Gut microbiota in adults with cystic fibrosis: Implications for the severity of the CFTR gene mutation and nutritional status

Activation of CFTR-specific T Cells in Cystic Fibrosis Mice Following Gene Transfer

BackgroundCystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed.ResultsThe CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (−0.383, Simpson’s Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity.ConclusionsThis is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.

Cystic fibrosis (CF) is a common recessive disorder caused by >1600 mutations in the CF transmembrane conductance regulator (CFTR) gene. About 13% of CFTR mutations are classified as "splicing mutations," but for almost 40% of these, their role in affecting the pre-mRNA splicing of the gene is not yet defined. In this work, we describe a new splicing mutation detected in three unrelated Italian CF patients. By DNA analyses and mRNA studies, we identified the c.1002-1110_1113delTAAG mutation localized in intron 6b of the CFTR gene. At the mRNA level, this mutation creates an aberrant inclusion of a sequence of 101 nucleotides between exons 6b and 7. This sequence corresponds to a portion of intron 6b and resembles a cryptic exon because it is characterized by an upstream ag and a downstream gt sequence, which are most probably recognized as 5'- and 3'-splice sites by the spliceosome. Through functional analysis of this splicing defect, we show that this mutation abolishes the interaction of the splicing regulatory protein heterogeneous nuclear ribonucleoprotein A2/B1 with an intronic splicing regulatory element and creates a new recognition motif for the SRp75 splicing factor, causing activation of the cryptic exon. Our results show that the c.1002-1110_1113delTAAG mutation creates a new intronic splicing regulatory element in intron 6b of the CFTR gene exclusively recognized by SRp75.

Molecular and Functional Analysis of the Large 5′ Promoter Region of CFTR Gene Revealed Pathogenic Mutations in CF and CFTR-Related Disorders

Cystic fibrosis (CF) is associated with fatty acid alterations characterized by low linoleic and docosahexaenoic acid. It is not clear whether these fatty acid alterations are directly linked to cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction or result from nutrient malabsorption. We hypothesized that if fatty acid alterations are a result of CFTR dysfunction, those alterations should be demonstrable in CF cell culture models. Two CF airway epithelial cell lines were used: 16HBE, sense and antisense CFTR cells, and C38/IB3-1 cells. Wild-type (WT) and CF cells were cultured in 10% fetal bovine serum (FBS) or 10% horse serum. Fatty acid levels were analyzed by GC-MS. Culture of both WT and CF cells in FBS resulted in very low linoleic acid levels. When cells were cultured in horse serum containing concentrations of linoleic acid matching those found in human plasma, physiological levels of linoleic acid were obtained and fatty acid alterations characteristic of CF tissues were then evident in CF compared with WT cells. Kinetic studies with radiolabeled linoleic acid demonstrated in CF cells increased conversion to longer and more-desaturated fatty acids such as arachidonic acid. In conclusion, these data demonstrate that CFTR dysfunction is associated with altered fatty acid metabolism in cultured airway epithelial cells.

Relative Contribution of Genetic and Nongenetic Modifiers to Intestinal Obstruction in Cystic Fibrosis

Gene Therapy for Cystic Fibrosis: Lessons Learned and Paths Forward

The field of personalized medicine, based on genetic information, represents a tremendous but largely unfulfilled opportunity for a future generation of therapies [1]. While better clinical outcomes have been realized using predictive biomarkers in some forms of cancer [2], the influence of genetic information on the treatment of most other human diseases has been limited. However, in the case of the inherited genetic disease cystic fibrosis (CF), pre-emptive possibilities have recently been uncovered. In particular, an investigational drug known as VX-770, has demonstrated great promise in clinical trials in patients with a specific cystic fibrosis transmembrane conductance regulator (CFTR) allele selected for clinical investigation based on data from in vitro studies [3,4]. This article highlights some of the opportunities and challenges associated with developing novel genotype-directed therapies for CF.

HIGHLIGHTS FROM THE LITERATURE

Fertility in Patients With Cystic Fibrosis

Nasal polyposis in atypical cystic fibrosis: A case report

The human gut microbiota comprises approximately 100 trillion microbial cells and produces a wide range of metabolites. Its composition is shaped by factors such as geography, dietary habits, and genetic background. Dysbiosis-an imbalance in this microbial ecosystem-has been associated with the development of metabolic diseases. This study aimed to characterize the gut microbiota composition in adults without diagnosed chronic diseases and assess its potential associations with cardiometabolic parameters. Volunteers over the age of 18 residing in Izmir province who met the inclusion criteria were enrolled in the study. Fecal and blood samples were collected from all participants. Bacterial DNA from fecal samples was extracted, and the full-length 16S rRNA was amplified. Full-length 16S rRNA PCR amplicons were sequenced using Oxford Nanopore Technologies. Taxonomic classification, Firmicutes/Bacteroidetes ratio, and Shannon index were determined using Massbiome Fecal Microbiome Analysis (Massive Bioinformatics, Türkiye). Dominant bacterial genera were also analyzed using the Epi2Me database. Blood samples were analyzed for metabolic health markers. Associations between bacterial taxa and blood-based metabolic parameters were examined statistically. A total of 82 participants were included in the study. According to BMI, 34 (41.4%) of the participants were classified as having a healthy weight, 23 (28.1%) as overweight, and 25 (30.5%) as obese. Segatella (Prevotella) copri was identified as the dominant species in most participants (51%). Other dominant species included Ruminococcus torques (13%), Faecalibacterium prausnitzii (13%), Faecalitalea cylindroides (5%), Bacteroides uniformis (4%), and Phocaeicola vulgatus (3%). S. copri was identified as the dominant bacterial species in 45 participants (54.8%) according to the Epi2Me database. The Shannon index and Firmicutes/Bacteroidetes ratio varied among the three BMI groups. Both Lachnospira and Ruminococcus genera had a significant negative correlation with BMI, indicating that higher levels of BMI are associated with lower abundances of these genera. In the regression analysis, Lachnospira was found to be less abundant at higher HbA1c levels. HOMA-IR was found to be a significant predictor for the relative abundance of Vescimonas. Ruthenibacterium is found to be more abundant at higher HDL levels. The dominant bacterial taxa differed from those reported in other populations, suggesting region-specific microbial profiles. Notably, specific gut microbial genera were associated with metabolic health indicators, including BMI, HbA1c, HOMA-IR, and HDL level. These findings underscore the potential role of gut microbiota in metabolic regulation and support the need for further region-specific research. This study is among the few in Türkiye focusing on healthy adults and contributes to the understanding of gut microbiota in relation to cardiometabolic parameters.

Chronic disruption of the intestinal microbiota in adult cystic fibrosis (CF) patients is associated with local and systemic inflammation, and has been linked to the risk of serious comorbidities. Supplementation with high amylose maize starch (HAMS) might provide clinical benefit by promoting commensal bacteria and the biosynthesis of immunomodulatory metabolites. However, whether the disrupted CF gut microbiota has the capacity to utilise these substrates is not known. We combined metagenomic sequencing, in vitro fermentation, amplicon sequencing, and metabolomics to define the characteristics of the faecal microbiota in adult CF patients and assess HAMS fermentation capacity. Compared to healthy controls, the faecal metagenome of adult CF patients had reduced bacterial diversity and prevalence of commensal fermentative clades. In vitro fermentation models seeded with CF faecal slurries exhibited reduced acetate levels compared to healthy control reactions, but comparable levels of butyrate and propionate. While the commensal genus Faecalibacterium was strongly associated with short chain fatty acid (SCFA) production by healthy microbiota, it was displaced in this role by Clostridium sensu stricto 1 in the microbiota of CF patients. A subset of CF reactions exhibited enterococcal overgrowth, resulting in lactate accumulation and reduced SCFA biosynthesis. The addition of healthy microbiota to CF faecal slurries failed to displace predominant CF taxa, or substantially influence metabolite biosynthesis. Despite significant microbiota disruption, the adult CF gut microbiota retains the capacity to exploit HAMS. Our findings highlight the potential for taxa associated with the altered CF gut microbiotato mediate prebiotic effects in microbial systems subject to ongoing perturbation, irrespective of the depletion of common commensal clades.

Chinese experts consensus statement: diagnosis and treatment of cystic fibrosis (2023)

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