Judith Coppinger

Examining both the biomarker potential and functionality of exosomes from CF patient lung cells

Dissection of the PI3K/Akt/mTOR signalling pathway as a therapeutic target in Cystic Fibrosis.

We are currently conducting a long term ongoing research study looking at the evolution of infection and inflammation in the airways of children with cystic fibrosis (CF). Every year, children with CF undergo a procedure called a bronchoscopy. A small camera is inserted into the patients airways which allows us to look inside a patient’s lungs and identify any damage present. Biological samples such as bronchoalveolar lavage (BAL) fluid from the lung as well as urine, blood and samples from the throat and nose are taken during the procedure and stored in a specialised ‘biobank’ . We also collect some of the patient’s clinical information. SHIELD CF is in place across three sites; OLCH Crumlin, Tallaght hospital and University hospital Limerick. There are over 8000 samples in the biobank already and these have contributed to more than 25 peer reviewed publications, helping us to understand various different aspects of CF lung disease.

In recent years we have come to understand that a vast array of bacteria lives in our airways – even in healthy people. It has become clear that the interaction between the healthy and harmful bacteria in the lungs is complex. We are conducting a long term and very wide-ranging study in children with CF looking at how these bacteria vary over time and whether they are related to lung inflammation, changes in antibiotic use and lung function at school age.

Bronchoalveolar lavage fluid is collected when salt water is instilled temporarily in the lungs during a bronchoscopy procedure. It collects the proteins and bacteria from the lower airways that otherwise could not be collected. This is potentially a very useful test for clinical trials of new medications in children with CF, but there are several different approaches internationally to the way the test is performed. This multicentre study seeks to determine if different ways of handling and processing the fluid impact on its utility as a marker of lung pathology.

The purpose of the CUBS study is to see if we can find proteins or ‘biomarkers’ in the urine that will help us to identify lung disease in children with CF. Biomarkers are biological molecules found in blood, other body fluids, or tissues that can be indicative of a particular disease or abnormal process such as inflammation. Lots of substances that are produced in the body are excreted, at least partially, in the urine. This has been shown to be true of biomarkers of lung damage in people with lung diseases. In some instances, urinary biomarkers have been shown to correlate well with lung infection or lung damage. This is of significant interest to doctors looking after children with CF as the collection of urine is a painless and harmless procedure, urine is always accessible and it is an easy fluid to work with. In the first part of the study, parents of children with CF will collect urine on a regular basis for 3 months at home and sent it to our partner lab in the UK (Mologic) to allow us to determine what the ‘normal’ range is (parents keep a symptom diary so we could determine when the children were well or sick). In the second part of this study, we will match urine collected with the corresponding bronchoalveolar lavage (BAL) fluid collected as part of the SHIELD CF project. We are trying to determine if there are substances in urine which are typically present at the time that we see a marker of lung damage called neutrophil elastase (NE) in the lung fluid. Earlier detection of lung damage and earlier intervention could prevent or slow down the progression of lung disease in children with CF.

The presence of certain compounds called ‘proteases’ have been shown to be a risk factor for lung damage in children with CF. Proteases are enzymes that can degrade healthy lung tissue if present in abnormal amounts. There are lots of different types of proteases, and little is known about some of these in children with CF. It is not yet known if particular proteases are associated with infection or damage to the lungs. The study is designed to establish the degree and pattern of proteases in the lungs of preschool children with CF, and to determine if specific proteases are associated with either pulmonary infection or clinical disease parameters. This study might help us to discover meaningful tests in due course to determine whether harmful proteins are present in young babies and children with CF.

Cystic fibrosis is a common inherited life threatening disease which is particularly common in Ireland. People with CF have a mutation in a gene that produces a protein called cystic fibrosis transmembrane conductance protein or CFTR. CFTR regulates the movement of salt in and out of cells. When CFTR doesn’t work well the result is thick, sticky mucus in the respiratory, digestive and reproductive systems, and inability to fight lung infections. Medications have now been designed to specifically target the CFTR protein. These are called CTR modulators. One such modulator is Orkambi, which has recently been approved to treat children over 6 years in Ireland. In this study we are using a new type of specialised lung function technique called ‘multiple breath washout’ (MBW) to look at the lung function of children aged 6-11 years with CF. Children will undergo MBW and a new form of low dose CT scanning called ‘spirometrically controlled CT’ before they commence on Orkmabi. In the first study of its kind in the world, we will be working with colleagues in Rotterdam, London and Cincinnati to assess the effects of Orkambi on the lung structure and lung function of these Irish children for two years following commencement of Orkambi in a real world setting.

The introduction of promising new medications to treat the basic defect in people with CF holds great promise to improve the survival and health of our patients with CF. New CF treatment such as Orkambi are currently only available for CF patients with the most common mutations. Furthermore only individuals with common or well-recognised mutations are being recruited to clinical trials of these new investigational medications. There are likely to be a significant group of children and adults with rarer mutations who may be left behind, with no prospect of having new drugs licensed for use in these people. What is required here is a patient specific ‘test’ to determine whether an individual may benefit from treatment with a given drug. The purpose of this research is to create a repository or “bank” of a type of stem cell called “induced pluripotent stem cells” or iPSCs. Stem cells are special kinds of cells that can renew themselves. Under certain experimental conditions, iPSCs can be directed to grow into any type of tissue or organ. In the case of this study, we are working with colleagues in RCSI and Boston University to develop a special type of lung cell which can readily be used to determine whether the child’s own lung cells may respond to new CF drugs. Ultimately, we would like to develop a test that can be offered to all patients with cystic fibrosis, particularly those with rare mutations not currently able to avail of approved drugs, to determine whether or not they will respond to a given drug.

Understanding early lung disease in CF is an international focus to try and tailor treatment to slow or prevent decline in lung function. In Ireland, we currently have limited capacity to formally assess early lung disease in this group. In recent years, there has been a move towards closer monitoring and active treatment in younger patients with CF, in an effort to improve long term survival. Lung Clearance Index (LCI) is a lung function measurement performed using the multiple breath washout (MBW) method. The MBW technique is an effort independent, low-risk, non-invasive procedure performed on spontaneously breathing children. The LCI is a value that is used to indicate the performance of the lungs, particularly the smaller airways. LCI is much more sensitive than other established tests for CF lung disease and can be performed in younger children. It is therefore a very helpful test for doctors looking after children with CF. We have recently acquired the equipment for MBW testing (N2) and wish to validate the test in a population of healthy Irish children and in children with CF, both when well and unwell and to compare our results with established values using this equipment. We are working with our colleage Dr Barry Linnane in Limerick, who has been using this device for a number of years.