Estimation of GFR in Patients With Cystic Fibrosis: A Cross-Sectional Study.

Can J Kidney Health Dis. 2020;7:2054358119899312

Authors: Wallace A, Price A, Fleischer E, Khoury M, Filler G

Abstract
Background: Patients with cystic fibrosis (CF) have frequent infectious complications requiring nephrotoxic medications, necessitating monitoring of renal function. Although adult studies have suggested that cystatin C (CysC)-based estimated glomerular filtration rate (eGFR) may be preferable due to reduced muscle mass of patients with CF, pediatric patients remain understudied.
Objective: Our objective was to determine which eGFR formula is best for estimating glomerular filtration rate (GFR) in pediatric patients with CF.
Methods: A total of 17 patients with CF treated with nephrotoxic antibiotics were recruited from the Children's Hospital at London Health Sciences Centre, London, Ontario, Canada. 99Tc DTPA GFR (measured GFR [mGFR]) was measured with 4-point measurements starting at 120 minutes using a 2-compartmental model with Brøchner-Mortensen correction, with simultaneous measurement of creatinine, urea, and CysC. The eGFR was calculated using 16 known equations based on creatinine, urea, CysC, or combinations of these. Primary outcome measures were correlation with mGFR, and agreement within 10% for various eGFR equations.
Results: Mean mGFR was 136 ± 21 mL/min/1.73 m2. Mean creatinine, CysC, and urea were 38 ± 10 μmol/L, 0.72 ± 0.08 mg/L, and 3.9 ± 1.4 mmol/L, respectively. The 2014 Grubb CysC eGFR had the best correlation coefficient (r = 0.75, P = .0004); however, only 35% were within 10%. The new Schwartz formula with creatinine and urea had the best agreement within 10%, but a relatively low correlation coefficient (r = 0.63, P = .0065, 64% within 10%).
Conclusions: Our study suggests that none of the eGFR formulae work well in this small cohort of pediatric patients with CF with preserved body composition, possibly due to inflammation causing false elevations of CysC. Based on the small numbers, we cannot conclude which eGFR formula is best.

PMID: 32002189 [PubMed]

Systematic comparison of the protein-protein interaction databases from a user's perspective.

J Biomed Inform. 2020 Jan 27;:103380

Authors: Kumar Bajpai A, Davuluri S, Tiwary K, Narayanan S, Oguru S, Basavaraju K, Dayalan D, Thirumurugan K, Acharya KK

Abstract
In absence of periodic systematic comparisons, biologists/bioinformaticians may be forced to make a subjective selection among the many protein-protein interaction (PPI) databases and tools. We conducted a comprehensive compilation and comparison of such resources. We compiled 375 PPI resources, short-listed 125 important ones (both lists are available at startbioinfo.com), and compared the features and coverage of 16 carefully-selected databases related to human PPIs. We quantitatively compared the coverage of 'experimentally verified' as well as 'total' (experimentally verified as well as predicted) PPIs for these 16 databases. Coverage was compared in two ways: (a) PPIs obtained in response to gene queries using the web interfaces were compared. As a query set, 108 genes expressed differently across tissues (specific to kidney, testis, and uterus, and ubiquitous - i.e., expressed in 43 human normal tissues) or associated with certain diseases (breast cancer, lung cancer, Alzheimer's, cystic fibrosis, diabetes, and cardiomyopathy) were chosen. The coverage was also compared for the well-studied genes versus the less-studied ones. The coverage of the databases for high-quality interactions was separately assessed using a set of literature curated experimentally-proven PPIs (gold standard PPI-set); (b) the back-end-data from 15 PPI databases was downloaded and compared. Combined results from STRING and UniHI covered around 84% of 'experimentally verified' PPIs. Approximately 94% of the 'total' PPIs available across the databases were retrieved by the combined use of hPRINT, STRING, and IID. Among the experimentally verified PPIs found exclusively in each database, STRING contributed around 71% of the hits. The coverage of certain databases was skewed for some gene-types. Analysis with the gold-standard PPI-set revealed that GPS-Prot, STRING, APID, and HIPPIE, each covered ∼70% of the curated interactions. The database usage frequencies did not always correlate with their respective advantages, thereby justifying the need for more frequent studies of this nature.

PMID: 32001390 [PubMed - as supplied by publisher]

Opportunities for machine learning to transform care for people with cystic fibrosis.

J Cyst Fibros. 2020 Jan;19(1):6-8

Authors: Abroshan M, Alaa AM, Rayner O, van der Schaar M

PMID: 32000972 [PubMed - in process]

Inhibition of Sphingolipid Synthesis as a Phenotype-Modifying Therapy in Cystic Fibrosis.

Cell Physiol Biochem. 2020 Jan 31;54(1):110-125

Authors: Mingione A, Cas MD, Bonezzi F, Caretti A, Piccoli M, Anastasia L, Ghidoni R, Paroni R, Signorelli P

Abstract
BACKGROUND/AIMS: Cystic Fibrosis (CF) is an inherited disease associated with a variety of mutations affecting the CFTR gene. A deletion of phenylalanine 508 (F508) affects more than 70% of patients and results in unfolded proteins accumulation, originating a proteinopathy responsible for inflammation, impaired trafficking, altered metabolism, cholesterol and lipids accumulation, impaired autophagy at the cellular level. Lung inflammation has been extensively related to the accumulation of the lipotoxin ceramide. We recently proved that inhibition of ceramide synthesis by Myriocin reduces inflammation and ameliorates the defence response against pathogens infection, which is downregulated in CF. Here, we aim at demonstrating the mechanisms of Myriocin therapeutic effects in Cystic Fibrosis broncho-epithelial cells.
METHODS: The effect of Myriocin treatment, on F508-CFTR bronchial epithelial cell line IB3-1 cells, was studied by evaluating the expression of key proteins and genes involved in autophagy and lipid metabolism, by western blotting and real time PCR. Moreover, the amount of glycerol-phospholipids, triglycerides, and cholesterols, sphingomyelins and ceramides were measured in treated and untreated cells by LC-MS. Finally, Sptlc1 was transiently silenced and the effect on ceramide content, autophagy and transcriptional activities was evaluated as above mentioned.
RESULTS: We demonstrate that Myriocin tightly regulates metabolic function and cell resilience to stress. Myriocin moves a transcriptional program that activates TFEB, major lipid metabolism and autophagy regulator, and FOXOs, central lipid metabolism and anti-inflammatory/anti-oxidant regulators. The activity of these transcriptional factors is associated with the induction of PPARs nuclear receptors activity, whose targets are genes involved in lipid transport compartmentalization and oxidation. Transient silencing of SPTCL1 recapitulates the effects induced by Myriocin.
CONCLUSION: Cystic Fibrosis bronchial epithelia accumulate lipids, exacerbating inflammation. Myriocin administration: i) activates the transcriptions of genes involved in enhancing autophagy-mediated stress clearance; ii) reduces the content of several lipid species and, at the same time, iii) enhances mitochondrial lipid oxidation. Silencing the expression of Sptlc1 reproduces Myriocin induced autophagy and transcriptional activities, demonstrating that the inhibition of sphingolipid synthesis drives a transcriptional program aimed at addressing cell metabolism towards lipid oxidation and at exploiting autophagy mediated clearance of stress. We speculate that regulating sphingolipid de novo synthesis can relieve from chronic inflammation, improving energy supply and anti-oxidant responses, indicating an innovative therapeutic strategy for CF.

PMID: 31999897 [PubMed - in process]

Elexacaftor/tezacaftor/ivacaftor (Trikafta) for cystic fibrosis.

Med Lett Drugs Ther. 2020 Jan 13;62(1589):5-7

Authors:

PMID: 31999662 [PubMed - in process]

Downregulation of CFTR Is Involved in the Formation of Hypertrophic Scars.

Biomed Res Int. 2020;2020:9526289

Authors: Zhou Y, Zhao Y, Du H, Suo Y, Chen H, Li H, Liang X, Li Q, Huang X

Abstract
Hypertrophic Scars (HTSs) are a complex fibroproliferative disorder, and their exact mechanism is still not fully understood. In this study, we first found that cystic fibrosis transmembrane conductance regulator (CFTR) expression was downregulated in human hypertrophic scars at the RNA and protein levels by microarray data analysis, RT-PCR, and immunofluorescence (IF) staining. To validate that this downregulation of CFTR is involved in the formation of HTSs, we then applied a mechanical overloading intervention in both wild type and CFTR-mutant mice (ΔF508). Our results showed thatΔF508 mice exhibited delayed wound healing and a significantly larger HTS on day 28. Masson staining revealed that there was more collagen deposition in the HTS, and Sirius red staining and IF staining showed a higher ratio of collagen 1/collagen 3 (Col1/Col3) in ΔF508 mice. Real-time RT-PCR showed that the proinflammatory markers were higher in ΔF508 mice in all phases of scar formation, whereas the proliferation marker was similar. Moreover, we harvested the fibroblasts from both mice. Western blotting showed that the expression of Col1 was the same in both mice, and the expression of Col3 was significantly lower in ΔF508 mice. However, in a mechanical overloading condition, the expression of Col1 was significantly higher in ΔF508 mice, and the expression of Col3 was the same in both mice. Taken together, our results indicate that the downregulation of CFTR might affect the function of fibroblasts, resulting in a lower level of collagen type 3 and a higher ratio of Col1/Col3, and thus aggravate the formation of HTSs in mechanical overloading conditions.

PMID: 31998800 [PubMed - in process]

Glycosylation changes in inflammatory diseases.

Adv Protein Chem Struct Biol. 2020;119:111-156

Authors: Groux-Degroote S, Cavdarli S, Uchimura K, Allain F, Delannoy P

Abstract
Glycosylation is one of the most important modifications of proteins and lipids, and cell surface glycoconjugates are thought to play important roles in a variety of biological functions including cell-cell and cell-substrate interactions, bacterial adhesion, cell immunogenicity and cell signaling. Alterations of glycosylation are observed in a number of inflammatory diseases. Pro-inflammatory cytokines have been shown to modulate cell surface glycosylation by regulating the expression of glycosyltransferases and sulfotransferases involved in the biosynthesis of glycan chains, inducing the expression of specific carbohydrate antigens at the cell surface that can be recognized by different types of lectins or by bacterial adhesins, contributing to the development of diseases. Glycosylation can also regulate biological functions of immune cells by recruiting leukocytes to inflammation sites with pro- or anti-inflammatory effects. Cell surface proteoglycans provide a large panel of binding sites for many mediators of inflammation, and regulate their bio-availability and functions. In this review, we summarize the current knowledge of the glycosylation changes occurring in mucin type O-linked glycans, glycosaminoglycans, as well as in glycosphingolipids, with a particular focus on cystic fibrosis and neurodegenerative diseases, and their consequences on cell interactions and disease progression.

PMID: 31997767 [PubMed - in process]

The current status and further prospects for lung magnetic resonance imaging in pediatric radiology.

Pediatr Radiol. 2020 Jan 29;:

Authors: Hirsch FW, Sorge I, Vogel-Claussen J, Roth C, Gräfe D, Päts A, Voskrebenzev A, Anders RM

Abstract
Lung MRI makes it possible to replace up to 90% of CT examinations with radiation-free magnetic resonance diagnostics of the lungs without suffering any diagnostic loss. The individual radiation exposure can thus be relevantly reduced. This applies in particular to children who repeatedly require sectional imaging of the lung, e.g., in tumor surveillance or in chronic lung diseases such as cystic fibrosis. In this paper we discuss various factors that favor the establishment of lung MRI in the clinical setting. Among the many sequences proposed for lung imaging, respiration-triggered T2-W turbo spin-echo (TSE) sequences have been established as a good standard for children. Additional sequences are mostly dispensable. The most important pulmonary findings are demonstrated here in the form of a detailed pictorial essay. T1-weighted gradient echo sequences with ultrashort echo time are a new option. These sequences anticipate signal loss in the lung and deliver CT-like images with high spatial resolution. When using self-gated T1-W ultrashort echo time 3-D sequences that acquire iso-voxel geometry in the sub-millimeter range, secondary reconstructions are possible.

PMID: 31996938 [PubMed - as supplied by publisher]

Author Correction: A human ciliopathy reveals essential functions for NEK10 in airway mucociliary clearance.

Nat Med. 2020 Jan 29;:

Authors: Chivukula RR, Montoro DT, Leung HM, Yang J, Shamseldin HE, Taylor MS, Dougherty GW, Zariwala MA, Carson J, Daniels MLA, Sears PR, Black KE, Hariri LP, Almogarri I, Frenkel EM, Vinarsky V, Omran H, Knowles MR, Tearney GJ, Alkuraya FS, Sabatini DM

Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.

PMID: 31996837 [PubMed - as supplied by publisher]

Mutation on lysX from Mycobacterium avium hominissuis impacts the host-pathogen interaction and virulence phenotype.

Virulence. 2020 Dec;11(1):132-144

Authors: Kirubakar G, Schäfer H, Rickerts V, Schwarz C, Lewin A

Abstract
The lysX gene from Mycobacterium avium hominissuis (MAH) is not only involved in cationic antimicrobial resistance but also regulates metabolic activity. An MAH lysX deficient mutant was shown to exhibit a metabolic shift at the extracellular state preadapting the bacteria to the conditions inside host-cells. It further showed stronger growth in human monocytes. In the present study, the LysX activity on host-pathogen interactions were analyzed. The lysX mutant from MAH proved to be more sensitive toward host-mediated stresses such as reactive oxygen species. Further, the lysX mutant exhibited increased inflammatory response in PBMC and multinucleated giant cell (MGC) formation in human macrophages during infection studies. Coincidentally, the lysX mutant strain revealed to be more reproductive in the Galleria mellonella infection model. Together, these data demonstrate that LysX plays a role in regulating the bacillary load in host organisms and the lack of lysX gene facilitates MAH adaptation to intracellular host-habitat, thereby suggesting an essential role of LysX in the modulation of host-pathogen interaction.

PMID: 31996090 [PubMed - in process]

Structural and Biophysical Analysis of the CLCA1 VWA Domain Suggests Mode of TMEM16A Engagement.

Cell Rep. 2020 Jan 17;:

Authors: Berry KN, Brett TJ

Abstract
The secreted protein calcium-activated chloride channel regulator 1 (CLCA1) utilizes a von Willebrand factor type A (VWA) domain to bind to and potentiate the calcium-activated chloride channel TMEM16A. To gain insight into this unique potentiation mechanism, we determined the 2.0-Å crystal structure of human CLCA1 VWA bound to Ca2+. The structure reveals the metal-ion-dependent adhesion site (MIDAS) in a high-affinity "open" conformation, engaging in crystal contacts that likely mimic how CLCA1 engages TMEM16A. The CLCA1 VWA contains a disulfide bond between α3 and α4 in close proximity to the MIDAS that is invariant in the CLCA family and unique in VWA structures. Further biophysical studies indicate that CLCA1 VWA is preferably stabilized by Mg2+ over Ca2+ and that α6 atypically extends from the VWA core. Finally, an analysis of TMEM16A structures suggests residues likely to mediate interaction with CLCA1 VWA.

PMID: 31995732 [PubMed - as supplied by publisher]

Intravital microscopic optical coherence tomography imaging to assess mucus mobilizing interventions for muco-obstructive lung disease in mice.

Am J Physiol Lung Cell Mol Physiol. 2020 Jan 29;:

Authors: Pieper M, Schulz-Hildebrandt H, Mall MA, Hüttmann G, König P

Abstract
Airway mucus obstruction is a hallmark of chronic lung diseases such as cystic fibrosis, asthma and COPD, and the development of more effective mucus mobilizing therapies remains an important unmet need for patients with these muco-obstructive lung diseases. However, methods for sensitive visualization and quantitative assessment of immediate effects of therapeutic interventions on mucus clearance in vivo are lacking. In this study, we determined if newly developed high-speed microscopic optical coherence tomography (mOCT) is sensitive to detect and compare in vivo effects of inhaled isotonic saline, hypertonic saline and bicarbonate on mucus mobilization and clearance in Scnn1b-transgenic mice with muco-obstructive lung disease. In vivomOCT imaging showed that inhaled isotonic saline-induced rapid mobilization of mucus that was mainly transported as chunks from the lower airways of Scnn1b-transgenic mice. Hypertonic saline mobilized a significantly greater amount of mucus that showed a more uniform distribution compared to isotonic saline. Addition of bicarbonate to isotonic saline had no effect on mucus mobilization, but also led to a more uniform mucus layer compared to treatment with isotonic saline alone. mOCT can detect differences in response to mucus mobilizing interventions in vivo, and may thus support the development of more effective therapies for patients with muco-obstructive lung diseases.

PMID: 31994896 [PubMed - as supplied by publisher]

Regulatory SNP rs5743417 impairs constitutive expression of human β-defensin 1 and has high frequency in Africans and Afro-Americans.

Int J Immunogenet. 2020 Jan 29;:

Authors: Cruz Díaz LA, Gutiérrez Ortega A, Chávez Álvarez RDC, Velarde Félix JS, Prado Montes de Oca E

Abstract
The prediction of regulatory single nucleotide polymorphisms (rSNPs) in proximal promoters of disease-related genes could be a useful tool for personalized medicine in both patient stratification and customized therapy. Using our previously reported method of rSNPs prediction (currently a software called SNPClinic v.1.0) as well as with PredictSNP tool, we performed in silico prediction of regulatory SNPs in the antimicrobial peptide human β-defensin 1 gene in three human cell lines from 1,000 Genomes Project (1kGP), namely A549 (epithelial cell line), HL-60 (neutrophils) and TH 1 (lymphocytes). These predictions were run in a proximal pseudo-promoter comprising all common alleles on each polymorphic site according to the 1,000 Genomes Project data (1kGP: ALL). Plasmid vectors containing either the major or the minor allele of a putative rSNP rs5743417 (categorized as regulatory by SNPClinic and confirmed by PredictSNP) and a non-rSNP negative control were transfected to lung A549 human epithelial cell line. We assessed functionality of rSNPs by qPCR using the Pfaffl method. In A549 cells, minor allele of the SNP rs5743417 G→A showed a significant reduction in gene expression, diminishing DEFB1 transcription by 33% when compared with the G major allele (p-value = .03). SNP rs5743417 minor allele has high frequency in Gambians (8%, 1kGP population: GWD) and Afro-Americans (3.3%, 1kGP population: ASW). This SNP alters three transcription factors binding sites (TFBSs) comprising SREBP2 (sterols and haematopoietic pathways), CREB1 (cAMP, insulin and TNF pathways) and JUND (apoptosis, senescence and stress pathways) in the proximal promoter of DEFB1. Further in silico analysis reveals that this SNP also overlaps with GS1-24F4.2, a lincRNA gene complementary to the X Kell blood group related 5 (XKR5) mRNA. The potential clinical impact of the altered constitutive expression of DEFB1 caused by rSNP rs5743417 in DEFB1-associated diseases as tuberculosis, COPD, asthma, cystic fibrosis and cancer in African and Afro-American populations deserves further research.

PMID: 31994826 [PubMed - as supplied by publisher]

Prevalence and Risk Factors for Iron Deficiency in Adults With Cystic Fibrosis.

Nutr Clin Pract. 2020 Jan 29;:

Authors: Gettle LS, Harden A, Bridges M, Albon D

Abstract
BACKGROUND: Iron deficiency is common in cystic fibrosis (CF), but previous prevalence studies often reported results confounded by acute exacerbations. This single-center retrospective study aimed to identify the prevalence of iron deficiency in a stable adult CF population, identify the risk factors associated with iron deficiency, and compare common laboratory indicators of iron status.
METHODS: Medical charts of 105 patients aged 18-67 were reviewed to determine the prevalence of anemia. Of these patients, a subgroup of 67 were included in analyses of iron deficiency, defined as serum ferritin < 12 ng/mL and/or percent transferrin saturation (TSAT) < 16%. Data on sex, age, body mass index, anemia status, vitamin deficiencies, presence of comorbidities, colonization with Pseudomonas aeruginosa, and use of acid blockers and CF transmembrane conductance regulator modulators were collected to evaluate relationship of iron deficiency with these clinical factors. κ agreements between serum iron, ferritin, transferrin, and TSAT were compared.
RESULTS: In this stable CF population, the prevalence of iron deficiency was 41.8% (n = 67), and the prevalence of anemia was 33.3% (n = 105). Iron deficiency was associated with presence of anemia (P < .001), vitamin A deficiency (P = .012), and moderate (P = .047) and severe lung disease (P = .045) compared with mild lung disease. Transferrin agreed poorly with other iron status indicators.
CONCLUSION: Iron deficiency is common in CF, although prevalence rates can vary widely depending on the laboratory parameters used. CF centers should consider routine screening for iron deficiency.

PMID: 31994790 [PubMed - as supplied by publisher]

Impaired counterregulatory responses to hypoglycaemia following oral glucose in adults with cystic fibrosis.

Diabetologia. 2020 Jan 29;:

Authors: Aitken ML, Szkudlinska MA, Boyko EJ, Ng D, Utzschneider KM, Kahn SE

Abstract
AIMS/HYPOTHESIS: The aim of this study was to determine the mechanism(s) for hypoglycaemia occurring late following oral glucose loading in patients with cystic fibrosis (CF).
METHODS: A 3 h 75 g OGTT was performed in 27 non-diabetic adults with CF who were classified based on this test as experiencing hypoglycaemia (glucose <3.3 mmol/l with or without symptoms or glucose <3.9 mmol/l with symptoms, n = 14) or not (n = 13). Beta cell function, incretin (glucagon-like peptide-1 [GLP-1] and glucose-dependent insulinotropic peptide [GIP]) and counterregulatory hormone responses (glucagon, catecholamines, growth hormone and cortisol) were assessed.
RESULTS: The two groups did not differ in age, weight or BMI. There were more male participants and individuals with pancreatic exocrine insufficiency in the hypoglycaemia group. Fasting plasma glucose did not differ between the two groups (5.3 ± 0.16 vs 5.3 ± 0.10 mmol/l). Both fasting insulin (20.7 ± 2.9 vs 36.5 ± 4.8 pmol/l; p = 0.009) and C-peptide (0.38 ± 0.03 vs 0.56 ± 0.05 nmol/l; p = 0.002) were lower in those who experienced hypoglycaemia. Following glucose ingestion, glucose concentrations were significantly lower in the hypoglycaemia group from 135 min onwards, with a nadir of 3.2 ± 0.2 vs 4.8 ± 0.3 mmol/l at 180 min (p < 0.001). The test was terminated early in three participants because of a glucose level <2.5 mmol/l. Insulin and C-peptide concentrations were also lower in the hypoglycaemia group, while incretin hormone responses were not different. Modelling demonstrated that those experiencing hypoglycaemia were more insulin sensitive (439 ± 17.3 vs 398 ± 13.1 ml min-1 m-2, p = 0.074 based on values until 120 min [n = 14]; 512 ± 18.9 vs 438 ± 15.5 ml min-1 m-2, p = 0.006 based on values until 180 min [n = 11]). In line with their better insulin sensitivity, those experiencing hypoglycaemia had lower insulin secretion rates (ISRfasting: 50.8 ± 3.2 vs 74.0 ± 5.9 pmol min-1 m-2, p = 0.002; ISROGTT: 44.9 ± 5.0 vs 63.4 ± 5.2 nmol/m2, p = 0.018) and beta cell glucose sensitivity (47.4 ± 4.5 vs 79.2 ± 7.5 pmol min-1 m-2 [mmol/l]-1, p = 0.001). Despite the difference in glucose concentrations, there were no significant increases in glucagon, noradrenaline, cortisol or growth hormone levels. Adrenaline increased by only 66% and 61% above baseline at 165 and 180 min when glucose concentrations were 3.8 ± 0.2 and 3.2 ± 0.2 mmol/l, respectively.
CONCLUSIONS/INTERPRETATION: Hypoglycaemia occurring late during an OGTT in people with CF was not associated with the expected counterregulatory hormone response, which may be a consequence of more advanced pancreatic dysfunction/destruction.

PMID: 31993716 [PubMed - as supplied by publisher]

Impact of Pseudomonas aeruginosa Isolation on Mortality and Outcomes in an Outpatient Chronic Obstructive Pulmonary Disease Cohort.

Open Forum Infect Dis. 2020 Jan;7(1):ofz546

Authors: Jacobs DM, Ochs-Balcom HM, Noyes K, Zhao J, Leung WY, Pu CY, Murphy TF, Sethi S

Abstract
Background: Tracheobronchial colonization by Pseudomonas aeruginosa (PA) has been shown to negatively impact outcomes in cystic fibrosis and bronchiectasis. There is uncertainty whether the same association is prevalent in chronic obstructive pulmonary disease (COPD), especially in the outpatient setting. Our objective was to determine (1) whether PA isolation is associated with mortality and (2) changes in exacerbation and hospitalization rates within a longitudinal cohort of COPD outpatients.
Methods: Pseudomonas aeruginosa colonization was ascertained in monthly sputum cultures in a prospective cohort of COPD patients from 1994 to 2014. All-cause mortality was compared between patients who were colonized during their follow-up period (PA + ) and those who remained free of colonization (PA - ); Cox proportional hazards models were used. Exacerbation and hospitalization rates were evaluated by 2-rate χ 2 and segmented regression analysis for 12 months before and 24 months after PA isolation.
Results: Pseudomonas aeruginosa was isolated from sputum in 73 of 181 (40%) patients. Increased mortality was seen with PA isolation: 56 of 73 (77%) PA +  patients died compared with 73 of 108 (68%) PA - patients (P = .004). In adjusted models, PA +  patients had a 47% higher risk of mortality (adjusted hazard ratio = 1.47; 95% confidence interval, 1.03-2.11; P = .04). Exacerbation rates were higher for the PA +  group during preisolation (15.4 vs 9.0 per 100 person-months, P < .001) and postisolation periods (15.7 vs 7.5, P < .001). Hospitalization rates were higher during the postisolation period among PA +  patients (6.25 vs 2.44, P < .001).
Conclusions: Tracheobronchial colonization by PA in COPD outpatients was associated with higher morbidity and mortality. This suggests that PA likely contributes to adverse clinical outcomes rather than just a marker of worsening disease.

PMID: 31993457 [PubMed]

Effects of Signal Disruption Depends on the Substrate Preference of the Lactonase.

Front Microbiol. 2019;10:3003

Authors: Mahan K, Martinmaki R, Larus I, Sikdar R, Dunitz J, Elias M

Abstract
Many bacteria produce and use extracellular signaling molecules such as acyl homoserine lactones (AHLs) to communicate and coordinate behavior in a cell-density dependent manner, via a communication system called quorum sensing (QS). This system regulates behaviors including but not limited to virulence and biofilm formation. We focused on Pseudomonas aeruginosa, a human opportunistic pathogen that is involved in acute and chronic lung infections and which disproportionately affects people with cystic fibrosis. P. aeruginosa infections are becoming increasingly challenging to treat with the spread of antibiotic resistance. Therefore, QS disruption approaches, known as quorum quenching, are appealing due to their potential to control the virulence of resistant strains. Interestingly, P. aeruginosa is known to simultaneously utilize two main QS circuits, one based on C4-AHL, the other with 3-oxo-C12-AHL. Here, we evaluated the effects of signal disruption on 39 cystic fibrosis clinical isolates of P. aeruginosa, including drug resistant strains. We used two enzymes capable of degrading AHLs, known as lactonases, with distinct substrate preference: one degrading 3-oxo-C12-AHL, the other degrading both C4-AHL and 3-oxo-C12-AHL. Two lactonases were used to determine the effects of signal disruption on the clinical isolates, and to evaluate the importance of the QS circuits by measuring effects on virulence factors (elastase, protease, and pyocyanin) and biofilm formation. Signal disruption results in at least one of these factors being inhibited for most isolates (92%). Virulence factor activity or production were inhibited by up to 100% and biofilm was inhibited by an average of 2.3 fold. Remarkably, the treatments led to distinct inhibition profiles of the isolates; the treatment with the lactonase degrading both signaling molecules resulted in a higher fraction of inhibited isolates (77% vs. 67%), and the simultaneous inhibition of more virulence factors per strain (2 vs. 1.5). This finding suggests that the lactonase AHL preference is key to its inhibitory spectrum and is an essential parameter to improve quorum quenching strategies.

PMID: 31993034 [PubMed]

Physical Activity Level and Perception of Exercise in Cystic Fibrosis.

Respir Care. 2020 Jan 28;:

Authors: Burnett DM, Barry AN, Mermis JD

Abstract
BACKGROUND: More patients with cystic fibrosis (CF) are living longer, and lifestyle-related behavior is becoming increasingly important for improving morbidity and mortality. Declining levels of exercise leads to low cardiorespiratory fitness, which is a strong, independent predictor of mortality in patients with CF. As a result, exercise training has become a commonly accepted form of treatment for patients with CF. The purpose of this study was to determine physical activity levels and perception of exercise in adult patients with CF.
METHODS: Adult patients from an in-patient CF unit were recruited to participate. A structured interview and self-report questionnaires were used to collect information on levels of physical activity and exercise perception including preferences, readiness, and barriers.
RESULTS: Forty-six adult patients with CF consented to participate in the interview and completed self-report questionnaires. Subjects self-reported that the majority (84%) of their time was spent performing physical activity at a moderate level, with mean ± SD of 11.8 ± 12.2 h per week of moderate physical activity. Vigorous physical activity was described as hard and very hard physical activity, with a mean ± SD of 1.8 ± 4.6 h (13%) and 0.4 ± 1.6 h (3%), respectively. Most of the adult subjects with CF preferred walking, and 65% of them felt that exercise was very important. Lack of energy, lack of good health, lack of self-discipline, and lack of time were noted as the most frequent barriers to exercise.
CONCLUSION: In this study, adult subjects with CF self-reported performing an adequate amount of moderate physical activity, although only a small proportion of time was spent at a vigorous level of physical activity. Clinicians providing rehabilitation have an opportunity to improve adherence to prescribed exercise by understanding the impact that physiological and psychological factors have on patients with CF. Further, motivating patients with CF to engage in more vigorous physical activity may provide a stimulus that improves clinical outcomes and potentially survival.

PMID: 31992663 [PubMed - as supplied by publisher]

Cystic fibrosis heterozygosity: Carrier state or haploinsufficiency?

Proc Natl Acad Sci U S A. 2020 Jan 28;:

Authors: Fisman D

PMID: 31992636 [PubMed - as supplied by publisher]

Interactions between the gut microbiome and host gene regulation in cystic fibrosis.

Genome Med. 2020 Jan 28;12(1):12

Authors: Dayama G, Priya S, Niccum DE, Khoruts A, Blekhman R

Abstract
BACKGROUND: Cystic fibrosis is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in the CFTR gene, leading to poor hydration of mucus and impairment of the respiratory, digestive, and reproductive organ functions. Advancements in medical care have led to markedly increased longevity of patients with cystic fibrosis, but new complications have emerged, such as early onset of colorectal cancer. Although the pathogenesis of colorectal cancer in cystic fibrosis remains unclear, altered host-microbe interactions might play a critical role. To investigate this, we characterized changes in the microbiome and host gene expression in the colonic mucosa of cystic fibrosis patients relative to healthy controls, and identified host gene-microbiome interactions in the colon of cystic fibrosis patients.
METHODS: We performed RNA-seq on colonic mucosa samples from cystic fibrosis patients and healthy controls to determine differentially expressed host genes. We also performed 16S rRNA sequencing to characterize the colonic mucosal microbiome and identify gut microbes that are differentially abundant between patients and healthy controls. Lastly, we modeled associations between relative abundances of specific bacterial taxa in the gut mucosa and host gene expression.
RESULTS: We find that 1543 genes, including CFTR, show differential expression in the colon of cystic fibrosis patients compared to healthy controls. These genes are enriched with functions related to gastrointestinal and colorectal cancer, such as metastasis of colorectal cancer, tumor suppression, p53, and mTOR signaling pathways. In addition, patients with cystic fibrosis show decreased gut microbial diversity, decreased abundance of butyrate producing bacteria, such as Ruminococcaceae and Butyricimonas, and increased abundance of other taxa, such as Actinobacteria and Clostridium. An integrative analysis identified colorectal cancer-related genes, including LCN2 and DUOX2, for which gene expression is correlated with the abundance of colorectal cancer-associated bacteria, such as Ruminococcaceae and Veillonella.
CONCLUSIONS: In addition to characterizing host gene expression and mucosal microbiome in cystic fibrosis patients, our study explored the potential role of host-microbe interactions in the etiology of colorectal cancer in cystic fibrosis. Our results provide biomarkers that may potentially serve as targets for stratifying risk of colorectal cancer in patients with cystic fibrosis.

PMID: 31992345 [PubMed - in process]