SLC6A14 impacts cystic fibrosis lung disease severity via mTOR and epithelial repair modulation

Abstract Cystic fibrosis (CF), due to variants in CFTR gene, is associated with chronic infection/inflammation responsible for airway epithelium alteration and lung function decline. Modifier genes induce phenotype variability between people with CF (pwCF) carrying the same CFTR variants. Among these, the gene encoding for the amino acid transporter SLC6A14 has been associated with lung disease severity and age of primary airway infection by the bacteria Pseudomonas aeruginosa. In this study, we investigated whether the single nucleotide polymorphism (SNP) rs3788766, located within SLC6A14 promoter, is associated with lung disease severity in a large French cohort of pwCF. We also studied the consequences of this SNP on SLC6A14 promoter activity using a luciferase reporter and the role of SLC6A14 in mammalian target of rapamycin (mTOR) signaling pathway and airway epithelial repair. We confirm that SLC6A14 rs3788766 SNP is associated with lung disease severity in pwCF (p=0.020; n=3,257, pancreatic insufficient, aged 6 to 40 years old), with the minor allele G being deleterious. In bronchial epithelial cell lines deficient for CFTR, SLC6A14 promoter activity is reduced in the presence of the rs3788766 G allele. SLC6A14 inhibition with a specific pharmacological blocker reduced 3H-arginine transport, mTOR phosphorylation and bronchial epithelial repair rates in wound healing assays. To conclude, our study highlights that SLC6A14 genotype might affect lung disease severity of people with cystic fibrosis via mTOR and epithelial repair mechanisms modulation in the lung.

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SLC6A14 impacts cystic fibrosis lung disease severity via mTOR and epithelial repair modulation

10.21203/rs.3.rs-591564/v2 ◽

2021 ◽

Author(s):

Julia Mercier ◽

Claire Calmel ◽

Julie Mésinèle ◽

Erika Sutanto ◽

Fatiha Merabtene ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Disease ◽

Disease Severity ◽

Promoter Activity ◽

Mammalian Target Of Rapamycin ◽

Luciferase Reporter ◽

Lung Function Decline ◽

Bronchial Epithelial ◽

Epithelial Repair ◽

Lung Disease Severity

Abstract Cystic fibrosis (CF), due to variants in CFTR gene, is associated with chronic infection/inflammation responsible for airway epithelium alteration and lung function decline. Modifier genes induce phenotype variability between people with CF (pwCF) carrying the same CFTR variants. Among these, the gene encoding for the amino acid transporter SLC6A14 has been associated with lung disease severity and age of primary airway infection by the bacteria Pseudomonas aeruginosa. In this study, we investigated whether the single nucleotide polymorphism (SNP) rs3788766, located within SLC6A14 promoter, is associated with lung disease severity in a large French cohort of pwCF. We also studied the consequences of this SNP on SLC6A14 promoter activity using a luciferase reporter and the role of SLC6A14 in mammalian target of rapamycin (mTOR) signaling pathway and airway epithelial repair. We confirm that SLC6A14 SNP rs3788766 is associated with lung disease severity in pwCF (p=0.020; n=3,257, pancreatic insufficient, aged 6 to 40 years old), with the minor allele G being deleterious. In bronchial epithelial cell lines deficient for CFTR, SLC6A14 promoter activity is reduced in the presence of the rs3788766 G allele. SLC6A14 inhibition with a specific pharmacological blocker reduced 3H-arginine transport, mTOR phosphorylation and bronchial epithelial repair rates in wound healing assays. To conclude, our study highlights that SLC6A14 genotype might affect lung disease severity of people with cystic fibrosis via mTOR and epithelial repair mechanisms modulation in the lung.

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SLC6A14 Modulates Lung Disease Severity in Cystic Fibrosis and Affects mTOR Phosphorylation and Bronchial Epithelial Repair

10.21203/rs.3.rs-591564/v1 ◽

2021 ◽

Author(s):

Julia Mercier ◽

Claire Calmel ◽

Julie Mésinèle ◽

Erika Sutanto ◽

Fatiha Merabtene ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Function ◽

Lung Disease ◽

Disease Severity ◽

Promoter Activity ◽

Mtor Signaling ◽

Bronchial Epithelial ◽

Epithelial Repair ◽

Mtor Phosphorylation ◽

Lung Disease Severity

Abstract Cystic fibrosis (CF), due to variants in CFTR gene, is associated with chronic infection/inflammation responsible for airway epithelium alteration and lung function decline. Modifier genes induce phenotype variability between people with CF (pwCF) carrying the same CFTR variants. Among these, the gene encoding for the amino acid transporter SLC6A14 has been associated with lung disease severity and age of primary airway infection by the bacteria Pseudomonas aeruginosa. In this study, we investigated whether the single nucleotide polymorphism (SNP) rs3788766, located within SLC6A14 promoter, is associated with lung disease severity in a large French cohort of pwCF. We also studied the consequences of this SNP on SLC6A14 promoter activity and the role of SLC6A14 in mammalian target of rapamycin (mTOR) signaling pathway and airway epithelial repair. We confirm that SLC6A14 SNP rs3788766 is associated with lung disease severity in pwCF (p=0.020; n=3,257, pancreatic insufficient, aged 6 to 40 years old), with the minor allele G being deleterious. In bronchial epithelial cell lines deficient for CFTR, SLC6A14 promoter activity is reduced in the presence of the rs3788766 G allele. SLC6A14 inhibition with a specific pharmacological blocker reduced 3H-arginine transport, mTOR phosphorylation and bronchial epithelial repair rates in wound healing assays. In conclusion, SLC6A14 rs3788766 G allele is associated with lower lung function in pwCF. SLC6A14, whose transcriptional promoter activity varies according to rs3788766 genotype, is involved in mTOR signaling and bronchial epithelial repair. This study suggests that SLC6A14 might influence CF lung phenotype via mTOR and epithelial repair mechanisms modulation.

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Single nucleotide variants in Pseudomonas aeruginosa populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis

10.1101/2021.10.04.21264421 ◽

2021 ◽

Author(s):

Morteza M Saber ◽

Jannik Donner ◽

Inès Levade ◽

Nicole Acosta ◽

Michael D Perkins ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Genetic Variation ◽

Lung Function ◽

Lung Disease ◽

Disease Severity ◽

Single Nucleotide Variants ◽

Lung Function Decline ◽

Single Nucleotide ◽

Lung Disease Severity

Complex polymicrobial communities inhabit the lungs of individuals with cystic fibrosis (CF) and contribute to the decline in lung function. However, the severity of lung disease and its progression in CF patients are highly variable and imperfectly predicted by host clinical factors at baseline, CFTR mutations in the host genome, or sputum polymicrobial community variation. The opportunistic pathogen Pseudomonas aeruginosa (Pa) dominates airway infections in the majority of CF adults. Here we hypothesized that genetic variation within Pa populations would be predictive of lung disease severity. To quantify Pa genetic variation within whole CF sputum samples, we used deep amplicon sequencing on a newly developed custom Ion AmpliSeq panel of 209 Pa genes previously associated with the host pathoadaptation and pathogenesis of CF infection. We trained machine learning models using Pa single nucleotide variants (SNVs), clinical and microbiome diversity data to classify lung disease severity at the time of sputum sampling, and to predict future lung function decline over five years in a cohort of 54 adult CF patients with chronic Pa infection. The models using Pa SNVs alone classified baseline lung disease with good sensitivity and specificity, with an area under the receiver operating characteristic curve (AUROC) of 0.87. While the models were less predictive of future lung function decline, they still achieved an AUROC of 0.74. The addition of clinical data to the models, but not microbiome community data, yielded modest improvements (baseline lung function: AUROC=0.92; lung function decline: AUROC=0.79), highlighting the predictive value of the AmpliSeq data. Together, our work provides a proof-of-principle that Pa genetic variation in sputum is strongly associated with baseline lung disease, moderately predicts future lung function decline, and provides insight into the pathobiology of Pa's effect on CF.

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DNA Methylation at ATP11A cg11702988 Is a Biomarker of Lung Disease Severity in Cystic Fibrosis: A Longitudinal Study

Genes ◽

10.3390/genes12030441 ◽

2021 ◽

Vol 12 (3) ◽

pp. 441

Author(s):

Fanny Pineau ◽

Davide Caimmi ◽

Sylvie Taviaux ◽

Maurane Reveil ◽

Laura Brosseau ◽

...

Keyword(s):

Cystic Fibrosis ◽

Dna Methylation ◽

Clinical Trials ◽

Lung Disease ◽

Disease Severity ◽

Genome Wide ◽

A Genome ◽

Lung Disease Severity ◽

Epigenetic Biomarker

Cystic fibrosis (CF) is a chronic genetic disease that mainly affects the respiratory and gastrointestinal systems. No curative treatments are available, but the follow-up in specialized centers has greatly improved the patient life expectancy. Robust biomarkers are required to monitor the disease, guide treatments, stratify patients, and provide outcome measures in clinical trials. In the present study, we outline a strategy to select putative DNA methylation biomarkers of lung disease severity in cystic fibrosis patients. In the discovery step, we selected seven potential biomarkers using a genome-wide DNA methylation dataset that we generated in nasal epithelial samples from the MethylCF cohort. In the replication step, we assessed the same biomarkers using sputum cell samples from the MethylBiomark cohort. Of interest, DNA methylation at the cg11702988 site (ATP11A gene) positively correlated with lung function and BMI, and negatively correlated with lung disease severity, P. aeruginosa chronic infection, and the number of exacerbations. These results were replicated in prospective sputum samples collected at four time points within an 18-month period and longitudinally. To conclude, (i) we identified a DNA methylation biomarker that correlates with CF severity, (ii) we provided a method to easily assess this biomarker, and (iii) we carried out the first longitudinal analysis of DNA methylation in CF patients. This new epigenetic biomarker could be used to stratify CF patients in clinical trials.

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