Digestive system involvement in cystic fibrosis

Modulation of Plasmatic Matrix Metalloprotease 9: A Promising New Tool for Understanding the Variable Clinical Responses of Patients with Cystic Fibrosis to Cystic Fibrosis Transmembrane Conductance Regulator Modulators

BACKGROUND

The most recent modulator combination, elexacaftor/tezacaftor/ivacaftor (Trikafta®), has been shown to improve clinical outcomes in most patients with cystic fibrosis (PwCF). Unfortunately, the clinical benefits are sometimes variable; thus, improving our knowledge of the possible causes of this variability can help reduce it.

METHODS

Circulating mononuclear cells (CMCs) and plasma were collected from 16 PwCF (including those on Trikafta® therapy) and 4 non-CF subjects. Cystic fibrosis transmembrane conductance regulator (CFTR) activity and matrix metalloprotease 9 (MMP9) expression were monitored before and after therapy, together with some clinical parameters. The relationship between MMP9 expression and the modulation of the extracellular-regulated 1/2 (ERK1/2) and nuclear factor-kB (NF-kB) pathways was also analyzed.

RESULTS

MMP9, markedly expressed in the CMCs and plasma of all the patients included in the study, was downregulated in the clinically responsive PwCF. In the non-responder, the MMP9 levels remained high. The modulation of MMP9 following treatment with Trikafta® may be controlled by the NF-kB pathway.

CONCLUSIONS

These data strongly suggest that MMP9 downregulation is a potential biomarker of therapy efficacy and that it could be useful in understanding the molecular events underlying the variable clinical responses of patients to Trikafta®. This knowledge could be helpful for future studies of personalized medicine and thereby ensure improvements in individual responses to therapies.

The Human Respiratory Microbiome: Current Understandings and Future Directions

Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.

A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis

BACKGROUND

This chapter reports the evaluation of two shotgun metaproteomic workflows. The methods were developed to investigate gut dysbiosis via analysis of the faecal microbiota from patients with cystic fibrosis (CF). We aimed to set up an unbiased and effective method to extract the entire proteome, i.e. to extract sufficient bacterial proteins from the faecal samples in combination with a maximum of host proteins giving information on the disease state.

METHODS

Two protocols were compared; the first method involves an enrichment of the bacterial proteins while the second method is a more direct method to generate a whole faecal proteome extract. The different extracts were analysed using denaturing polyacrylamide gel electrophoresis followed by liquid chromatography-tandem mass spectrometry aiming a maximal coverage of the bacterial protein content in faecal samples.

RESULTS AND CONCLUSIONS

In all extracts, microbial proteins are detected, and in addition, nonbacterial proteins are detected in all samples providing information about the host status. Our study demonstrates the huge influence of the used protein extraction method on the obtained result and shows the need for a standardised and appropriate sample preparation for metaproteomic analysis. To address questions on the health status of the patients, a whole protein extract is preferred over a method to enrich the bacterial fraction. In addition, the method of the whole protein fraction is faster, which gives the possibility to analyse more biological replicates.

A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis

Cystic Fibrosis (CF) and its treatment result in an altered gut microbiota composition compared to non-CF controls. However, the impact of this on gut microbiota functionality has not been extensively characterised. Our aim was to conduct a proof-of-principle study to investigate if measurable changes in gut microbiota functionality occur in adult CF patients compared to controls. Metagenomic DNA was extracted from faecal samples from six CF patients and six non-CF controls and shotgun metagenomic sequencing was performed on the MiSeq platform. Metabolomic analysis using gas chromatography-mass spectrometry was conducted on faecal water. The gut microbiota of the CF group was significantly different compared to the non-CF controls, with significantly increased Firmicutes and decreased Bacteroidetes. Functionality was altered, with higher pathway abundances and gene families involved in lipid (e.g. PWY 6284 unsaturated fatty acid biosynthesis (p = 0.016)) and xenobiotic metabolism (e.g. PWY-5430 meta-cleavage pathway of aromatic compounds (p = 0.004)) in CF patients compared to the controls. Significant differences in metabolites occurred between the two groups. This proof-of-principle study demonstrates that measurable changes in gut microbiota functionality occur in CF patients compared to controls. Larger studies are thus needed to interrogate this further.

Increased risk of colorectal neoplasia in adult patients with cystic fibrosis: a matched case-control study

OBJECTIVE

As the lifespan of patients with cystic fibrosis (CF) increases, concerns regarding the occurrence of bowel cancer have arisen. However, previous cohort studies have yielded contradictory results as to the risk of colorectal cancer (CRC) in the CF population. The aim of this study was to determine whether CF is associated with an increased risk of colorectal neoplasia.

METHODS

We performed a matched case-control study at a statewide CF center. Cases were adult CF patients undergoing colonoscopy in a 5-year period from 2007 to 2012. Controls were matched in a 2:1 ratio for age, gender, and colonoscopy indication.

RESULTS

A total of 50 patients with CF who underwent colonoscopy were identified. Among CF patients, there were 5 (10%) cases with CRC, 1 (2%) with ileal adenocarcinoma, 13 (26%) with adenomas, and 16(32%) with advanced adenomas. In contrast, there was 1 (1%) case with CRC, 11 (11%) with adenomas, and 6 (6%) with advanced adenomas identified among controls. Compared to controls, CF was associated with a 10-fold increased risk of CRC (odds ratio [OR] = 10.0, 95% confidence interval [CI]: 1.2-85.6; p = 0.03), threefold increased risk of adenomas (OR = 3.34, 95%CI: 1.23-9.08; p = 0.018], and sevenfold increased risk of advanced adenomas (OR = 6.95, 95% CI: 2.30-21.01; p = 0.001). Moreover, the quality of bowel preparation was significantly worse in CF patients with a fourfold (p = 0.01) increased likelihood of a poor preparation.

CONCLUSIONS

Our data suggest that CF patients are at significantly increased risk of CRC compared to age, sex, and colonoscopy-indication matched controls. Consideration should be given to the introduction of a CRC surveillance program in the CF population.

Cystic fibrosis, gastroduodenal inflammation, duodenal ulcer, and H. pylori infection: the "cystic fibrosis paradox" revisited

BACKGROUND

In cystic fibrosis (CF) patients a duodenal impaired bicarbonate secretion and unbuffered gastric acid are always described and the development of duodenal ulceration is uncommon (CF paradox). Helicobacter pylori (HP) infection is the main cause for duodenal ulceration and its prevalence in CF patients is controversial.

AIM

The objective of this study is to evaluate HP prevalence, gastric histology, and duodenal ulceration in adult FC patients.

METHODS

32 adult CF patients were submitted to (13)C-urea breath test and serum immunoblotting test for HP diagnosis. Among them, 20 patients were submitted to endoscopy.

RESULTS

19/32 (68%) patients showed positive serology. Endoscopy showed erosive duodenitis (15%), and duodenal ulcer scar in 10%. On duodenal histology, 94.5%, showed active inflammation and 66.7% gastric metaplasia.

CONCLUSION

HP infection prevalence in adult CF patients was similar to that of general Brazilian population. CF patients have all the duodenal spectrum of alterations, including duodenal ulcer. CF paradox may not exist.

Cross-sectional and longitudinal comparisons of the predominant fecal microbiota compositions of a group of pediatric patients with cystic fibrosis and their healthy siblings

Although only poorly documented, it can be assumed that intensive antibiotic treatments of chronic lung infections in patients with cystic fibrosis (CF) also affect the diversity and metabolic functioning of the gastrointestinal microbiota and potentially lead to a state of dysbiosis. A better knowledge of the differences in gut microbiota composition and stability between patients with CF and healthy subjects could lead to optimization of current antibiotic therapies and/or development of add-on therapies. Using conventional culturing and population fingerprinting by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA amplicons, we compared the predominant fecal microbiota of 21 patients with CF and 24 healthy siblings in a cross-sectional study. General medium counts, as well as counts on media specific for lactic acid bacteria, clostridia, Bifidobacterium spp., Veillonella spp., and Bacteroides-Prevotella spp., were consistently higher in sibling samples than in CF samples, whereas the reverse was found for enterobacterial counts. DGGE fingerprinting uncovered large intersubject variations in both study groups. On the other hand, the cross-sectional data indicated that the predominant fecal microbiota of patients and siblings had comparable species richness. In addition, a longitudinal study was performed on 7 or 8 consecutive samples collected over a 2-year period from two patients and their respective siblings. For these samples, DGGE profiling indicated an overall trend toward lower temporal stability and lower species richness in the predominant fecal CF microbiota. The observed compositional and dynamic perturbations provide the first evidence of a general dysbiosis in children with CF compared to their siblings.

The switch of intestinal Slc26 exchangers from anion absorptive to HCOFormula secretory mode is dependent on CFTR anion channel function

CFTR has been recognized to function as both an anion channel and a key regulator of Slc26 anion transporters in heterologous expression systems. Whether this regulatory relationship between CFTR and Slc26 transporters is seen in native intestine, and whether this effect is coupled to CFTR transport function or other features of this protein, has not been studied. The duodena of anesthetized CFTR-, NHE3-, Slc26a6-, and Scl26a3-deficient mice and wild-type (WT) littermates were perfused, and duodenal bicarbonate (HCO(3)(-)) secretion (DBS) and fluid absorptive or secretory rates were measured. The selective NHE3 inhibitor S1611 or genetic ablation of NHE3 significantly reduced fluid absorptive rates and increased DBS. Slc26a6 (PAT1) or Slc26a3 (DRA) ablation reduced the S1611-induced DBS increase and reduced fluid absorptive rates, suggesting that the effect of S1611 or NHE3 ablation on HCO(3)(-) secretion may be an unmasking of Slc26a6- and Slc26a3-mediated Cl(-)/HCO(3)(-) exchange activity. In the absence of CFTR expression or after application of the CFTR(inh)-172, fluid absorptive rates were similar to those of WT, but S1611 induced virtually no increase in DBS, demonstrating that CFTR transport activity, and not just its presence, is required for Slc26-mediated duodenal HCO(3)(-) secretion. A functionally active CFTR is an absolute requirement for Slc26-mediated duodenal HCO(3)(-) secretion, but not for Slc26-mediated fluid absorption, in which these transporters operate in conjunction with the Na(+)/H(+) exchanger NHE3. This suggests that Slc26a6 and Slc26a3 need proton recycling via NHE3 to operate in the Cl(-) absorptive mode and Cl(-) exit via CFTR to operate in the HCO(3)(-) secretory mode.