Cystic Fibrosis Research News № 10

October 2022

Antimicrobial peptides may be the key to fight off AMR

How can we kill bacteria that are resistant to traditional antibiotics? Some scientists are betting that it’s best to go natural – or at least mimic nature – to beat off antimicrobial resistance (AMR). Researchers from the University of Warwick are the latest to design and test synthetic antimicrobial peptides (AMP) that target common CF pathogens P. aeruginosa and S. aureus.

AMPs are small peptides produced by living organisms. As a component of the innate immune system, they serve as an early line of defense against invading pathogens. In CF, it is thought that AMP activity is compromised – contributing to the failure to clear infections. Thus, treating CF patients with synthetic AMPs could make up for some of the immune system’s lost effectiveness.

The University of Warwick study sought not only to synthesize new, effective AMPs, but also to develop an effective protocol to screen for AMPs that are likely to be effective for CF patients. After synthesizing a class of compounds called acrylamide copolymers to serve as synthetic AMPs, the researchers testedd them against a battery of assays. They employed synthetic cystic fibrosis medium rather than traditional culture medium, assessed the effect of the AMPs on two different strains of both S. aureus and P. aeruginosa, and even used an in vivo model (larva of the moth species G. mellonella) to gauge both efficacy and toxicity of their AMP compounds. In the end, they identified two powerful lead candidates, and showed that they work by disrupting bacterial membrane stability.

Other teams have been working on similar problems with different approaches. Researchers from the University of Minnesota tested their own synthetic peptide (DGL13K) against the same two species of bacteria – taking advantage of the G. mellonella model as well as a mouse model. Another team of researchers from Brazil put their synthetic AMP (Adevonin) to the test against a broader range of gram-negative and gram-positive bacteria, also using the G. mellonella model, and concluded that it was hard on bacteria but soft on human fibroblasts in cell culture. A study in China has brought new methods to the synthesis of AMPs, using an approach called ‘click chemistry’ that relies on high yield, stereospecific, and relatively simple chemical reactions. The technique, originally developed in 2001 by chemist and Nobel laureate Barry Sharpless, has seen renewed interest lately in academic and industry circles.

Ultimately, synthetic AMP development is but one approach being explored to treat antimicrobial-resistant infections in CF. Yale University launched its Center for Phage Biology and Therapy earlier this year, with a special focus on treatment of CF patients (Yale researchers already have a phase I/II clinical trial underway). Recently the CF Foundation awarded funding to Destiny Pharma for its investigational small molecule compound XF-73 to treat drug-resistant MRSA infections. And with debate ongoing in congress about the passage of the PASTEUR Act, which aims to provide economic incentives for antimicrobial research and development, CF researchers, clinicians, and patient advocates alike are hopeful that bacteria-fighting efforts will soon receive another shot in the arm.

Featured Studies:

International CF Centers Seek Out Better Liver Disease Diagnosis

Study results were recently published in the Journal of Cystic Fibrosis  by a team of Swedish researchers who set out to establish a better method for liver disease screening. The approach, called shear wave elastography (SWE), is being heralded as a more effective, non-invasive way to diagnose this common CF complication. This is not the first team of scientists who have sought to establish the merits of SWE: studies in Australia and Italy, have aimed to do the same. 

Clinicians have long recognized liver disease as a major, life-limiting complication of CF. Yearly screening is carried out at CF centers. But there remains ongoing debate over the best way to monitor liver health; up to now clinics have adopted a range of methods from screening for blood biomarkers to ultrasound imaging. For those researchers comparing liver screening methods and weighing their pros and cons, the end goal is to find the optimal method and promote it broadly so that all CF centers can benefit. A superior diagnostic method, employed at a single center, may allow for earlier detection and treatment of liver disease for a few patients each year. This itself is a very positive development. But if this superior method were rolled out at many CF centers across the world, it could positively impact hundreds, or even thousands of patients.

So, what makes SWE better than other approaches for liver disease screening? The Swedish authors, led by Helga Elidottir from Lund University noted that other approaches are either less effective or too invasive. There is evidence that the ultrasound approach is more sensitive than blood-based biochemical tests, yet the ultrasound may not detect cirrhosis (scarring of the liver). A biopsy, the current ‘gold standard’ diagnostic method, does detect cirrhosis – but it requires surgery. SWE is more attractive than biopsy because of what it measures: liver stiffness.  As SWE is non-invasive, no surgery is necessary to assess the stiffness of the liver. Drawing from data in the Swedish national CF registry, the researchers showed that in subjects who had both been biopsied and evaluated with SWE, cirrhosis and increased liver stiffness tended to be observed together. In other words, it is possible to detect the presence of cirrhosis without a biopsy – the increased liver stiffness gives it away.

Other research centers have recently implemented SWE into their clinical programs and and with demonstrated value. The aforementioned team in Naples, Italy compared SWE to APRI, FIB-5, and GPR, and found SWE superior at detecting liver disease. In Brisbane, Australia, SWE was actually combined with APRI, and the study found that the two indicators together were better predictors of liver disease than either method used alone.

All three groups of researchers mention the importance of verifying their findings in multi-center studies. This would help raise the profile of SWE screening further and demonstrate that it is worth employing broadly as a diagnostic approach. Recent multi-center study efforts in other domains of CF research may prove a helpful model for SWE advocates. A study in March 2022 published in the journal Frontiers in Cellular and Infection Microbiology, for example, described results from a 13-Center effort that compared the airway microbiome of nearly 100 CF patients (and controls) across the US. Another recent study published in January 2022 (Pediatric Pulmonology) drew on data from the multicenter FIRST study, including 160 infants at 5 US CF centers, to show that vitamin D insufficiency is prevalent in young CF children (< 3 years of age).

Featured Studies:

Electrode-Based Diagnostics for Earlier Detection (and Eradication) of P. aeruginosa

In a positive trend for the CF community, the number of patients developing chronic P. aeruginosa infection has decreased over the past several decades. This long-standing trend owes to a number of factors. One is the success of infection control measures. Hospitals and CF clinics take great pains to physically distance CF patients, encourage mask-wearing, and meticulously clean examination rooms after patient use. Another is the success of early eradication therapy, which treats the bacterium before it can really dig into the lungs and establish antibiotic-resistant biofilms. But here there is still room to improve. A successful course of early eradication therapy requires that the infection is detected as quickly as possible, yet many patients do not clear the initial infection in time. Scientists are working to develop new diagnostic methods that rapidly and reliably detect biomarkers of P. aeruginosa infection, that will result in faster diagnosis and treatment for patients, hopefully clearing infection before it becomes chronic.

Similarly, researchers in Austria are developing an electrode-based diagnostic tool. It works by detecting a panel of molecules secreted by P. aeruginosa cells. Several of these molecules are quorum sensing compounds (used for inter-bacterial communication), while others are virulence factors that enable competition with the host or other bacteria. As the authors note in their recent publication, traditional diagnostic methods like lab culture or mass spectrometry require a lot of time and/or resources, including expensive medical equipment and highly trained personnel. But this new electrode-based method will allow for much faster ‘point-of-care’ testing that can be completed during a routine medical examination without additional laboratory work. It would even allow for large-scale testing in the hospital, or environmental sampling. These are measures that could help stifle an outbreak before it affects many people with CF.

Other researchers too are working to perfect electrode-based techniques and enable better infection diagnosis. Part of this project involves testing different types of electrodes. The Austrian team utilized screen-printed electrodes made of carbon and silver. Another group in Cork, Ireland is working with a boron-doped diamond electrode to detect a similar panel of P. aeruginosa molecules. While still other research is expoloring experimental techniques without electrodes that would allow for similarly rapid detection. At the University of Nottingham in the UK, for example, a diagnostic protocol is being developed based on a classic, quick-and-easy laboratory technique called thin-layer chromatography. The core technology of chromatography – the separation of a mixture into identifiable component parts by passage through a medium – is actually what powers rapid COVID tests.

In addition, there have been similar efforts over the past several years to determine whether another rapid, non-invasive approach – the detection of breath-based biomarkers – could be useful for P. aeruginosa diagnosis. The same principle is now being explored for detection of Non-tuberculosis mycobacteria (NTM), another CF pathogen. Clinicians face a similar issue wherein NTM detection has traditionally depended on relatively slow diagnosis by culture in the lab. These diagnostic efforts should fall on receptive ears (and open wallets). Over the past several years the Cystic Fibrosis Foundation has awarded upwards of $100 million through its Infection Research Initiative, with the stated aim of improving “the detection, diagnosis, treatment, and outcomes of CF-related infections.” And in the aftermath of a global pandemic, there is broader public interest too in diagnostic measures that can recognize and curb the spread of infection before it gets too far out of hand.

Featured Studies:

Clinical Trial Watch

Denver, Colorado. Soon Recruiting. Clinicians are constantly searching for the most effective method to diagnose CF lung symptoms so they can be managed as early as possible. In this spirit, a new trial will test the power of electrical impedance tomography (EIT) to detect changes in the lung. They will compare EIT to the CT scan, which is the current diagnostic standard. The trial will assess whether EIT provides useful information about structural changes in the lung that may indicate worsening disease, and determine how well EIT can gauge response to treatment for pulmonary exacerbations. Specifically, EIT will be assessed for its ability to detect air trapping (an abnormal retention of air in the lungs) and consolidation (when the air filling the small airways has been replaced with some other fluid or solid material) (Sponsor: University of Colorado, Denver).

Liverpool, UK. Recruiting. The ‘gamification’ of healthcare – combining a patient’s daily treatment routine with game-like elements to make the treatment more enjoyable (and effective) – has become somewhat of a hot topic in medical circles. The principle is now being applied to the treatment of CF, where clinicians are concerned about adherence to daily therapies. A new trial will test the Playphysio®(Pp) system, which was developed by Will Jackson, software engineer and father of a child with CF. The system integrates with physical therapy devices, providing games to play during therapy, and actually incorporates aspects of the therapy itself into those games,for example, the game prompts users to pause during treatment and cough to clear out mucus in the lungs. The system also tracks adherence to therapy over time. The trial will compare patients who receive the device to patients who do not to see if the device improves adherence (Sponsor: Alder Hey Children's NHS Foundation Trust).

Portsmouth, UK. Soon Recruiting. Aside from gamifying therapy to make it more enjoyable, researchers also want to know if cardio exercise can stand in for traditional airway clearance. This interest in exercise as a form of airway clearance has emerged directly from the CF community. Many patients, especially with the advent of highly effective modulator therapy, have questioned whether they can simply exercise (including forced ‘huff coughing’, to clear mucus in the lungs) instead of using airway clearance devices. Many patients, after all, are exercising anyway as part of their health routine. A new study will help address this point by splitting patients up into two groups – half will be instructed to replace chest physiotherapy with aerobic exercise (including huff coughing), and the other half will continue with their usual care. In the end, the study will assess lung function parameters (FEV1, FVC) as well as the direct feedback of people with CF as to what therapy routine they would prefer going forward (Sponsor: University Hospital Southampton NHS Foundation Trust).

Baltimore, Maryland. Recruiting. People with CF-related diabetes, like diabetes patients in general, are at high risk of an eye disorder called diabetic retinopathy. The condition ultimately results in blindness, and it is important that diabetics receive eye exams at least once a year. The ACCESS 2 clinical trial is now recruiting patients to test the effectiveness of a special camera with AI software for diabetic eye exams. The camera will be compared to the current standard – examination by actual retinal specialists – to see whether the device can match their diagnosis (Sponsor: Johns Hopkins University).

Beyond the Bench

Krystal Biotech Granted IND Approval for CF Gene Therapy Drug. The company’s drug candidate, KB407, is a viral vector that delivers two copies of the CFTR gene to lung cells, where it is transcribed into functional CFTR protein. Initial New Drug (IND) approval will allow Krystal Biotech to commence a phase 1 clinical trial, which they hope to start running this year. In the words of Senior Vice President of Clinical Development at the company Dr. Hubert Chen, the gene therapy drug will “treat the root cause of the disease regardless of an individual patient’s mutation by giving the body instructions to produce its own functional protein” (Krystal Biotech).

CFF Grant Funds Novel Stem Cell Research. The Foundation’s Harry Schwachman Clinical Investigator Award (aimed at exceptional physician-scientists in the realm of CF research) will go to Dr. Andrew Berical at Boston University School of Medicine. The grant will provide nearly $400 thousand dollars in funding over four years. Berical’s research revolves around using stem cells to enable more personalized CF drug testing. With a team of fellow researchers, he has developed a platform that takes stem cells from patients with different CFTR mutations, differentiates them into airway epithelial cells, and uses them to test the effects of CFTR modulators. The platform has the potential to be used in personalized drug testing for a wide range of different diseases (Boston University).

Carbon Biosciences Launches with $38 Million Series A. In June the Boston-based company Carbon Biosciences announced it will advance novel parvovirus vectors that can deliver larger gene therapy payloads with enhanced tissue specificity and with minimal neutralizing immunity. Carbon's lead candidate, CGT-100, targets lung tissue with demonstrated upper airway tissue tropism. Carbon benefits from a collaborative agreement between the Cystic Fibrosis Foundation and the Longwood Fund. (Carbon Biosciences)

Gene Therapy Groups Get the Golden Ticket. In Other CF Foundation News, the first ever CFF “Golden Ticket” Competition has concluded – awarding two Biotech companies (Avecris and Nosis Biological Sciences) one year of free lab and office space – provided by Bakar Labs –  as well as access to additional CFF resources. The two companies are working to develop genetic therapies for CF, joining Krystal Biotech (mentioned above) and other early stage players. But while the companies are working in the same space, their tech is different. Avecris is developing a gene therapy delivery vehicle – but unlike Krystal Biotech they are working on a non-viral  (instead of a viral) vector. Nosis is creating a machine learning-based drug screening platform that aims to improve the safety and delivery success of gene therapy (Cystic Fibrosis Foundation).

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.