Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease.

Microorganisms. 2020 Jul 04;8(7):

Authors: Bacci G, Taccetti G, Dolce D, Armanini F, Segata N, Di Cesare F, Lucidi V, Fiscarelli E, Morelli P, Casciaro R, Negroni A, Mengoni A, Bevivino A

Abstract
Although the cystic fibrosis (CF) lung microbiota has been characterized in several studies, little is still known about the temporal changes occurring at the whole microbiome level using untargeted metagenomic analysis. The aim of this study was to investigate the taxonomic and functional temporal dynamics of the lower airway microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with advanced lung disease regularly attending three Italian CF Centers, given a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing both strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes across clinical status. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of both traditional and atypical CF pathogens. A large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status, and consistently detected in the lung microbiome of all subjects independently from known antibiotic exposure. In conclusion, an overall stability in the microbiome-associated genes was found despite taxonomic fluctuations of the communities.

PMID: 32635564 [PubMed]

Mental health and cystic fibrosis: Time to move from secondary prevention to predictive medicine.

Pediatr Pulmonol. 2020 Jul 07;:

Authors: Amerio A, Sibilla F, Pescini R, Ciprandi R, Casciaro R, Grimaldi Filioli P, Porcelli C, Odone A, Costanza A, Aguglia A, Serafini G, Amore M, Castellani C, Cresta F

PMID: 32634297 [PubMed - as supplied by publisher]

The histone-like protein AlgP regulon is distinct in mucoid and nonmucoid Pseudomonas aeruginosa and does not include alginate biosynthesis genes.

Microbiology. 2020 Jul 07;:

Authors: Cross AR, Csatary EE, Raghuram V, Diggle FL, Whiteley M, Wuest WM, Goldberg JB

Abstract
The opportunistic bacterial pathogen Pseudomonas aeruginosa causes acute and chronic infections that are notoriously difficult to treat. In people with cystic fibrosis, P. aeruginosa can cause lifelong lung infections, and isolation of mucoid P. aeruginosa, resulting from the overproduction of alginate, is associated with chronic infection. The histone-like protein AlgP has previously been implicated in the control of alginate gene expression in mucoid strains, but this regulation is unclear. To explore AlgP in further detail, we deleted algP in mucoid strains and demonstrated that the deletion of algP did not result in a nonmucoid phenotype or a decrease in alginate production. We showed that the algP promoter is expressed by both the nonmucoid strain PAO1 and the isogenic mucoid strain PDO300, suggesting that there may be genes that are differentially regulated between these strains. In support of this, using RNA sequencing, we identified a small AlgP regulon that has no significant overlap between PAO1 and PDO300 and established that alginate genes were not differentially regulated by the deletion of algP. Of note, we found that deleting algP in PAO1 increased expression of the nitric oxide operon norCBD and the nitrous oxide reductase genes nosRZ and subsequently promoted growth of PAO1 under anaerobic conditions. Altogether, we have defined a narrow regulon of genes controlled by AlgP and provided evidence that alginate production is not greatly affected by AlgP, countering the long-standing premise in the field.

PMID: 32634088 [PubMed - as supplied by publisher]

Apolipoprotein E polymorphism and vitamin K status in cystic fibrosis patients not supplemented with vitamin K.

Eur Rev Med Pharmacol Sci. 2020 Jun;24(12):7077-7082

Authors: Krzyżanowska-Jankowska P, Walkowiak D, Drzymała-Czyż S, Rohovyk N, Bober L, Walkowiak J

Abstract
OBJECTIVE: ApoE alleles have been shown to significantly correlate with vitamin K status, however, data concerning this phenomenon in cystic fibrosis (CF) are scarce. This study aimed to investigate the effect of ApoE polymorphism on vitamin K status in a unique group of CF patients who had never received vitamin K supplementation.
PATIENTS AND METHODS: The study group consisted of 93 CF patients aged from 3 months to 32 years. Vitamin K status was assessed by the concentration of prothrombin induced by vitamin K absence (PIVKA-II) and the percentage of undercarboxylated osteocalcin (u-OC). The clinical status was evaluated in all patients.
RESULTS: Fifty-four (65.1%) out of 83 patients had a pathological PIVKA-II concentration (≥2 ng/ml) and an abnormal percentage of u-OC (≥20%). There were no differences in the clinical parameters, including PIVKA-II concentration (p=0.7752) and u-OC percentage (p=0.8395), between patients with genotypes ApoE2/3, ApoE3/3 and ApoE3/4. Moreover, the frequency of vitamin K deficiency did not significantly differ in CF patients with ApoE2/3, ApoE3/3 and ApoE3/4 genotypes (66.7 vs. 69.9 vs. 80%, p=0.8411; 87.5 vs. 89.6 vs. 100%, p=1.000, respectively).
CONCLUSIONS: The presence of the ApoE4 allele does not influence the vitamin K status in CF patients who have never received vitamin K supplementation.

PMID: 32633402 [PubMed - in process]

Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome.

Thorax. 2020 Jul 06;:

Authors: Nelson MT, Wolter DJ, Eng A, Weiss EJ, Vo AT, Brittnacher MJ, Hayden HS, Ravishankar S, Bautista G, Ratjen A, Blackledge M, McNamara S, Nay L, Majors C, Miller SI, Borenstein E, Simon RH, LiPuma JJ, Hoffman LR

Abstract
RATIONALE: The most common antibiotic used to treat people with cystic fibrosis (PWCF) is inhaled tobramycin, administered as maintenance therapy for chronic Pseudomonas aeruginosa lung infections. While the effects of inhaled tobramycin on P. aeruginosa abundance and lung function diminish with continued therapy, this maintenance treatment is known to improve long-term outcomes, underscoring how little is known about why antibiotics work in CF infections, what their effects are on complex CF sputum microbiomes and how to improve these treatments.
OBJECTIVES: To rigorously define the effect of maintenance tobramycin on CF sputum microbiome characteristics.
METHODS AND MEASUREMENTS: We collected sputum from 30 PWCF at standardised times before, during and after a single month-long course of maintenance inhaled tobramycin. We used traditional culture, quantitative PCR and metagenomic sequencing to define the dynamic effects of this treatment on sputum microbiomes, including abundance changes in both clinically targeted and untargeted bacteria, as well as functional gene categories.
MAIN RESULTS: CF sputum microbiota changed most markedly by 1 week of antibiotic therapy and plateaued thereafter, and this shift was largely driven by changes in non-dominant taxa. The genetically conferred functional capacities (ie, metagenomes) of subjects' sputum communities changed little with antibiotic perturbation, despite taxonomic shifts, suggesting functional redundancy within the CF sputum microbiome.
CONCLUSIONS: Maintenance treatment with inhaled tobramycin, an antibiotic with demonstrated long-term mortality benefit, primarily impacted clinically untargeted bacteria in CF sputum, highlighting the importance of monitoring the non-canonical effects of antibiotics and other treatments to accurately define and improve their clinical impact.

PMID: 32631930 [PubMed - as supplied by publisher]

Scnn1b-transgenic BALB/c mice as a model of Pseudomonas aeruginosa infections of the cystic fibrosis lung.

Infect Immun. 2020 Jul 06;:

Authors: Brao KJ, Wille BP, Lieberman J, Ernst RK, Shirtliff ME, Harro JM

Abstract
The opportunistic pathogen Pseudomonas aeruginosa is responsible for much of the morbidity and mortality associated with cystic fibrosis (CF), a condition that predisposes patients to chronic lung infections. P. aeruginosa lung infections are difficult to treat because P. aeruginosa adapts to the CF lung, can develop multidrug resistance, and can form biofilms. Despite the clinical significance of P. aeruginosa, modeling P. aeruginosa infections in CF has been challenging. Here, we characterize Scnn1b-transgenic (Tg) BALB/c mice as P. aeruginosa lung infection models. Scnn1b-Tg mice overexpress the epithelial Na+ channel (ENaC) in their lungs, driving increased sodium absorption that causes lung pathology similar to CF. We intranasally infected Scnn1b-Tg mice and wildtype littermates with the laboratory P. aeruginosa strain PAO1 and CF clinical isolates, then assessed differences in bacterial clearance, cytokine responses, and histological features up to 12 days post-infection. Scnn1b-Tg mice carried higher bacterial burdens when infected with biofilm-grown rather than planktonic PAO1; Scnn1b-Tg mice also cleared infections slower than their wildtype littermates. Infection with PAO1 elicited significant increases in pro-inflammatory and Th17-linked cytokines on Day 3. Scnn1b-Tg mice infected with non-mucoid early CF isolates maintained bacterial burdens and mounted immune responses similar to PAO1-infected Scnn1b-Tg mice. In contrast, Scnn1b-Tg mice infected with a mucoid CF isolate carried high bacterial burdens, produced significantly more IL-1β, IL-13, IL-17, IL-22 and KC, and showed severe immune cell infiltration into the bronchioles. Taken together, these results show the promise of Scnn1b-Tg mice as models of early P. aeruginosa colonization in the CF lung.

PMID: 32631918 [PubMed - as supplied by publisher]

Pro con debates in clinical medicine infection prevention and control in cystic fibrosis: One size fits all? The argument in favour.

Paediatr Respir Rev. 2020 Jun 16;:

Authors: Haggie S, Fitzgerald DA

Abstract
This article advocates for a universal approach to infection control measures in cystic fibrosis. The central tenets of infection control include hand hygiene, contact precautions, regular microbiological surveillance and adopting inpatient, outpatient, domestic and social practices to minimise acquisition of common CF pathogens. Infection control measures should be proactive and prospective, assuming all patients harbour aggressive pathogens, and not relying on past culture results. The challenges of implementing these policies include cost, equipment, education, consistency, meticulousness all whilst balancing additional procedures to a busy clinical workload.

PMID: 32631758 [PubMed - as supplied by publisher]

KLF4 Acts as a wt-CFTR Suppressor through an AKT-Mediated Pathway.

Cells. 2020 Jul 02;9(7):

Authors: Sousa L, Pankonien I, Clarke LA, Silva I, Kunzelmann K, Amaral MD

Abstract
Cystic Fibrosis (CF) is caused by >2000 mutations in the CF transmembrane conductance regulator (CFTR) gene, but one mutation-F508del-occurs in ~80% of patients worldwide. Besides its main function as an anion channel, the CFTR protein has been implicated in epithelial differentiation, tissue regeneration, and, when dysfunctional, cancer. However, the mechanisms that regulate such relationships are not fully elucidated. Krüppel-like factors (KLFs) are a family of transcription factors (TFs) playing central roles in development, stem cell differentiation, and proliferation. Herein, we hypothesized that these TFs might have an impact on CFTR expression and function, being its missing link to differentiation. Our results indicate that KLF4 (but not KLF2 nor KLF5) is upregulated in CF vs. non-CF cells and that it negatively regulates wt-CFTR expression and function. Of note, F508del-CFTR expressing cells are insensitive to KLF4 modulation. Next, we investigated which KLF4-related pathways have an effect on CFTR. Our data also show that KLF4 modulates wt-CFTR (but not F508del-CFTR) via both the serine/threonine kinase AKT1 (AKT) and glycogen synthase kinase 3 beta (GSK3β) signaling. While AKT acts positively, GSK3β is a negative regulator of CFTR. This crosstalk between wt-CFTR and KLF4 via AKT/ GSK3β signaling, which is disrupted in CF, constitutes a novel mechanism linking CFTR to the epithelial differentiation.

PMID: 32630830 [PubMed - in process]

Cystic Fibrosis: Overview of the Current Development Trends and Innovative Therapeutic Strategies.

Pharmaceutics. 2020 Jul 02;12(7):

Authors: Almughem FA, Aldossary AM, Tawfik EA, Alomary MN, Alharbi WS, Alshahrani MY, Alshehri AA

Abstract
Cystic Fibrosis (CF), an autosomal recessive genetic disease, is caused by a mutation in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). This mutation reduces the release of chloride ions (Cl-) in epithelial tissues, and hyperactivates the epithelial sodium channels (ENaC) which aid in the absorption of sodium ions (Na+). Consequently, the mucus becomes dehydrated and thickened, making it a suitable medium for microbial growth. CF causes several chronic lung complications like thickened mucus, bacterial infection and inflammation, progressive loss of lung function, and ultimately, death. Until recently, the standard of clinical care in CF treatment had focused on preventing and treating the disease complications. In this review, we have summarized the current knowledge on CF pathogenesis and provided an outlook on the current therapeutic approaches relevant to CF (i.e., CFTR modulators and ENaC inhibitors). The enormous potential in targeting bacterial biofilms using antibiofilm peptides, and the innovative therapeutic strategies in using the CRISPR/Cas approach as a gene-editing tool to repair the CFTR mutation have been reviewed. Finally, we have discussed the wide range of drug delivery systems available, particularly non-viral vectors, and the optimal properties of nanocarriers which are essential for successful drug delivery to the lungs.

PMID: 32630625 [PubMed]

Full Rescue of F508del-CFTR Processing and Function by CFTR Modulators Can Be Achieved by Removal of Two Regulatory Regions.

Int J Mol Sci. 2020 Jun 25;21(12):

Authors: Uliyakina I, Botelho HM, da Paula AC, Afonso S, Lobo MJ, Felício V, Farinha CM, Amaral MD

Abstract
Cystic Fibrosis (CF) is caused by mutations in the CF Transmembrane conductance Regulator (CFTR), the only ATP-binding cassette (ABC) transporter functioning as a channel. Unique to CFTR is a regulatory domain which includes a highly conformationally dynamic region-the regulatory extension (RE). The first nucleotide-binding domain of CFTR contains another dynamic region-regulatory insertion (RI). Removal of RI rescues the trafficking defect of CFTR with F508del, the most common CF-causing mutation. Here we aimed to assess the impact of RE removal (with/without RI or genetic revertants) on F508del-CFTR trafficking and how CFTR modulator drugs VX-809/lumacaftor and VX-770/ivacaftor rescue these variants. We generated cell lines expressing ΔRE and ΔRI CFTR (with/without genetic revertants) and assessed CFTR expression, stability, plasma membrane levels, and channel activity. Our data demonstrated that ΔRI significantly enhanced rescue of F508del-CFTR by VX-809. While the presence of the RI seems to be precluding full rescue of F508del-CFTR processing by VX-809, this region appears essential to rescue its function by VX-770, suggesting some contradictory role in rescue of F508del-CFTR by these two modulators. This negative impact of RI removal on VX-770-stimulated currents on F508del-CFTR can be compensated by deletion of the RE which also leads to the stabilization of this mutant. Despite both regions being conformationally dynamic, RI precludes F508del-CFTR processing while RE affects mostly its stability and channel opening.

PMID: 32630527 [PubMed - in process]

Clinical and Genotypical Features of False-Negative Patients in 26 Years of Cystic Fibrosis Neonatal Screening in Tuscany, Italy.

Diagnostics (Basel). 2020 Jul 01;10(7):

Authors: Taccetti G, Botti M, Terlizzi V, Cavicchi MC, Neri AS, Galici V, Mergni G, Centrone C, Peroni DG, Festini F

Abstract
Cystic fibrosis (CF) is a life-threatening and common genetic disorder. Cystic fibrosis newborn screening (CF NBS) has been implemented in many countries over the last 30 years, becoming a widely accepted public health strategy in economically developed countries. False-negative (FN) cases can occur after CF NBS, with the number depending on the method. We evaluated the delayed diagnosis of CF, identifying the patients who had false-negative CF NBS results over 26 years (1992-2018) in Tuscany, Italy. The introduction of DNA analysis to the newborn screening protocol improved the sensitivity of the test and reduced the FNs. Our experience showed that, overall, at least 8.7% of cases of CF received FNs (18 cases) and were diagnosed later, with an average age of 6.6 years (range: 4 months to 22 years). Respiratory symptoms and salt-loss syndrome (metabolic hypochloremic alkalosis) are suggestive symptoms of CF and were commons events in FN patients. In Tuscany, a region with a high CFTR allelic heterogeneity, the salt-loss syndrome was a common event in FNs. Therefore, we provided evidence to support the claim that the FN patients had CFTR mutations rarer compared with the true-positive cases. We underline the importance of vigilance toward clinical manifestations suggestive of CF on the part of the primary care providers and hospital physicians in a region with an efficient newborn screening program.

PMID: 32630227 [PubMed]

Nonsense Suppression Therapy: New Hypothesis for the Treatment of Inherited Bone Marrow Failure Syndromes.

Int J Mol Sci. 2020 Jun 30;21(13):

Authors: Bezzerri V, Api M, Allegri M, Fabrizzi B, Corey SJ, Cipolli M

Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of cancer-prone genetic diseases characterized by hypocellular bone marrow with impairment in one or more hematopoietic lineages. The pathogenesis of IBMFS involves mutations in several genes which encode for proteins involved in DNA repair, telomere biology and ribosome biogenesis. The classical IBMFS include Shwachman-Diamond syndrome (SDS), Diamond-Blackfan anemia (DBA), Fanconi anemia (FA), dyskeratosis congenita (DC), and severe congenital neutropenia (SCN). IBMFS are associated with high risk of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and solid tumors. Unfortunately, no specific pharmacological therapies have been highly effective for IBMFS. Hematopoietic stem cell transplantation provides a cure for aplastic or myeloid neoplastic complications. However, it does not affect the risk of solid tumors. Since approximately 28% of FA, 24% of SCN, 21% of DBA, 20% of SDS, and 17% of DC patients harbor nonsense mutations in the respective IBMFS-related genes, we discuss the use of the nonsense suppression therapy in these diseases. We recently described the beneficial effect of ataluren, a nonsense suppressor drug, in SDS bone marrow hematopoietic cells ex vivo. A similar approach could be therefore designed for treating other IBMFS. In this review we explain in detail the new generation of nonsense suppressor molecules and their mechanistic roles. Furthermore, we will discuss strengths and limitations of these molecules which are emerging from preclinical and clinical studies. Finally we discuss the state-of-the-art of preclinical and clinical therapeutic studies carried out for IBMFS.

PMID: 32630050 [PubMed - in process]

Emerging Resistance of Gram Negative Pathogens in Community-Acquired Pneumonia.

Semin Respir Crit Care Med. 2020 Aug;41(4):480-495

Authors: Amati F, Restrepo MI

Abstract
In recent decades, there has been a growing interest about the role of gram negative bacteria in community-acquired pneumonia (CAP), especially Pseudomonas aeruginosa, Enterobacteriaceae, and Acinetobacter baumannii. The prevalence of these pathogens differs largely according to the local ecology and the geographical location. Identifying gram negative bacteria, and in particular resistant gram negative bacteria, is of paramount importance in patients with CAP because these pathogens are associated with higher clinical severity and unfavorable outcomes. The use of individualized risk factors to predict each pathogen is a helpful strategy that needs to be locally validated. However, it should be taken into account that most of the risk factors identified in the literature are heterogeneously defined or lack consistency. New diagnostic techniques, such as molecular testing, are promising methods for early detection of these gram negative pathogens. The increasing mechanisms of resistance to antibiotics of these pathogens have limited our therapeutic approach. This narrative review focuses on the epidemiology, risk factors, diagnosis, and therapeutic options for the most relevant gram negative bacteria that cause CAP.

PMID: 32629487 [PubMed - as supplied by publisher]

Characterization of the Mechanism of Action of RDR01752, a Novel Corrector of F508del-CFTR.

Biochem Pharmacol. 2020 Jul 03;:114133

Authors: Lopes-Pacheco M, Silva IAL, Turner MJ, Carlile GW, Sondo E, Thomas DY, Pedemonte N, Hanrahan JW, Amaral MD

Abstract
Despite progress in developing pharmacotherapies to rescue F508del-CFTR, the most prevalent Cystic Fibrosis (CF)-causing mutation, individuals homozygous for this mutation still face several disease-related symptoms. Thus, more potent compound combinations are still needed. Here, we investigated the mechanism of action (MoA) of RDR01752, a novel F508del-CFTR trafficking corrector. F508del-CFTR correction by RDR01752 was assessed by biochemical, immunofluorescence microscopy and functional assays in cell lines and in intestinal organoids. To determine the MoA of RDR01752, we assessed its additive effects to those of genetic revertants of F508del-CFTR, the FDA-approved corrector drugs VX-809 and VX-661, and low temperature. Our data demonstrated that RDR01752 rescues F508del-CFTR processing and plasma membrane (PM) expression to similar levels of VX-809 in cell lines, although RDR01752 produced lower functional rescue. However, in functional assays using intestinal organoids (F508del/F508del), RDR01752, VX-809 and VX-661 had similar efficacy. RDR01752 demonstrated additivity to revertants 4RK and G550E, but not to R1070W, as previously shown for VX-809. RDR01752 was also additive to low temperature. Co-treatment of RDR01752 and VX-809 did not increase F508del-CFTR PM expression and function compared to each corrector alone. The lack of additivity of RDR01752 with the genetic revertant R1070W suggests that this compound has the same effect as the insertion of tryptophan at 1070, i.e., filling the pocket at the NBD1:ICL4 interface in F508del-CFTR, similarly to VX-809. Combination of RDR01752 with correctors mimicking the rescue by revertants G550E or 4RK could thus maximize rescue of F508del-CFTR.

PMID: 32628927 [PubMed - as supplied by publisher]

Treatment of Nontuberculous Mycobacterial Pulmonary Disease: An Official ATS/ERS/ESCMID/IDSA Clinical Practice Guideline: Executive Summary.

Clin Infect Dis. 2020 Jul 06;:

Authors: Daley CL, Iaccarino JM, Lange C, Cambau E, Wallace RJ, Andrejak C, Böttger EC, Brozek J, Griffith DE, Guglielmetti L, Huitt GA, Knight SL, Leitman P, Marras TK, Olivier KN, Santin M, Stout JE, Tortoli E, van Ingen J, Wagner D, Winthrop KL

Abstract
Nontuberculous mycobacteria (NTM) represent over 190 species and subspecies, some of which can produce disease in humans of all ages and can affect both pulmonary and extrapulmonary sites. This guideline focuses on pulmonary disease in adults (without cystic fibrosis or human immunodeficiency virus infection) caused by the most common NTM pathogens such as Mycobacterium avium complex, Mycobacterium kansasii, and Mycobacterium xenopi among the slowly growing NTM and Mycobacterium abscessus among the rapidly growing NTM. A panel of experts was carefully selected by leading international respiratory medicine and infectious diseases societies (ATS, ERS, ESCMID, IDSA) and included specialists in pulmonary medicine, infectious diseases and clinical microbiology, laboratory medicine, and patient advocacy. Systematic reviews were conducted around each of 22 PICO (Population, Intervention, Comparator, Outcome) questions and the recommendations were formulated, written, and graded using the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach. Thirty-one evidence-based recommendations about treatment of NTM pulmonary disease are provided. This guideline is intended for use by healthcare professionals who care for patients with NTM pulmonary disease, including specialists in infectious diseases and pulmonary diseases.

PMID: 32628747 [PubMed - as supplied by publisher]

Paracellular bicarbonate flux across human cystic fibrosis airway epithelia tempers changes in airway surface liquid pH.

J Physiol. 2020 Jul 05;:

Authors: Thornell IM, Rehman T, Pezzulo AA, Welsh MJ

Abstract
KEY POINTS: Cl- and HCO3 - had similar paracellular permeabilities in human airway epithelia. PCl /PNa of airway epithelia was unaltered by pH 7.4 vs. pH 6.0 solutions. Under basal conditions, calculated paracellular HCO3 - flux was secretory. Cytokines that increased airway surface liquid pH decreased or reversed paracellular HCO3 - flux. HCO3 - flux through the paracellular pathway may counterbalance effects of cellular H+ and HCO3 - secretion.
ABSTRACT: Airway epithelia control the pH of airway surface liquid (ASL), thereby optimizing respiratory defenses. Active H+ and HCO3 - secretion by airway epithelial cells produce an ASL that is acidic compared to the interstitial space. The paracellular pathway could provide a route for passive HCO3 - flux that also modifies ASL pH. However, there is limited information about paracellular HCO3 - flux, and it remains uncertain whether an acidic pH produced by loss of CFTR anion channels or proinflammatory cytokines might alter paracellular pathway function. To investigate paracellular HCO3 - transport, we studied differentiated primary cultures of human cystic fibrosis (CF) and non-CF airway epithelia. The paracellular pathway was pH-insensitive at pH 6.0 vs. pH 7.4 and was equally permeable to Cl- and HCO3 - . Under basal conditions at pH ∼6.6, calculated paracellular HCO3 - flux was weakly secretory. Treating epithelia with IL-17 plus TNFα alkalinized ASL pH to ∼7.0, increased paracellular HCO3 - permeability, and paracellular HCO3 - flux was negligible. Applying IL-13 increased ASL pH to ∼7.4 without altering paracellular HCO3 - permeability, and calculated paracellular HCO3 - flux was absorptive. These results suggest that HCO3 - flux through the paracellular pathway counterbalances, in part, changes in ASL pH produced via cellular mechanisms. As the pH of ASL increases towards that of basolateral liquid, paracellular HCO3 - flux becomes absorptive, tempering the alkaline pH generated by transcellular HCO3 - secretion. This article is protected by copyright. All rights reserved.

PMID: 32627187 [PubMed - as supplied by publisher]

Methods for Extraction and Detection of Pf Bacteriophage DNA from the Sputum of Patients with Cystic Fibrosis.

Phage. 2020 Jun 01;1(2):100-108

Authors: Burgener EB, Secor PR, Tracy MC, Sweere JM, Bik EM, Milla CE, Bollyky PL

Abstract
Background: There is increasing interest in the pulmonary microbiome's bacterial and viral communities, particularly in the context of chronic airway infections in cystic fibrosis (CF). However, the isolation of microbial DNA from the sputum from patients with CF is technically challenging and the optimal protocols for the analysis of viral species, including bacteriophage, from clinical samples remains difficult. Materials and Methods: In this study, we evaluate a set of methods developed for processing and analyzing sputum from patients with CF with the goal of detecting Pf bacteriophage virion-derived nucleic acid. We evaluate the impact of bead beating, deoxyribonuclease digestion, and heating steps in these protocols focusing on the quantitative assessment of Pseudomonas aeruginosa and Pf bacteriophage in sputum. Results: Based on these comparative data, we describe an optimized protocol for processing sputum from patients with CF and isolating DNA for polymerase chain reaction or sequencing-based studies. Conclusion: These studies demonstrate the assessment of a specific bacteriophage and bacteria in sputum from patients with CF.

PMID: 32626852 [PubMed]

Urine lipoarabinomannan as a marker for low-risk of NTM infection in the CF airway.

J Cyst Fibros. 2020 Jul 02;:

Authors: De P, Amin AG, Graham B, Martiniano SL, Caceres SM, Poch KR, Jones MC, Saavedra MT, Malcolm KC, Nick JA, Chatterjee D

Abstract
BACKGROUND: Individuals with Cystic fibrosis (CF) are the most vulnerable population for pulmonary infection with nontuberculous mycobacteria (NTM). Screening, diagnosis, and assessment of treatment response currently depend on traditional culture techniques, but sputum analysis for NTM in CF is challenging, and associated with a low sensitivity. The cell wall lipoarabinomannan (LAM), a lipoglycan found in all mycobacterial species, and has been validated as a biomarker in urine for active Mycobacterium tuberculosis infection.
METHODS: Urine from a CF cohort (n = 44) well-characterized for NTM infection status by airway cultures was analyzed for LAM by gas chromatography/mass spectrometry. All subjects with positive sputum cultures for NTM had varying amounts of LAM in their urine. No LAM was detected in subjects who never had a positive culture (14/45). One individual initially classified as NTM sputum negative subsequently developed NTM disease 657 days after the initial urine LAM testing. Repeat urine LAM testing turned positive, correlating to her positive NTM status. Subjects infected with subspecies of M. abscessus had greater LAM quantities than those infected with M. avium complex (MAC). There was no correlation with disease activity or treatment status and LAM quantity. A TB Capture ELISA using anti-LAM antibodies demonstrated very poor sensitivity in identifying individuals with positive NTM sputum cultures.
CONCLUSION: These findings support the conclusion that urine LAM related to NTM infection may be a useful screening test to determine patients at low risk for having a positive NTM sputum culture, as part of a lifetime screening strategy in the CF population.

PMID: 32624408 [PubMed - as supplied by publisher]

Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells.

Nucleic Acids Res. 2020 04 17;48(7):3513-3524

Authors: NandyMazumdar M, Yin S, Paranjapye A, Kerschner JL, Swahn H, Ge A, Leir SH, Harris A

Abstract
The CFTR gene lies within an invariant topologically associated domain (TAD) demarcated by CTCF and cohesin, but shows cell-type specific control mechanisms utilizing different cis-regulatory elements (CRE) within the TAD. Within the respiratory epithelium, more than one cell type expresses CFTR and the molecular mechanisms controlling its transcription are likely divergent between them. Here, we determine how two extragenic CREs that are prominent in epithelial cells in the lung, regulate expression of the gene. We showed earlier that these CREs, located at -44 and -35 kb upstream of the promoter, have strong cell-type-selective enhancer function. They are also responsive to inflammatory mediators and to oxidative stress, consistent with a key role in CF lung disease. Here, we use CRISPR/Cas9 technology to remove these CREs from the endogenous locus in human bronchial epithelial cells. Loss of either site extinguished CFTR expression and abolished long-range interactions between these sites and the gene promoter, suggesting non-redundant enhancers. The deletions also greatly reduced promoter interactions with the 5' TAD boundary. We show substantial recruitment of RNAPII to the -35 kb element and identify CEBPβ as a key activator of airway expression of CFTR, likely through occupancy at this CRE and the gene promoter.

PMID: 32095812 [PubMed - indexed for MEDLINE]

Inhibition of Pseudomonas aeruginosa biofilm formation and expression of virulence genes by selective epimerization in the peptide Esculentin-1a(1-21)NH2.

FEBS J. 2019 10;286(19):3874-3891

Authors: Casciaro B, Lin Q, Afonin S, Loffredo MR, de Turris V, Middel V, Ulrich AS, Di YP, Mangoni ML

Abstract
Pseudomonas aeruginosa is a pathogenic bacterium known to cause serious human infections, especially in immune-compromised patients. This is due to its unique ability to transform from a drug-tolerant planktonic to a more dangerous and treatment-resistant sessile life form, called biofilm. Recently, two derivatives of the frog skin antimicrobial peptide esculentin-1a, i.e. Esc(1-21) and its D-amino acids containing diastereomer Esc(1-21)-1c, were characterized for their powerful anti-Pseudomonal activity against both forms. Prevention of biofilm formation already in its early stages could be even more advantageous for counteracting infections induced by this bacterium. In this work, we studied how the diastereomer Esc(1-21)-1c can inhibit Pseudomonas biofilm formation in comparison to the parent peptide and two clinically-used conventional antibiotics, i.e. colistin and aztreonam, when applied at dosages below the minimal growth inhibitory concentration. Biofilm prevention was correlated to the peptides' ability to inhibit Pseudomonas motility and to reduce the production of virulent metabolites, for example, pyoverdine and rhamnolipids. Furthermore, the molecular mechanism underlying these activities was evaluated by studying the peptides' effect on the expression of key genes involved in the virulence and motility of bacteria, as well as by monitoring the peptides' binding to the bacterial signaling nucleotide ppGpp. Our results demonstrate that the presence of only two D-amino acids in Esc(1-21)-1c is sufficient to downregulate ppGpp-mediated expression of biofilm-associated genes, presumably as a result of higher peptide stability and therefore prolonged interaction with the nucleotide. Overall, these studies should assist efficient design and optimization of new anti-infective agents with multiple pharmacologically beneficial properties.

PMID: 31144441 [PubMed - indexed for MEDLINE]