Cystic Fibrosis Research News № 8

July 2022

Translational Advances

Antimicrobials Progress Through All Stages of the Therapeutic Pipeline

Over the last month, several antimicrobial drug candidates have been proposed that may combat common, clinically relevant CF pathogens, including the discovery of new drug targets and improving the half-life of drugs in the body.

Researchers at Rama University in India have identified new protein epitopes in the fungal species A. fumigatus. Epitopes are components of fungal proteins that bind molecules on the surface of T cells and initiate an immune response. In this case, the idea is to use fungal epitopes to design vaccines that will stimulate the immune system to preemptively fight off any fungal infection . The group at Rama identified the epitopes by using a suite of machine learning and artificial neural network (ANN) algorithms capable of predicting the “allergenicity” of fungal proteins, their chemical properties (e.g., half-life, molecular weight), and their capacity to bind the MHC-II complex, which is found on the surface of T cells (1).

Other researchers have  advanced drug candidates to treat Pseudomonas aeruginosa infections. A multi-university team in China set out to modify the properties of an existing anti-pseudomonal antimicrobial drug: cyclo(L-Trp-L-Ser). In previous studies the compound had been shown to inhibit Pseudomonas quorum sensing, a molecular messaging system that individual bacteria use to communicate with other bacterial cells in the surrounding area. This communication helps the bacteria to form biofilms and coordinate their response to host cells. The recent study  led by Yinglu Wang and Lile Pan discovered that by adding an extra sugar group to cyclo(L-Trp-L-Ser), the anti-quorum sensing activity of the compound was greatly enhanced,  and its ability to eliminate pre-formed bacterial biofilms was increased by a factor of 10. The scientists believe that the compound may have potential as an adjuvant to existing antibiotics, allowing for more effective treatment of persistent, drug-resistant infections (2).

A team in New Zealand recently published results of their work  that targeted more effective inhaled antibiotic delivery. The established antibiotic ceftazidime was used as a spray dyer to formulate microparticles that are easier to inhale. These microparticles were then fortified with amino acids to enhance their chemical stability in the lungs. After using a suite of experimental techniques to analyze the drug particle properties (X ray-diffraction, IR spectroscopy, electron microscopy), the researchers ultimately discovered that the addition of the amino acid leucine best improved the aerosolization of the microparticles (converting them into a fine, inhalable spray), and that tryptophan improved particle stability. This approach to enhancing inhaled drug delivery may prove useful for other inhaled drugs, whether antimicrobial in nature or not (3).

Additional Studies:

  • Polypeptide drug PP-007 helps resolve lung inflammation, reducing neutrophil recruitment and muting pro-inflammatory cytokine levels in CF mice (4
  • Scientists discover the mechanism of action for 1PBC, a TMEM16A pore blocker, as inhibition of the TMEM16A chloride channel as a potential therapeutic approach when CFTR modulator therapy is not viable (5)
  • A nanoparticle formulation to extend the half-life of DNA-ase in the CF lung is proposed. DNA-ase (Pulmozyme®) has long been approved for the treatment of CF. The drug thins mucus by cutting up extracellular DNA (6

Clinical Progress

The Path to Personalized CF Care 

The long and arduous road to effective CF treatment begins with diagnosis ; not just the initial diagnosis of CF, but also the lifelong diagnosis and treatment of infections and pulmonary exacerbations. New studies are improving the landscape of CF diagnostics, providing a broader understanding of the impact of individual genetic and environmental circumstances. Taken together, these research advances permit CF care teams to provide more informed prescriptions to treat exacerbations and improve overall patient health.

For newborn screening, a group of Canadian researchers have developed a “rapid assay”  that measures sweat chloride levels in under 5 minutes. The sweat test has long been a standard diagnostic test for cystic fibrosis - as elevated sweat chloride levels are a hallmark of CF. However, it is not adequate for diagnosing infants that produce relatively little sweat, as the traditional sweat test is not sensitive enough to detect sweat chloride at low volume. The assay uses a technique called “capillary electrophoresis with indirect UV detection” (CE-iUV), and study results show that it can reliably measure sweat chloride at low volumes and successfully distinguish CF infant sweat from the sweat of non-CF infants (1)

A team in France has been searching for more effective diagnostic markers for M. abscessus infection. M. abscessus is a relatively rare but concerning CF pathogen that has demonstrated antibiotic resistance and has been associated with lung function decline in prior studies. This group sought to understand  whether IgA status (which measures the IgA antibody produced by the immune system’s B cells) differs between M. abscessus positive and M. abscessus negative in CF patients. The researchers found that detection of M. abscessus positive did in fact exhibit significantly higher IgA levels in CF patients. This implies that IgA may be used as a reliable infection biomarker, and as the study noted, IgA can be paired with traditional bacterial culture as a supplement to diagnose infections that the bacterial culture fails to detect (2)

Understanding a patient’s CFTR mutations, and their association with specific CF symptoms and comorbidities, can inform treatment prescriptions over the patient’s lifetime.  

In sunny Italy, a team of researchers  have studied the F508del/5T;TG12 genotype, which combines the F508del, with the rarer mutation 5T;TG12. The study indicates that patients with this genotype present a broad array of symptoms – from severe to very mild. The team performed a systematic analysis of long-term data from patients at 10 Italian CF centers to understand long-term trends in the symptoms of individuals with this mutation. They discovered a tendency towards mild lung disease with pancreatic insufficiency and relatively low prevalence of complications like CF-related diabetes. Patients in this group also tended to be diagnosed with CF later in life, as their symptoms were mild and did not allow for conclusive diagnosis at an early age. Knowing how their symptoms tend to unfold, clinicians can now monitor this patient group more effectively and catch emerging symptoms. Further studies along these same lines may provide the benefits for individuals with other combinations of CF mutations (3).

Additional Studies:

  • Respiratory viral infections in CF infants are not associated with worsened structural lung disease at an early age (4)
  • ETI modulator treatment is associated with mental health symptoms such as low mood, insomnia, and “brain fog”. Adjustment of ETI dose is associated with mental health improvements in the study population (5)
  • Analyzing the stool samples of CF infants, study finds that stool frequency and consistency is not significantly different from healthy infants. Constipation was found to be less common in infants receiving acid suppression therapy or exclusive formula feeding (vs. breastfeeding) – a finding that may help manage GI symptoms in all infants (6)  

Mastering the Microbiome

Studies of Bacterial Evolution Point the Way to Potential Drug Targets 

A key focus for microbiologists working in CF is to understand how important CF pathogens such as Pseudomonas aeruginosa, Staphylococcusaureus, as well as more recent pathogens of concern, colonize and adapt to the unique biological niche of the CF lung. For long-term infections, these bacteria may have decades of time to adapt. Understanding what molecular changes occur in the bacteria over time, allowing them to evade destruction by the host immune system and contribute to lung deterioration, is essential to identify future targets for antimicrobial drugs. Understanding the biological factors that allow bacteria to damage and persist in the CF lungs, new therapeutics can be developed to target these factors and break a pathogen’s hold on the patient’s lungs. 

A recent study from the Institut Necker in France found new insights about the way that persistent S. aureus infection causes lung damage in young CF patients, where S. aureus tends to be most prevalent, and whereas P. aeruginosa typically begins to dominate the microbial community during adolescence. Given this, it is possible that early infection with S. aureus paves the way for later P. aeruginosa infection by creating more hospitable conditions for infection. To investigate the evolution of S. aureus and its effect on the airways, the French group gathered sequential isolates of the bacteria from the lungs of 15 young CF patients over time. They found that the phenotype of S. aureus did indeed evolve over time, with later isolates more adept at causing pro-inflammatory cytokine secretion in the lungs.  They also showed that this cytokine secretion was dependent on the S. aureus protein Spa and acted through the TNF-alpha receptor 1 signaling pathway in airway epithelial cells. Both the Spa protein and the signaling pathway may serve as potential therapeutic targets (1).

At the Dartmouth-Hitchcock Medical Center in the USA, scientists have identified changes in the behavior of P. aeruginosa that occur when it colonizes the CF lung over the long term. They examined  the factors that contribute to the development of lasR- mutant P. aeruginosa strains. LasR loss of functionis a common occurrence in chronic infection isolates, and the presence of lasR mutant Pseudomonas tends to be associated with worsened lung disease.  A novel finding was that the presence of another quorum sensing gene, CbrAB, is required for lineages of lasR- bacterial cells to evolve. It follows from this research that targeting the CbrAB gene might prevent evolution of lasR mutant strains or harm these strains if they have already evolved (2).

Another study in Canada found that the peptidoglycan (PG) composition of epidemic strains of Pseudomonas isolated from CF patients,was significantly different from the PG composition of common laboratory strains. Both strains were grown in laboratory conditions that resembled the CF lung (using synthetic CF sputum medium) to make the experiment more relevant to biological conditions. The results suggest that PG composition has some influence on the bacteria’s ability to colonize the CF lungs effectively, and it may be possible to use PG as a therapeutic target (3).

Additional Studies:

  • Researchers re-analyzed the genomes of 111 Stenotrophomonas isolates and reported that isolates previously classified as S. maltophilia really belong to multiple different species groups (S. maltophilia, S. pavanii, and a number of novel, unclassified species). The researchers found variation in the antibiotic resistance and virulence genes of these different species, meaning that more precise detection of Stenotrophomonas bacteria could better inform treatment decisions and the prescription of antibiotics (4).
  • New computational models explain the biology of Pseudomonas biofilms. Using prior experimental data, a study modeled interactions between Pseudomonas quorum sensing molecules called QSAIs and the extracellular polymeric substance (EP), secreted by the bacteria, that constitutes much of the biofilm matrix. Future drugs could be designed to disrupt these interaction (5).
  • 17.8% of sputum samples analyzed in a study exhibit increases in total bacterial load after antibiotic treatment. This means that antibiotic treatment can actually be beneficial to bacterial communities, even if antibiotics alone can kill a single species. The finding could help inform antibiotic prescriptions that take into account the unique profile of each patient’s lung microbiome (6).

Clinical Trial Watch

Quebec, Canada. Recruiting. Diabetes is common within the CF population, as certain biological features of CF predispose patients towards endocrine pancreatic dysfunction – the failure to secrete the blood glucose-regulating molecule insulin. A new trial aims to determine how CFTR gene variant and presence/absence of exocrine pancreatic insufficiency are associated with hypoglycemic episodes in type 1 diabetics. Though not explicitly focused on people with CF, the outcomes of this trial will be useful for CF and non-CF diabetics alike. Knowing what biological factors contribute to the onset of diabetes and its symptoms will improve monitoring and treatment of the disease (Sponsors: Institut de Recherches Cliniques de Montreal, Juvenile Diabetes Research Foundation). 

Amsterdam, Netherlands. Recruiting. Yearly screening for CF-related diabetes (CFRD) is a common experience in CF clinics in the United States. Typically, patients attending an appointment are instructed to drink 75g of glucose solution (essentially, highly concentrated sugar water) and have their blood glucose monitored over the course of two hours to assess how well their body produces insulin and manages blood sugar. Patients often voice discomfort while drinking the glucose solution, with many reporting nausea and vomiting. This trial will test how well a more palatable, commercially available sports drink high in sugar compares to the traditional use of glucose solution to diagnose CFRD. The trial will measure blood glucose level 2 hours after drinking either the glucose solution or the sports drink, and see whether blood glucose levels are comparable (Sponsor: Universiteit van Amsterdam). 

USA, 5 Sites. Soon Recruiting. Another common, life-shortening CF comorbidity is colorectal cancer (CRC). People with CF have a 5-10x greater risk of CRC than the general population. Akin to the glucose solution trial above, this trial will compare three CRC diagnostic methods: multi-target DNA, quantitative FIT, and colonoscopy (the current standard test method). If the first two methods, which are both stool-based and therefore far less invasive then a colonoscopy, are just as effective at diagnosing CRC then they would allow for easier, more frequent cancer screening. The study will enroll patients from the NICE-CF cohort: a group of middle aged – elderly CF patients that are eligible for routine colon cancer screening. Key outcome measures will be the sensitivity and specificity for the diagnostic test (Sponsors: University of Washington, CFF). 

USA, 2 Sites. Soon Recruiting. People with CF have daily airway clearance regimens, using medical devices like the “vest” machine (Hill-Rom, Electromed, etc.) or Acapella® in the home to loosen the sticky mucus in the lungs and relieve pulmonary symptoms. However, with the onset of highly effective modulator therapy, many CF patients and clinicians alike are questioning whether the 1-2 hours per day spent on airway clearance are still necessary. This trial will compare the ability of “symptom-driven” airway clearance (i.e., just perform airway clearance when symptoms start to pick up – for example, when dealing with a cold) to “continuous” airway clearance (the standard model – perform airway clearance twice every day). Several measures of lung function (FEV1, FVC, MRI) will serve as primary outcomes to show whether “symptom-driven” airway clearance can keep patients as healthy as continuous airway clearance (Sponsor: University of Missouri-Columbia). 

Beyond the Bench: CF Business News

AbbVie’s Bid to Challenge Vertex Triple Combo Falls Short. AbbVie’s trial to test the efficacy of adding a novel corrector to their existing two-piece corrector-potentiator combo therapy has not met positive expectations. The additional corrector compound, which was recently acquired from the drug company Galapagos, did not significantly improve patient outcomes. AbbVie will move forward with its double combination therapy for now, and in the near future, hopes to bring in other novel corrector compounds from its clinical pipeline to build a more effective triple combo therapy. Beyond the facilities of AbbVie and Vertex, the hunt is on for new modulator compounds with different mechanisms of action. A French research team recently published promising preclinical results (cell culture, mice) for their molecule c407, which stabilizes delta-F508 mutant CFTR specifically (Fierce Biotech, University of Paris)

New Antimicrobial Drugs to Beat Back Antimicrobial Resistance. Biotech firm ContraFect Corporation recently presented data at the European Congress of Clinical Microbiology & Infectious Disease demonstrating the bacteria-killing potential of their direct lytic agent (DLA) drug CF-370, which works by destabilizing the bacterial cell wall. The drug performed well at killing an extensively drug resistant (XDR) variant of Pseudomonas aeruginosa. In related news, the company Beyond Air released promising data on the efficacy of their medical device, the LungFit PRO®. The device provides patients with inhaled nitric oxide (NO), which is known to have anti-inflammatory and antibacterial properties. Early clinical studies suggest that non-tuberculosis mycobacteria– a class of dangerous bacteria that tend to infect people with CF – are harmed by NO exposure. In early trials of the device, patients have reported improvement in a wide range of physiological symptoms – from respiratory health to digestive function (ContraFect, BeyondAir).

Grant Funding for CF Stem Cell Research. It is well established that rampant bacterial infection contributes to inflammation in the CF lungs – but scientists now believe that another biological source may contribute to inflammation as well: pro-inflammatory stem cell populations in the lung. Two stem cell researchers at the University of Houston have been awarded $2.7 million dollars in total from the NIH to conduct new research projects on this topic. Their work will help define the molecular characteristics of pro-inflammatory stem cells in the CF lung, and hopefully give rise to the development of new drugs that target these stem cells (University of Houston).

mRNA Therapy Proves Promising as a Next-Gen CF Drug Approach. As an alternative to small molecule CF modulator drugs that interface with mutant CFTR protein and rescue its function – there is also the prospect of replacing the mutant CFTR gene altogether with a functional copy. This approach would rescue CFTR function regardless of a patient’s individual CFTR mutation. Introducing mRNA transcripts encoding the CFTR gene into lung cells is one way to accomplish this feat – and the biotech company ReCode Therapeutics has recently published promising results using this approach. The company used its SORT lipid nanoparticle platform to encapsulate and deliver CFTR mRNA to lung epithelial cells in the lab and found that the delivered drug consistently rescued CFTR function. As trials of the platform progress, the goal is to gain approval for the platform’s use as an inhaled therapeutic (ReCode Therapeutics).

A Call to Action

Cystic fibrosis (CF) research is very much dependent on the strength of the CF community. It’s not simply an effort carried out by scientists in white lab coats - although there are many of them, and their work has enormous impact. Advances in research also depend on the technicians and engineers who operate the laboratory equipment that enables drug discovery, and the industrial machinery that allows drug development. Research depends on both business and marketing professionals, those who make biopharma companies viable and promote clinical trials. Successful research further depends on clinical trial coordinators, who carry out studies and work tirelessly to recruit and support patients throughout the complicated trial process. Particularly for rare diseases like cystic fibrosis, research depends on the work of foundations and patient advocates, which includes in the United States organizations such as the CF Foundation, Emily’s Entourage, CFRI, and the Boomer Esiason Foundation, as well as countless other across the globe, and hundreds of committed clinicians and researchers. Most importantly, research depends on people with CF and their devoted families and friends.

There can be no progress in CF research without patients willing to participate in clinical trials: not only to test new drugs, but also to provide, quite literally, their flesh and blood. It is with the help of patient samples that scientists can understand the damage that CF inflicts upon the human body, and also how drugs developed by the research community can remedy these damages.

This newsletter aims to pull all of these threads together; allowing the CF community to more fully appreciate how well the aims of its many members are aligned (and it extends an invitation to all readers not yet a part of the CF community, to embrace the cause and take up the task of pushing CF research forward). There’s something here for everyone - those interested in the clinical side of CF care, or in drug development, or the technical work performed in CF-centered laboratories. The newsletter also has as its objective to showcase new clinical trials; an opportunity for patients and clinicians to take part. Wherever and whoever you are in the world, you too may push CF research forward - either by direct participation, or simply by reading and sharing this newsletter with others.