by the CF Trust (UK) and the CF Foundation (US) are working to develop gene editing tools for CF. As well as researching how the genes can be edited and corrected, this SRC is considering different approaches for how to treat patients:
- Coating ‘gene editing molecules’ in nanoparticles, which could then be inhaled into the lungs as an aerosol.
- Collecting cells from the patients, editing them in the lab to correct the mutation, growing up large numbers of these ‘corrected’ cells, and then transplanting them back into the patients.
So far, this work is all in the early preclinical development stage. This involves evaluation in animal models. Much more time and effort will be required to confirm whether these approaches are feasible, effective, and safe for use in humans.
Stem cells and disease modelling
Stem cells can play an important role in understanding CF. Researchers are currently collecting cells from patients with different CFTR mutations and converting them into a form of stem cell called induced pluripotent stem cells (iPSCs). These cells can be grown into different types of lung cells in the lab. This allows researchers to study how each CFTR mutation affects the cells of the lung and to understand the mechanisms by which different mutations act.
These cells can also be used to develop disease models, allowing scientists to test new therapies and drugs. Testing on cells derived from different individuals means that scientists can gain a broader understanding of how different individuals may respond to a therapy. This means researchers have a more balanced view of the potential effects before they apply the therapy to trial participants. Cell therapies
Scientists are also exploring using tissue engineering techniques to develop lung grafts from stem cells for patients with CF. Like the techniques above, this would involve collecting lung cells from patients living with CF to generate patient-specific stem cells. These cells would have the mutation corrected in the lab before being grown in large numbers and used to generate healthy lung tissue. This tissue could potentially be used as a graft to replace severely damaged lung tissue. This research is in the very early stages, and it will take several years of pre-clinical work to confirm whether this approach may be viable.
You can read more about tissue engineering below.
Find out more
The Cystic Fibrosis Trust provides information for patients and carers about CF, including information about ongoing research.
The Strategic Research Centre for CF is a group of UK-based researchers collaborating to develop personalised cell therapies for cyistic fibrosis.
The UK Respiratory Gene Therapy Consortium is conducting researching into gene therapy-based approaches to CF.